diff --git a/biolink-model.graphql b/biolink-model.graphql index d00e249d67..b47ec53e21 100644 --- a/biolink-model.graphql +++ b/biolink-model.graphql @@ -1,5 +1,5 @@ # metamodel_version: 1.7.0 -# version: 3.3.2 +# version: 3.4.0 type AccessibleDnaRegion implements GenomicEntity, ChemicalEntityOrGeneOrGeneProduct, PhysicalEssence, OntologyClass { id: String! @@ -86,9 +86,9 @@ interface AnatomicalEntityToAnatomicalEntityAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -121,9 +121,9 @@ type AnatomicalEntityToAnatomicalEntityOntogenicAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -157,9 +157,9 @@ type AnatomicalEntityToAnatomicalEntityPartOfAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -206,7 +206,7 @@ type Article xref: [Uriorcurie] id: String! name: LabelType - publicationType: String! + publicationType: [String]! publishedIn: Uriorcurie! isoAbbreviation: String volume: String @@ -227,9 +227,9 @@ type Association qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -308,9 +308,9 @@ type BehaviorToBehavioralFeatureAssociation implements EntityToPhenotypicFeature qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -474,7 +474,7 @@ type Book meshTerms: [Uriorcurie] xref: [Uriorcurie] name: LabelType - publicationType: String! + publicationType: [String]! id: String! type: [String] } @@ -499,7 +499,7 @@ type BookChapter xref: [Uriorcurie] id: String! name: LabelType - publicationType: String! + publicationType: [String]! publishedIn: Uriorcurie! volume: String chapter: String @@ -538,9 +538,9 @@ type CaseToPhenotypicFeatureAssociation implements EntityToPhenotypicFeatureAsso qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -568,6 +568,52 @@ type CaseToPhenotypicFeatureAssociation implements EntityToPhenotypicFeatureAsso hasPercentage: Double } +type CausalGeneToDiseaseAssociation implements EntityToDiseaseAssociationMixin, GeneToEntityAssociationMixin + { + id: String! + iri: IriType + name: LabelType + description: NarrativeText + hasAttribute: [Attribute] + negated: Boolean + qualifiers: [OntologyClass] + publications: [Publication] + hasEvidence: [EvidenceType] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] + timepoint: TimeType + originalSubject: String + originalPredicate: Uriorcurie + originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] + type: [String] + category: [CategoryType] + subjectAspectQualifier: GeneOrGeneProductOrChemicalEntityAspectEnum + objectDirectionQualifier: DirectionQualifierEnum + predicate: PredicateType! + frequencyQualifier: FrequencyValue + severityQualifier: SeverityValue + onsetQualifier: Onset + sexQualifier: BiologicalSex + hasCount: Integer + hasTotal: Integer + hasQuotient: Double + hasPercentage: Double + subject: GeneOrGeneProduct! + object: Disease! + } + type Cell { id: String! @@ -609,9 +655,9 @@ type CellLineAsAModelOfDiseaseAssociation implements ModelToDiseaseAssociationMi qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -648,9 +694,9 @@ type CellLineToDiseaseOrPhenotypicFeatureAssociation implements CellLineToEntity qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -715,9 +761,9 @@ type ChemicalAffectsGeneAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -784,9 +830,9 @@ type ChemicalEntityAssessesNamedThingAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -824,9 +870,9 @@ type ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -887,9 +933,9 @@ type ChemicalGeneInteractionAssociation implements ChemicalToEntityAssociationMi qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -959,9 +1005,9 @@ type ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation im qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -996,9 +1042,9 @@ type ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation implements qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -1049,9 +1095,9 @@ type ChemicalToChemicalAssociation implements ChemicalToEntityAssociationMixin qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -1083,9 +1129,9 @@ type ChemicalToChemicalDerivationAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -1122,9 +1168,9 @@ type ChemicalToDiseaseOrPhenotypicFeatureAssociation implements ChemicalToEntity qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -1162,9 +1208,9 @@ type ChemicalToPathwayAssociation implements ChemicalToEntityAssociationMixin qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -1454,9 +1500,9 @@ type ContributorAssociation negated: Boolean publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -1480,6 +1526,52 @@ type ContributorAssociation qualifiers: [OntologyClass] } +type CorrelatedGeneToDiseaseAssociation implements EntityToDiseaseAssociationMixin, GeneToEntityAssociationMixin + { + id: String! + iri: IriType + name: LabelType + description: NarrativeText + hasAttribute: [Attribute] + negated: Boolean + qualifiers: [OntologyClass] + publications: [Publication] + hasEvidence: [EvidenceType] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] + timepoint: TimeType + originalSubject: String + originalPredicate: Uriorcurie + originalObject: String + subjectCategory: OntologyClass + objectCategory: OntologyClass + subjectClosure: [String] + objectClosure: [String] + subjectCategoryClosure: [OntologyClass] + objectCategoryClosure: [OntologyClass] + subjectNamespace: String + objectNamespace: String + subjectLabelClosure: [String] + objectLabelClosure: [String] + retrievalSourceIds: [RetrievalSource] + type: [String] + category: [CategoryType] + subjectAspectQualifier: GeneOrGeneProductOrChemicalEntityAspectEnum + objectDirectionQualifier: DirectionQualifierEnum + predicate: PredicateType! + frequencyQualifier: FrequencyValue + severityQualifier: SeverityValue + onsetQualifier: Onset + sexQualifier: BiologicalSex + hasCount: Integer + hasTotal: Integer + hasQuotient: Double + hasPercentage: Double + subject: GeneOrGeneProduct! + object: Disease! + } + type Dataset { id: String! @@ -1646,9 +1738,9 @@ type DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation implements Diseas qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -1683,9 +1775,9 @@ type DiseaseOrPhenotypicFeatureToLocationAssociation implements DiseaseOrPhenoty qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -1725,9 +1817,9 @@ type DiseaseToExposureEventAssociation implements DiseaseToEntityAssociationMixi qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -1759,9 +1851,9 @@ type DiseaseToPhenotypicFeatureAssociation implements EntityToPhenotypicFeatureA qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -1850,7 +1942,7 @@ type DrugLabel xref: [Uriorcurie] id: String! name: LabelType - publicationType: String! + publicationType: [String]! } interface DrugToEntityAssociationMixin @@ -1871,9 +1963,9 @@ type DrugToGeneAssociation implements DrugToEntityAssociationMixin qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -1919,13 +2011,12 @@ type DruggableGeneToDiseaseAssociation implements EntityToDiseaseAssociationMixi name: LabelType description: NarrativeText hasAttribute: [Attribute] - object: NamedThing! negated: Boolean qualifiers: [OntologyClass] publications: [Publication] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -1943,12 +2034,20 @@ type DruggableGeneToDiseaseAssociation implements EntityToDiseaseAssociationMixi retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] - subject: GeneOrGeneProduct! - predicate: PredicateType! - hasEvidence: [DruggableGeneCategoryEnum] + subjectAspectQualifier: GeneOrGeneProductOrChemicalEntityAspectEnum + objectDirectionQualifier: DirectionQualifierEnum frequencyQualifier: FrequencyValue severityQualifier: SeverityValue onsetQualifier: Onset + sexQualifier: BiologicalSex + hasCount: Integer + hasTotal: Integer + hasQuotient: Double + hasPercentage: Double + object: Disease! + subject: GeneOrGeneProduct! + predicate: PredicateType! + hasEvidence: [DruggableGeneCategoryEnum] } interface Entity @@ -1976,9 +2075,9 @@ type EntityToDiseaseAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -2043,9 +2142,9 @@ type EntityToPhenotypicFeatureAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -2212,9 +2311,9 @@ type ExonToTranscriptRelationship qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -2256,9 +2355,9 @@ type ExposureEventToOutcomeAssociation implements EntityToOutcomeAssociationMixi qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -2293,9 +2392,9 @@ type ExposureEventToPhenotypicFeatureAssociation implements EntityToPhenotypicFe qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -2389,9 +2488,9 @@ type FunctionalAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -2451,15 +2550,13 @@ type GeneAsAModelOfDiseaseAssociation implements ModelToDiseaseAssociationMixin, name: LabelType description: NarrativeText hasAttribute: [Attribute] - predicate: PredicateType! - object: NamedThing! negated: Boolean qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -2477,10 +2574,19 @@ type GeneAsAModelOfDiseaseAssociation implements ModelToDiseaseAssociationMixin, retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] - subject: GeneOrGeneProduct! + subjectAspectQualifier: GeneOrGeneProductOrChemicalEntityAspectEnum + objectDirectionQualifier: DirectionQualifierEnum + predicate: PredicateType! frequencyQualifier: FrequencyValue severityQualifier: SeverityValue onsetQualifier: Onset + sexQualifier: BiologicalSex + hasCount: Integer + hasTotal: Integer + hasQuotient: Double + hasPercentage: Double + object: Disease! + subject: GeneOrGeneProduct! } interface GeneExpressionMixin @@ -2522,9 +2628,9 @@ type GeneHasVariantThatContributesToDiseaseAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -2542,6 +2648,16 @@ type GeneHasVariantThatContributesToDiseaseAssociation retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] + subjectAspectQualifier: GeneOrGeneProductOrChemicalEntityAspectEnum + objectDirectionQualifier: DirectionQualifierEnum + frequencyQualifier: FrequencyValue + severityQualifier: SeverityValue + onsetQualifier: Onset + sexQualifier: BiologicalSex + hasCount: Integer + hasTotal: Integer + hasQuotient: Double + hasPercentage: Double subjectFormOrVariantQualifier: String subject: GeneOrGeneProduct! object: Disease! @@ -2567,23 +2683,20 @@ interface GeneProductMixin xref: [Uriorcurie] } -type GeneToDiseaseAssociation +type GeneToDiseaseAssociation implements EntityToDiseaseAssociationMixin, GeneToEntityAssociationMixin { id: String! iri: IriType name: LabelType description: NarrativeText hasAttribute: [Attribute] - subject: NamedThing! - predicate: PredicateType! - object: NamedThing! negated: Boolean qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -2601,6 +2714,19 @@ type GeneToDiseaseAssociation retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] + subjectAspectQualifier: GeneOrGeneProductOrChemicalEntityAspectEnum + objectDirectionQualifier: DirectionQualifierEnum + predicate: PredicateType! + frequencyQualifier: FrequencyValue + severityQualifier: SeverityValue + onsetQualifier: Onset + sexQualifier: BiologicalSex + hasCount: Integer + hasTotal: Integer + hasQuotient: Double + hasPercentage: Double + subject: GeneOrGeneProduct! + object: Disease! } type GeneToDiseaseOrPhenotypicFeatureAssociation implements EntityToPhenotypicFeatureAssociationMixin, GeneToEntityAssociationMixin @@ -2614,9 +2740,9 @@ type GeneToDiseaseOrPhenotypicFeatureAssociation implements EntityToPhenotypicFe qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -2665,9 +2791,9 @@ type GeneToExpressionSiteAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -2704,9 +2830,9 @@ interface GeneToGeneAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -2739,9 +2865,9 @@ type GeneToGeneCoexpressionAssociation implements GeneExpressionMixin qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -2779,9 +2905,9 @@ type GeneToGeneFamilyAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -2815,9 +2941,9 @@ type GeneToGeneHomologyAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -2851,9 +2977,9 @@ type GeneToGeneProductRelationship qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -2888,9 +3014,9 @@ type GeneToGoTermAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -2924,9 +3050,9 @@ type GeneToPathwayAssociation implements GeneToEntityAssociationMixin qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -2948,23 +3074,20 @@ type GeneToPathwayAssociation implements GeneToEntityAssociationMixin object: Pathway! } -type GeneToPhenotypeAssociation +type GeneToPhenotypeAssociation implements EntityToPhenotypicFeatureAssociationMixin, GeneToEntityAssociationMixin { id: String! iri: IriType name: LabelType description: NarrativeText hasAttribute: [Attribute] - subject: NamedThing! - predicate: PredicateType! - object: NamedThing! negated: Boolean qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -2982,6 +3105,19 @@ type GeneToPhenotypeAssociation retrievalSourceIds: [RetrievalSource] type: [String] category: [CategoryType] + subjectAspectQualifier: GeneOrGeneProductOrChemicalEntityAspectEnum + objectDirectionQualifier: DirectionQualifierEnum + predicate: PredicateType! + frequencyQualifier: FrequencyValue + severityQualifier: SeverityValue + onsetQualifier: Onset + sexQualifier: BiologicalSex + hasCount: Integer + hasTotal: Integer + hasQuotient: Double + hasPercentage: Double + subject: GeneOrGeneProduct! + object: PhenotypicFeature! } type GeneticInheritance @@ -3049,9 +3185,9 @@ type GenomicSequenceLocalization qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -3106,9 +3242,9 @@ type GenotypeAsAModelOfDiseaseAssociation implements ModelToDiseaseAssociationMi qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -3145,9 +3281,9 @@ type GenotypeToDiseaseAssociation implements GenotypeToEntityAssociationMixin, E qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -3189,9 +3325,9 @@ type GenotypeToGeneAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -3225,9 +3361,9 @@ type GenotypeToGenotypePartAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -3262,9 +3398,9 @@ type GenotypeToPhenotypicFeatureAssociation implements EntityToPhenotypicFeature qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -3305,9 +3441,9 @@ type GenotypeToVariantAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -3496,9 +3632,9 @@ type InformationContentEntityToNamedThingAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -3521,30 +3657,6 @@ type InformationContentEntityToNamedThingAssociation predicate: PredicateType! } -type InformationResource - { - iri: IriType - type: [String] - hasAttribute: [Attribute] - providedBy: [String] - category: [CategoryType]! - license: String - rights: String - format: String - creationDate: Date - informationResourceStatus: InformationResourceStatusEnum - name: LabelType - id: String! - xref: [Uriorcurie] - synonym: [LabelType] - description: NarrativeText - } - -type InformationResourceCollection - { - informationResources: [InformationResource] - } - type Invertebrate { id: String! @@ -3579,7 +3691,7 @@ type JournalArticle xref: [Uriorcurie] id: String! name: LabelType - publicationType: String! + publicationType: [String]! publishedIn: Uriorcurie! isoAbbreviation: String volume: String @@ -3600,6 +3712,23 @@ type LifeStage hasAttribute: [Attribute] } +type LogOddsAnalysisResult + { + id: String! + iri: IriType + type: [String] + name: LabelType + description: NarrativeText + hasAttribute: [Attribute] + providedBy: [String] + xref: [Uriorcurie] + category: [CategoryType]! + license: String + rights: String + format: String + creationDate: Date + } + type MacromolecularComplex implements MacromolecularMachineMixin { id: String! @@ -3631,9 +3760,9 @@ type MacromolecularMachineToBiologicalProcessAssociation implements Macromolecul qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -3667,9 +3796,9 @@ type MacromolecularMachineToCellularComponentAssociation implements Macromolecul qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -3708,9 +3837,9 @@ type MacromolecularMachineToMolecularActivityAssociation implements Macromolecul qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -3775,9 +3904,9 @@ type MaterialSampleDerivationAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -3814,9 +3943,9 @@ type MaterialSampleToDiseaseOrPhenotypicFeatureAssociation implements MaterialSa qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -3898,9 +4027,9 @@ type MolecularActivityToChemicalEntityAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -3934,9 +4063,9 @@ type MolecularActivityToMolecularActivityAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -3969,9 +4098,9 @@ type MolecularActivityToPathwayAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -4065,9 +4194,9 @@ type NamedThingAssociatedWithLikelihoodOfNamedThingAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -4253,9 +4382,9 @@ type OrganismTaxonToEnvironmentAssociation implements OrganismTaxonToEntityAssoc qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -4290,9 +4419,9 @@ type OrganismTaxonToOrganismTaxonAssociation implements OrganismTaxonToEntityAss qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -4325,9 +4454,9 @@ type OrganismTaxonToOrganismTaxonInteraction qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -4362,9 +4491,9 @@ type OrganismTaxonToOrganismTaxonSpecialization qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -4399,9 +4528,9 @@ type OrganismToOrganismAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -4450,9 +4579,9 @@ type OrganismalEntityAsAModelOfDiseaseAssociation implements ModelToDiseaseAssoc qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -4491,9 +4620,9 @@ type PairwiseGeneToGeneInteraction qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -4526,9 +4655,9 @@ type PairwiseMolecularInteraction qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -4573,7 +4702,7 @@ type Patent xref: [Uriorcurie] id: String! name: LabelType - publicationType: String! + publicationType: [String]! } interface PathognomonicityQuantifier @@ -4837,9 +4966,9 @@ type PopulationToPopulationAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -4895,7 +5024,7 @@ type PredicateMapping objectDerivativeQualifier: String objectContextQualifier: String causalMechanismQualifier: CausalMechanismQualifierEnum - anatomicalContextQualifier: AnatomicalContextQualifierEnum + anatomicalContextQualifier: String speciesContextQualifier: OrganismTaxon exactMatch: [NamedThing] narrowMatch: [NamedThing] @@ -4922,7 +5051,7 @@ type PreprintPublication xref: [Uriorcurie] id: String! name: LabelType - publicationType: String! + publicationType: [String]! } type Procedure implements ActivityAndBehavior @@ -5040,7 +5169,7 @@ type Publication xref: [Uriorcurie] id: String! name: LabelType - publicationType: String! + publicationType: [String]! } type QuantityValue @@ -5061,9 +5190,9 @@ type ReactionToCatalystAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -5100,9 +5229,9 @@ type ReactionToParticipantAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -5265,9 +5394,9 @@ type SequenceAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -5299,9 +5428,9 @@ type SequenceFeatureRelationship qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -5351,9 +5480,9 @@ interface SequenceVariantModulatesTreatmentAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -5393,7 +5522,7 @@ type Serial meshTerms: [Uriorcurie] xref: [Uriorcurie] name: LabelType - publicationType: String! + publicationType: [String]! isoAbbreviation: String volume: String issue: String @@ -5592,9 +5721,9 @@ type TaxonToTaxonAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -5676,9 +5805,9 @@ type TranscriptToGeneRelationship qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -5743,9 +5872,9 @@ type VariantAsAModelOfDiseaseAssociation implements ModelToDiseaseAssociationMix qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -5782,9 +5911,9 @@ type VariantToDiseaseAssociation implements VariantToEntityAssociationMixin, Ent qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -5827,9 +5956,9 @@ type VariantToGeneAssociation implements VariantToEntityAssociationMixin qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -5863,9 +5992,9 @@ type VariantToGeneExpressionAssociation implements GeneExpressionMixin qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -5904,9 +6033,9 @@ type VariantToPhenotypicFeatureAssociation implements VariantToEntityAssociation qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -5947,9 +6076,9 @@ type VariantToPopulationAssociation implements VariantToEntityAssociationMixin, qualifiers: [OntologyClass] publications: [Publication] hasEvidence: [EvidenceType] - knowledgeSource: InformationResource - primaryKnowledgeSource: InformationResource - aggregatorKnowledgeSource: [InformationResource] + knowledgeSource: String + primaryKnowledgeSource: String + aggregatorKnowledgeSource: [String] timepoint: TimeType originalSubject: String originalPredicate: Uriorcurie @@ -6024,7 +6153,7 @@ type WebPage xref: [Uriorcurie] id: String! name: LabelType - publicationType: String! + publicationType: [String]! } type Zygosity diff --git a/biolink-model.owl.ttl b/biolink-model.owl.ttl index a62a5b8775..9225233437 100644 --- a/biolink-model.owl.ttl +++ b/biolink-model.owl.ttl @@ -93,7 +93,6 @@ biolink:GeneToEntityAssociationMixin, biolink:GenomicEntity, biolink:GenotypeToEntityAssociationMixin, - biolink:InformationResourceCollection, biolink:MacromolecularMachineMixin, biolink:MacromolecularMachineToEntityAssociationMixin, biolink:MappingCollection, @@ -109,13 +108,12 @@ biolink:SubjectOfInvestigation, biolink:ThingWithTaxon, biolink:VariantToEntityAssociationMixin ; - dct:license "https://creativecommons.org/publicdomain/zero/1.0/" ; - pav:version "3.3.2" ; - linkml:generation_date "2023-05-04T23:01:41" ; - linkml:metamodel_version "1.7.0" ; - linkml:source_file "biolink-model.yaml" ; - linkml:source_file_date "2023-05-04T23:00:24" ; - linkml:source_file_size 355095 . + linkml:classes "{'mapping collection': ClassDefinition(name='mapping collection', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/MappingCollection', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A collection of deprecated mappings.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['predicate mappings'], slot_usage={}, attributes={}, class_uri='biolink:MappingCollection', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'predicate mapping': ClassDefinition(name='predicate mapping', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/PredicateMapping', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['mapped predicate', 'subject aspect qualifier', 'subject direction qualifier', 'subject form or variant qualifier', 'subject part qualifier', 'subject derivative qualifier', 'subject context qualifier', 'predicate', 'qualified predicate', 'object aspect qualifier', 'object direction qualifier', 'object form or variant qualifier', 'object part qualifier', 'object derivative qualifier', 'object context qualifier', 'causal mechanism qualifier', 'anatomical context qualifier', 'species context qualifier', 'exact match', 'narrow match', 'broad match'], slot_usage={}, attributes={}, class_uri='biolink:PredicateMapping', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ontology class': ClassDefinition(name='ontology class', id_prefixes=['MESH', 'UMLS', 'KEGG.BRITE'], definition_uri='https://w3id.org/biolink/vocab/OntologyClass', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[\"This is modeled as a mixin. 'ontology class' should not be the primary type of a node in the KG. Instead you should use an informative bioloink category, such as AnatomicalEntity (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL), etc\", \"Note that formally this is a metaclass. Instances of this class are instances in the graph, but can be the object of 'type' edges. For example, if we had a node in the graph representing a specific brain of a specific patient (e.g brain001), this could have a category of bl:Sample, and by typed more specifically with an ontology class UBERON:nnn, which has as category bl:AnatomicalEntity\"], examples=[Example(value='UBERON:0000955', description=\"the class 'brain' from the Uberon anatomy ontology\", object=None)], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=['https://github.com/biolink/biolink-model/issues/486'], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['owl:Class', 'schema:Class'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id'], slot_usage={}, attributes={}, class_uri='biolink:OntologyClass', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'annotation': ClassDefinition(name='annotation', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Annotation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Biolink Model root class for entity annotations.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='biolink:Annotation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'quantity value': ClassDefinition(name='quantity value', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/QuantityValue', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='annotation', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['has unit', 'has numeric value'], slot_usage={}, attributes={}, class_uri='biolink:QuantityValue', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'attribute': ClassDefinition(name='attribute', id_prefixes=['EDAM-DATA', 'EDAM-FORMAT', 'EDAM-OPERATION', 'EDAM-TOPIC'], definition_uri='https://w3id.org/biolink/vocab/Attribute', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['samples'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['SIO:000614'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='named thing', abstract=None, mixin=None, mixins=['ontology class'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has attribute type', 'has quantitative value', 'has qualitative value', 'iri'], slot_usage={'name': SlotDefinition(name='name', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=\"The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.\", alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:Attribute', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'chemical role': ClassDefinition(name='chemical role', id_prefixes=['CHEBI'], definition_uri='https://w3id.org/biolink/vocab/ChemicalRole', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='\\tA role played by the molecular entity or part thereof within a chemical context.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='CHEBI:35469', description=None, object=None)], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['CHEBI:51086'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='attribute', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has attribute type', 'has quantitative value', 'has qualitative value', 'iri'], slot_usage={}, attributes={}, class_uri='biolink:ChemicalRole', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'biological sex': ClassDefinition(name='biological sex', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/BiologicalSex', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['PATO:0000047'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='attribute', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has attribute type', 'has quantitative value', 'has qualitative value', 'iri'], slot_usage={}, attributes={}, class_uri='biolink:BiologicalSex', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'phenotypic sex': ClassDefinition(name='phenotypic sex', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/PhenotypicSex', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['PATO:0001894'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='biological sex', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has attribute type', 'has quantitative value', 'has qualitative value', 'iri'], slot_usage={}, attributes={}, class_uri='biolink:PhenotypicSex', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'genotypic sex': ClassDefinition(name='genotypic sex', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GenotypicSex', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['PATO:0020000'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='biological sex', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has attribute type', 'has quantitative value', 'has qualitative value', 'iri'], slot_usage={}, attributes={}, class_uri='biolink:GenotypicSex', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'severity value': ClassDefinition(name='severity value', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/SeverityValue', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='describes the severity of a phenotypic feature or disease', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='attribute', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has attribute type', 'has quantitative value', 'has qualitative value', 'iri'], slot_usage={}, attributes={}, class_uri='biolink:SeverityValue', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'relationship quantifier': ClassDefinition(name='relationship quantifier', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/RelationshipQuantifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='biolink:RelationshipQuantifier', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'sensitivity quantifier': ClassDefinition(name='sensitivity quantifier', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/SensitivityQuantifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='relationship quantifier', abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='biolink:SensitivityQuantifier', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'specificity quantifier': ClassDefinition(name='specificity quantifier', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/SpecificityQuantifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='relationship quantifier', abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='biolink:SpecificityQuantifier', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'pathognomonicity quantifier': ClassDefinition(name='pathognomonicity quantifier', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/PathognomonicityQuantifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A relationship quantifier between a variant or symptom and a disease, which is high when the presence of the feature implies the existence of the disease', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='specificity quantifier', abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='biolink:PathognomonicityQuantifier', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'frequency quantifier': ClassDefinition(name='frequency quantifier', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/FrequencyQuantifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='relationship quantifier', abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['has count', 'has total', 'has quotient', 'has percentage'], slot_usage={}, attributes={}, class_uri='biolink:FrequencyQuantifier', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'chemical or drug or treatment': ClassDefinition(name='chemical or drug or treatment', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ChemicalOrDrugOrTreatment', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='biolink:ChemicalOrDrugOrTreatment', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'entity': ClassDefinition(name='entity', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Entity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Root Biolink Model class for all things and informational relationships, real or imagined.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'category', 'type', 'name', 'description', 'has attribute'], slot_usage={}, attributes={}, class_uri='biolink:Entity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'named thing': ClassDefinition(name='named thing', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/NamedThing', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a databased entity or concept/class', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['BFO:0000001', 'WIKIDATA:Q35120', 'UMLSSG:OBJC', 'STY:T071', 'dcid:Thing'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category'], slot_usage={'category': SlotDefinition(name='category', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=True, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern='^biolink:[A-Z][A-Za-z]+$', structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:NamedThing', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'relationship type': ClassDefinition(name='relationship type', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An OWL property used as an edge label', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='ontology class', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id'], slot_usage={}, attributes={}, class_uri='biolink:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'taxonomic rank': ClassDefinition(name='taxonomic rank', id_prefixes=['TAXRANK'], definition_uri='https://w3id.org/biolink/vocab/TaxonomicRank', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['WIKIDATA:Q427626'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='ontology class', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id'], slot_usage={}, attributes={}, class_uri='biolink:TaxonomicRank', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'organism taxon': ClassDefinition(name='organism taxon', id_prefixes=['NCBITaxon', 'MESH', 'UMLS'], definition_uri='https://w3id.org/biolink/vocab/OrganismTaxon', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['model_organism_database'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['taxon', 'taxonomic classification'], structured_aliases={}, mappings=[], exact_mappings=['WIKIDATA:Q16521', 'STY:T001', 'bioschemas:Taxon'], close_mappings=[], related_mappings=[], narrow_mappings=['dcid:BiologicalSpecies'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='named thing', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=['NCBITaxon'], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'organism taxon_has taxonomic rank'], slot_usage={'has taxonomic rank': SlotDefinition(name='has taxonomic rank', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['WIKIDATA:P105'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=False, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='taxonomic rank', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:OrganismTaxon', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'event': ClassDefinition(name='event', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Event', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Something that happens at a given place and time.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['NCIT:C25499', 'STY:T051'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='named thing', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category'], slot_usage={}, attributes={}, class_uri='biolink:Event', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'administrative entity': ClassDefinition(name='administrative entity', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/AdministrativeEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='named thing', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category'], slot_usage={}, attributes={}, class_uri='biolink:AdministrativeEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'study result': ClassDefinition(name='study result', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/StudyResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=\"A collection of data items from a study that are about a particular study subject or experimental unit (the 'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation of this data as evidence.\", alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"The data/metadata included in a Study Result object are typically a subset of data from a larger study data set, that are selected by a curator because they may be useful as evidence for deriving knowledge about a specific focus of the study. The notion of a 'study' here is defined broadly to include any research activity at any scale that is aimed at generating knowledge or hypotheses. This may include a single assay or computational analyses, or a larger scale clinical trial or experimental research investigation.\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='information content entity', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'license', 'rights', 'format', 'creation date'], slot_usage={}, attributes={}, class_uri='biolink:StudyResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'study': ClassDefinition(name='study', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Study', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a detailed investigation and/or analysis', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['NCIT:C63536'], close_mappings=['SIO:001066', 'SEPIO:0000004'], related_mappings=[], narrow_mappings=['SIO:000994'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='activity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category'], slot_usage={}, attributes={}, class_uri='biolink:Study', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'study variable': ClassDefinition(name='study variable', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/StudyVariable', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a variable that is used as a measure in the investigation of a study', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['STATO:0000258', 'SIO:000367'], related_mappings=[], narrow_mappings=['NCIT:C142192'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='information content entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'license', 'rights', 'format', 'creation date'], slot_usage={}, attributes={}, class_uri='biolink:StudyVariable', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'common data element': ClassDefinition(name='common data element', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/CommonDataElement', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. (https://cde.nlm.nih.gov/home)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['NCIT:C19984'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='information content entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'license', 'rights', 'format', 'creation date'], slot_usage={}, attributes={}, class_uri='biolink:CommonDataElement', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'concept count analysis result': ClassDefinition(name='concept count analysis result', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ConceptCountAnalysisResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of a concept count analysis.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='study result', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'license', 'rights', 'format', 'creation date'], slot_usage={}, attributes={}, class_uri='biolink:ConceptCountAnalysisResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'observed expected frequency analysis result': ClassDefinition(name='observed expected frequency analysis result', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ObservedExpectedFrequencyAnalysisResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of a observed expected frequency analysis.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='study result', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'license', 'rights', 'format', 'creation date'], slot_usage={}, attributes={}, class_uri='biolink:ObservedExpectedFrequencyAnalysisResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'relative frequency analysis result': ClassDefinition(name='relative frequency analysis result', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/RelativeFrequencyAnalysisResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of a relative frequency analysis.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='study result', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'license', 'rights', 'format', 'creation date'], slot_usage={}, attributes={}, class_uri='biolink:RelativeFrequencyAnalysisResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'text mining result': ClassDefinition(name='text mining result', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/TextMiningResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of text mining.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='study result', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'license', 'rights', 'format', 'creation date'], slot_usage={}, attributes={}, class_uri='biolink:TextMiningResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'chi squared analysis result': ClassDefinition(name='chi squared analysis result', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ChiSquaredAnalysisResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of a chi squared analysis.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='study result', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'license', 'rights', 'format', 'creation date'], slot_usage={}, attributes={}, class_uri='biolink:ChiSquaredAnalysisResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'log odds analysis result': ClassDefinition(name='log odds analysis result', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/LogOddsAnalysisResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of a log odds ratio analysis.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='study result', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'license', 'rights', 'format', 'creation date'], slot_usage={}, attributes={}, class_uri='biolink:LogOddsAnalysisResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'agent': ClassDefinition(name='agent', id_prefixes=['isbn', 'ORCID', 'ScopusID', 'ResearchID', 'GSID', 'isni'], definition_uri='https://w3id.org/biolink/vocab/Agent', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='person, group, organization or project that provides a piece of information (i.e. a knowledge association)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['group'], structured_aliases={}, mappings=[], exact_mappings=['prov:Agent', 'dct:Agent'], close_mappings=[], related_mappings=[], narrow_mappings=['UMLSSG:ORGA', 'STY:T092', 'STY:T093', 'STY:T094', 'STY:T095', 'STY:T096'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='administrative entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['iri', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'affiliation', 'address', 'agent_id', 'agent_name'], slot_usage={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=\"Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code.\", alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=['isbn', 'ORCID', 'ScopusID', 'ResearchID', 'GSID', 'isni'], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=True, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'name': SlotDefinition(name='name', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='it is recommended that an author\\'s \\'name\\' property be formatted as \"surname, firstname initial.\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:Agent', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'information content entity': ClassDefinition(name='information content entity', id_prefixes=['doi'], definition_uri='https://w3id.org/biolink/vocab/InformationContentEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a piece of information that typically describes some topic of discourse or is used as support.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['information', 'information artefact', 'information entity'], structured_aliases={}, mappings=[], exact_mappings=['IAO:0000030'], close_mappings=[], related_mappings=[], narrow_mappings=['UMLSSG:CONC', 'STY:T077', 'STY:T078', 'STY:T079', 'STY:T080', 'STY:T081', 'STY:T082', 'STY:T089', 'STY:T102', 'STY:T169', 'STY:T171', 'STY:T185'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='named thing', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'license', 'rights', 'format', 'creation date'], slot_usage={}, attributes={}, class_uri='biolink:InformationContentEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'dataset': ClassDefinition(name='dataset', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Dataset', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='an item that refers to a collection of data from a data source.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['IAO:0000100', 'dctypes:Dataset', 'schema:dataset', 'dcid:Dataset'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='information content entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'license', 'rights', 'format', 'creation date'], slot_usage={}, attributes={}, class_uri='biolink:Dataset', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'dataset distribution': ClassDefinition(name='dataset distribution', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/DatasetDistribution', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='an item that holds distribution level information about a dataset.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['dcat:Distribution'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='information content entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'license', 'rights', 'format', 'creation date', 'distribution download url'], slot_usage={}, attributes={}, class_uri='biolink:DatasetDistribution', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'dataset version': ClassDefinition(name='dataset version', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/DatasetVersion', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='an item that holds version level information about a dataset.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='information content entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'license', 'rights', 'format', 'creation date', 'has dataset', 'ingest date', 'has distribution'], slot_usage={}, attributes={}, class_uri='biolink:DatasetVersion', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'dataset summary': ClassDefinition(name='dataset summary', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/DatasetSummary', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='an item that holds summary level information about a dataset.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='information content entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'license', 'rights', 'format', 'creation date', 'source web page', 'source logo'], slot_usage={}, attributes={}, class_uri='biolink:DatasetSummary', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'confidence level': ClassDefinition(name='confidence level', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ConfidenceLevel', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Level of confidence in a statement', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['CIO:0000028', 'SEPIO:0000187'], close_mappings=['SEPIO:0000167'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='information content entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=['cio'], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'license', 'rights', 'format', 'creation date'], slot_usage={}, attributes={}, class_uri='biolink:ConfidenceLevel', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'evidence type': ClassDefinition(name='evidence type', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/EvidenceType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Class of evidence that supports an association', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['evidence code'], structured_aliases={}, mappings=[], exact_mappings=['ECO:0000000'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='information content entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=['eco'], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'license', 'rights', 'format', 'creation date'], slot_usage={}, attributes={}, class_uri='biolink:EvidenceType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'publication': ClassDefinition(name='publication', id_prefixes=['PMID', 'PMC', 'doi', 'NLMID'], definition_uri='https://w3id.org/biolink/vocab/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP). ', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['model_organism_database'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['IAO:0000311'], close_mappings=[], related_mappings=[], narrow_mappings=['IAO:0000013', 'STY:T170'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='information content entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['iri', 'type', 'description', 'has attribute', 'provided by', 'named thing_category', 'license', 'rights', 'format', 'creation date', 'authors', 'publication_pages', 'summary', 'keywords', 'mesh terms', 'xref', 'publication_id', 'publication_name', 'publication_publication type'], slot_usage={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=\"Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.\", alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'name': SlotDefinition(name='name', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=\"the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).\", alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'publication type': SlotDefinition(name='publication type', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=True, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'pages': SlotDefinition(name='pages', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'book': ClassDefinition(name='book', id_prefixes=['isbn', 'NLMID'], definition_uri='https://w3id.org/biolink/vocab/Book', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='This class may rarely be instantiated except if use cases of a given knowledge graph support its utility.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['model_organism_database'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='publication', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['iri', 'description', 'has attribute', 'provided by', 'named thing_category', 'license', 'rights', 'format', 'creation date', 'authors', 'publication_pages', 'summary', 'keywords', 'mesh terms', 'xref', 'publication_name', 'publication_publication type', 'book_id', 'book_type'], slot_usage={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Books should have industry-standard identifier such as from ISBN.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=True, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'type': SlotDefinition(name='type', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=\"Should generally be set to an ontology class defined term for 'book'.\", alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:Book', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'book chapter': ClassDefinition(name='book chapter', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/BookChapter', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['model_organism_database'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='publication', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['iri', 'type', 'description', 'has attribute', 'provided by', 'named thing_category', 'license', 'rights', 'format', 'creation date', 'authors', 'publication_pages', 'summary', 'keywords', 'mesh terms', 'xref', 'publication_id', 'publication_name', 'publication_publication type', 'book chapter_published in', 'volume', 'chapter'], slot_usage={'published in': SlotDefinition(name='published in', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The enclosing parent book containing the chapter should have industry-standard identifier from ISBN.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=True, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:BookChapter', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'serial': ClassDefinition(name='serial', id_prefixes=['issn', 'NLMID'], definition_uri='https://w3id.org/biolink/vocab/Serial', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='This class may rarely be instantiated except if use cases of a given knowledge graph support its utility.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['model_organism_database'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['journal'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='publication', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['iri', 'description', 'has attribute', 'provided by', 'named thing_category', 'license', 'rights', 'format', 'creation date', 'authors', 'publication_pages', 'summary', 'keywords', 'mesh terms', 'xref', 'publication_name', 'publication_publication type', 'iso abbreviation', 'volume', 'issue', 'serial_id', 'serial_type'], slot_usage={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Serials (journals) should have industry-standard identifier such as from ISSN.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=True, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'type': SlotDefinition(name='type', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=\"Should generally be set to an ontology class defined term for 'serial' or 'journal'.\", alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:Serial', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'article': ClassDefinition(name='article', id_prefixes=['PMID'], definition_uri='https://w3id.org/biolink/vocab/Article', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a piece of writing on a particular topic presented as a stand-alone section of a larger publication\\t ', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['model_organism_database'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['SIO:000154', 'fabio:article'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='publication', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['iri', 'type', 'description', 'has attribute', 'provided by', 'named thing_category', 'license', 'rights', 'format', 'creation date', 'authors', 'publication_pages', 'summary', 'keywords', 'mesh terms', 'xref', 'publication_id', 'publication_name', 'publication_publication type', 'article_published in', 'article_iso abbreviation', 'volume', 'issue'], slot_usage={'published in': SlotDefinition(name='published in', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The enclosing parent serial containing the article should have industry-standard identifier from ISSN.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=True, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'iso abbreviation': SlotDefinition(name='iso abbreviation', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=\"Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent.\", alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:Article', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'journal article': ClassDefinition(name='journal article', id_prefixes=['PMID', 'PMCID', 'doi'], definition_uri='https://w3id.org/biolink/vocab/JournalArticle', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='an article, typically presenting results of research, that is published in an issue of a scientific journal.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['IAO:0000013', 'fabio:JournalArticle'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='article', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['iri', 'type', 'description', 'has attribute', 'provided by', 'named thing_category', 'license', 'rights', 'format', 'creation date', 'authors', 'publication_pages', 'summary', 'keywords', 'mesh terms', 'xref', 'publication_id', 'publication_name', 'publication_publication type', 'article_published in', 'article_iso abbreviation', 'volume', 'issue'], slot_usage={}, attributes={}, class_uri='biolink:JournalArticle', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'patent': ClassDefinition(name='patent', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Patent', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time. ', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['SIO:000153', 'IAO:0000313', 'fabio:Patent'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='publication', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['iri', 'type', 'description', 'has attribute', 'provided by', 'named thing_category', 'license', 'rights', 'format', 'creation date', 'authors', 'publication_pages', 'summary', 'keywords', 'mesh terms', 'xref', 'publication_id', 'publication_name', 'publication_publication type'], slot_usage={}, attributes={}, class_uri='biolink:Patent', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'web page': ClassDefinition(name='web page', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/WebPage', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, and/or other features.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['SIO:000302', 'NCIT-OBO:C142749', 'fabio:WebPage'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='publication', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['iri', 'type', 'description', 'has attribute', 'provided by', 'named thing_category', 'license', 'rights', 'format', 'creation date', 'authors', 'publication_pages', 'summary', 'keywords', 'mesh terms', 'xref', 'publication_id', 'publication_name', 'publication_publication type'], slot_usage={}, attributes={}, class_uri='biolink:WebPage', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'preprint publication': ClassDefinition(name='preprint publication', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/PreprintPublication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=\"a document reresenting an early version of an author's original scholarly work, such as a research paper or a review, prior to formal peer review and publication in a peer-reviewed scholarly or scientific journal.\", alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['EFO:0010558', 'fabio:Preprint'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='publication', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['iri', 'type', 'description', 'has attribute', 'provided by', 'named thing_category', 'license', 'rights', 'format', 'creation date', 'authors', 'publication_pages', 'summary', 'keywords', 'mesh terms', 'xref', 'publication_id', 'publication_name', 'publication_publication type'], slot_usage={}, attributes={}, class_uri='biolink:PreprintPublication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'drug label': ClassDefinition(name='drug label', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/DrugLabel', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a document accompanying a drug or its container that provides written, printed or graphic information about the drug, including drug contents, specific instructions or warnings for administration, storage and disposal instructions, etc. ', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['NCIT-OBO:C41203'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='publication', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['iri', 'type', 'description', 'has attribute', 'provided by', 'named thing_category', 'license', 'rights', 'format', 'creation date', 'authors', 'publication_pages', 'summary', 'keywords', 'mesh terms', 'xref', 'publication_id', 'publication_name', 'publication_publication type'], slot_usage={}, attributes={}, class_uri='biolink:DrugLabel', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'retrieval source': ClassDefinition(name='retrieval source', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/RetrievalSource', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='information content entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'named thing_category', 'license', 'rights', 'format', 'creation date', 'retrieval source_resource id', 'retrieval source_resource role', 'retrieval source_upstream resource ids', 'xref'], slot_usage={'resource id': SlotDefinition(name='resource id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=True, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'resource role': SlotDefinition(name='resource role', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=True, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'upstream resource ids': SlotDefinition(name='upstream resource ids', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:RetrievalSource', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'physical essence or occurrent': ClassDefinition(name='physical essence or occurrent', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/PhysicalEssenceOrOccurrent', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a physical or processual entity.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='biolink:PhysicalEssenceOrOccurrent', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'physical essence': ClassDefinition(name='physical essence', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/PhysicalEssence', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='physical essence or occurrent', abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='biolink:PhysicalEssence', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'physical entity': ClassDefinition(name='physical entity', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/PhysicalEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An entity that has material reality (a.k.a. physical essence).', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['STY:T072'], close_mappings=[], related_mappings=[], narrow_mappings=['STY:T073'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='named thing', abstract=None, mixin=None, mixins=['physical essence'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category'], slot_usage={}, attributes={}, class_uri='biolink:PhysicalEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'occurrent': ClassDefinition(name='occurrent', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Occurrent', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A processual entity.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['BFO:0000003'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='physical essence or occurrent', abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='biolink:Occurrent', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'activity and behavior': ClassDefinition(name='activity and behavior', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ActivityAndBehavior', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Activity or behavior of any independent integral living, organization or mechanical actor in the world', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['UMLSSG:ACTI'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='occurrent', abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='biolink:ActivityAndBehavior', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'activity': ClassDefinition(name='activity', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Activity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['prov:Activity', 'NCIT:C43431', 'STY:T052'], close_mappings=[], related_mappings=[], narrow_mappings=['STY:T056', 'STY:T057', 'STY:T064', 'STY:T066', 'STY:T062', 'STY:T065', 'STY:T058'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='named thing', abstract=None, mixin=None, mixins=['activity and behavior'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category'], slot_usage={}, attributes={}, class_uri='biolink:Activity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'procedure': ClassDefinition(name='procedure', id_prefixes=['CPT'], definition_uri='https://w3id.org/biolink/vocab/Procedure', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A series of actions conducted in a certain order or manner', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['UMLSSG:PROC', 'dcid:MedicalProcedure'], close_mappings=[], related_mappings=[], narrow_mappings=['STY:T059', 'STY:T060', 'STY:T061', 'STY:T063'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='named thing', abstract=None, mixin=None, mixins=['activity and behavior'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category'], slot_usage={}, attributes={}, class_uri='biolink:Procedure', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'phenomenon': ClassDefinition(name='phenomenon', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Phenomenon', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['UMLSSG:PHEN'], close_mappings=[], related_mappings=[], narrow_mappings=['STY:T034', 'STY:T038', 'STY:T069'], broad_mappings=['STY:T067', 'STY:T068', 'STY:T070'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='named thing', abstract=None, mixin=None, mixins=['occurrent'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category'], slot_usage={}, attributes={}, class_uri='biolink:Phenomenon', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'device': ClassDefinition(name='device', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Device', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=['UMLSSG:DEVI', 'STY:T074', 'STY:T075', 'STY:T203', 'STY:T122'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='named thing', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category'], slot_usage={}, attributes={}, class_uri='biolink:Device', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'diagnostic aid': ClassDefinition(name='diagnostic aid', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/DiagnosticAid', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A device or substance used to help diagnose disease or injury', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['STY:T130', 'SNOMED:2949005'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='named thing', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category'], slot_usage={}, attributes={}, class_uri='biolink:DiagnosticAid', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'study population': ClassDefinition(name='study population', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/StudyPopulation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A group of people banded together or treated as a group as participants in a research study.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['WIKIDATA:Q7229825'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='population of individual organisms', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'provided by', 'xref', 'named thing_category', 'in taxon', 'organismal entity_has attribute'], slot_usage={}, attributes={}, class_uri='biolink:StudyPopulation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'subject of investigation': ClassDefinition(name='subject of investigation', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/SubjectOfInvestigation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An entity that has the role of being studied in an investigation, study, or experiment', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='biolink:SubjectOfInvestigation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'material sample': ClassDefinition(name='material sample', id_prefixes=['BIOSAMPLE', 'GOLD.META'], definition_uri='https://w3id.org/biolink/vocab/MaterialSample', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO]', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['biospecimen', 'sample', 'biosample', 'physical sample'], structured_aliases={}, mappings=[], exact_mappings=['OBI:0000747', 'SIO:001050'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='physical entity', abstract=None, mixin=None, mixins=['subject of investigation'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category'], slot_usage={}, attributes={}, class_uri='biolink:MaterialSample', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'planetary entity': ClassDefinition(name='planetary entity', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/PlanetaryEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Any entity or process that exists at the level of the whole planet', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='named thing', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category'], slot_usage={}, attributes={}, class_uri='biolink:PlanetaryEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'environmental process': ClassDefinition(name='environmental process', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/EnvironmentalProcess', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['ENVO:02500000'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='planetary entity', abstract=None, mixin=None, mixins=['occurrent'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category'], slot_usage={}, attributes={}, class_uri='biolink:EnvironmentalProcess', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'environmental feature': ClassDefinition(name='environmental feature', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/EnvironmentalFeature', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['ENVO:01000254'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='planetary entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category'], slot_usage={}, attributes={}, class_uri='biolink:EnvironmentalFeature', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'geographic location': ClassDefinition(name='geographic location', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GeographicLocation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a location that can be described in lat/long coordinates', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['UMLSSG:GEOG', 'STY:T083'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='planetary entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'latitude', 'longitude'], slot_usage={}, attributes={}, class_uri='biolink:GeographicLocation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'geographic location at time': ClassDefinition(name='geographic location at time', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GeographicLocationAtTime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a location that can be described in lat/long coordinates, for a particular time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='geographic location', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'latitude', 'longitude', 'timepoint'], slot_usage={}, attributes={}, class_uri='biolink:GeographicLocationAtTime', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'thing with taxon': ClassDefinition(name='thing with taxon', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ThingWithTaxon', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; genes, their products and other molecular entities; body parts; biological processes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['in taxon'], slot_usage={}, attributes={}, class_uri='biolink:ThingWithTaxon', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'biological entity': ClassDefinition(name='biological entity', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/BiologicalEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['bioentity'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=['WIKIDATA:Q28845870', 'STY:T050', 'SIO:010046', 'STY:T129'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='named thing', abstract=True, mixin=None, mixins=['thing with taxon'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon'], slot_usage={}, attributes={}, class_uri='biolink:BiologicalEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'genomic entity': ClassDefinition(name='genomic entity', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GenomicEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['translator_minimal'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=['STY:T028', 'GENO:0000897'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['has biological sequence'], slot_usage={}, attributes={}, class_uri='biolink:GenomicEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'epigenomic entity': ClassDefinition(name='epigenomic entity', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/EpigenomicEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['translator_minimal'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['has biological sequence'], slot_usage={}, attributes={}, class_uri='biolink:EpigenomicEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'molecular entity': ClassDefinition(name='molecular entity', id_prefixes=['PUBCHEM.COMPOUND', 'CHEMBL.COMPOUND', 'UNII', 'CHEBI', 'DRUGBANK', 'MESH', 'CAS', 'DrugCentral', 'GTOPDB', 'HMDB', 'KEGG.COMPOUND', 'ChemBank', 'PUBCHEM.SUBSTANCE', 'SIDER.DRUG', 'INCHI', 'INCHIKEY', 'KEGG.GLYCAN', 'KEGG.DRUG', 'KEGG.ENVIRON', 'KEGG', 'UMLS'], definition_uri='https://w3id.org/biolink/vocab/MolecularEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A molecular entity is a chemical entity composed of individual or covalently bonded atoms.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['translator_minimal'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=['STY:T088', 'STY:T085', 'CHEBI:23367', 'bioschemas:MolecularEntity'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='chemical entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'trade name', 'available from', 'max tolerated dose', 'is toxic', 'has chemical role', 'is metabolite'], slot_usage={}, attributes={}, class_uri='biolink:MolecularEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'chemical entity': ClassDefinition(name='chemical entity', id_prefixes=['UNII', 'CHEBI', 'MESH', 'CAS', 'UMLS', 'ncats.drug', 'PHARMGKB.CHEMICAL'], definition_uri='https://w3id.org/biolink/vocab/ChemicalEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A chemical entity is a physical entity that pertains to chemistry or biochemistry.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['translator_minimal'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['CHEBI:24431', 'SIO:010004', 'WIKIDATA:Q79529', 'STY:T103'], close_mappings=[], related_mappings=[], narrow_mappings=['WIKIDATA:Q43460564'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='named thing', abstract=None, mixin=None, mixins=['physical essence', 'chemical or drug or treatment', 'chemical entity or gene or gene product', 'chemical entity or protein or polypeptide'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'trade name', 'available from', 'max tolerated dose', 'is toxic', 'has chemical role'], slot_usage={}, attributes={}, class_uri='biolink:ChemicalEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'small molecule': ClassDefinition(name='small molecule', id_prefixes=['PUBCHEM.COMPOUND', 'CHEMBL.COMPOUND', 'UNII', 'CHEBI', 'DRUGBANK', 'MESH', 'CAS', 'DrugCentral', 'GTOPDB', 'HMDB', 'KEGG.COMPOUND', 'ChemBank', 'PUBCHEM.SUBSTANCE', 'SIDER.DRUG', 'INCHI', 'INCHIKEY', 'KEGG.GLYCAN', 'KEGG.DRUG', 'KEGG.ENVIRON', 'KEGG', 'BIGG.METABOLITE', 'UMLS', 'foodb.compound'], definition_uri='https://w3id.org/biolink/vocab/SmallMolecule', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion).', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['model_organism_database', 'translator_minimal'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['chemical substance'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=['STY:T196', 'CHEBI:59999', 'bioschemas:ChemicalSubstance', 'STY:T123', 'STY:T131', 'STY:T125', 'STY:T197', 'STY:T109', 'STY:T118', 'STY:T111', 'STY:T119', 'STY:T124', 'STY:T115', 'STY:T110', 'STY:T127'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='molecular entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'trade name', 'available from', 'max tolerated dose', 'is toxic', 'has chemical role', 'is metabolite', 'small molecule_id'], slot_usage={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='CHEBI:29101', description='sodium ion', object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:SmallMolecule', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'chemical mixture': ClassDefinition(name='chemical mixture', id_prefixes=['PUBCHEM.COMPOUND', 'CHEMBL.COMPOUND', 'UNII', 'CHEBI', 'DRUGBANK', 'MESH', 'CAS', 'DrugCentral', 'GTOPDB', 'HMDB', 'KEGG.COMPOUND', 'ChemBank', 'PUBCHEM.SUBSTANCE', 'SIDER.DRUG', 'INCHI', 'INCHIKEY', 'KEGG.GLYCAN', 'KEGG.DRUG', 'KEGG', 'KEGG.ENVIRON', 'UMLS'], definition_uri='https://w3id.org/biolink/vocab/ChemicalMixture', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A chemical mixture is a chemical entity composed of two or more molecular entities.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['translator_minimal'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['dcid:ChemicalCompound'], related_mappings=[], narrow_mappings=['NCIT:C20401', 'SNOMEDCT:49616005'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='chemical entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'trade name', 'available from', 'max tolerated dose', 'is toxic', 'has chemical role', 'is supplement', 'highest FDA approval status', 'drug regulatory status world wide', 'routes of delivery'], slot_usage={}, attributes={}, class_uri='biolink:ChemicalMixture', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'nucleic acid entity': ClassDefinition(name='nucleic acid entity', id_prefixes=['PUBCHEM.COMPOUND', 'CHEMBL.COMPOUND', 'UNII', 'CHEBI', 'MESH', 'CAS', 'GTOPDB', 'HMDB', 'KEGG', 'KEGG.COMPOUND', 'ChemBank', 'PUBCHEM.SUBSTANCE', 'INCHI', 'INCHIKEY', 'KEGG.GLYCAN', 'KEGG.ENVIRON'], definition_uri='https://w3id.org/biolink/vocab/NucleicAcidEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['model_organism_database', 'translator_minimal'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['sequence feature', 'genomic entity'], structured_aliases={}, mappings=[], exact_mappings=['SO:0000110'], close_mappings=[], related_mappings=[], narrow_mappings=['STY:T086', 'STY:T114'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='molecular entity', abstract=None, mixin=None, mixins=['genomic entity', 'thing with taxon', 'physical essence', 'ontology class'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'trade name', 'available from', 'max tolerated dose', 'is toxic', 'has chemical role', 'is metabolite', 'has biological sequence', 'in taxon'], slot_usage={}, attributes={}, class_uri='biolink:NucleicAcidEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'regulatory region': ClassDefinition(name='regulatory region', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/RegulatoryRegion', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['regulatory element'], structured_aliases={}, mappings=[], exact_mappings=['SO:0005836', 'SIO:001225', 'WIKIDATA:Q3238407'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='biological entity', abstract=None, mixin=None, mixins=['genomic entity', 'chemical entity or gene or gene product', 'physical essence', 'ontology class'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon', 'has biological sequence'], slot_usage={}, attributes={}, class_uri='biolink:RegulatoryRegion', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'accessible dna region': ClassDefinition(name='accessible dna region', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/AccessibleDnaRegion', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['dnase-seq accessible region', 'atac-seq accessible region'], structured_aliases={}, mappings=[], exact_mappings=['SO:0002231'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='regulatory region', abstract=None, mixin=None, mixins=['genomic entity', 'chemical entity or gene or gene product', 'physical essence', 'ontology class'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon', 'has biological sequence'], slot_usage={}, attributes={}, class_uri='biolink:AccessibleDnaRegion', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'transcription factor binding site': ClassDefinition(name='transcription factor binding site', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/TranscriptionFactorBindingSite', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['tf binding site', 'binding site'], structured_aliases={}, mappings=[], exact_mappings=['SO:0000235'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='regulatory region', abstract=None, mixin=None, mixins=['genomic entity', 'chemical entity or gene or gene product', 'physical essence', 'ontology class'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon', 'has biological sequence'], slot_usage={}, attributes={}, class_uri='biolink:TranscriptionFactorBindingSite', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'molecular mixture': ClassDefinition(name='molecular mixture', id_prefixes=['PUBCHEM.COMPOUND', 'CHEMBL.COMPOUND', 'UNII', 'CHEBI', 'DRUGBANK', 'MESH', 'CAS', 'DrugCentral', 'GTOPDB', 'HMDB', 'KEGG.COMPOUND', 'ChemBank', 'PUBCHEM.SUBSTANCE', 'SIDER.DRUG', 'INCHI', 'INCHIKEY', 'KEGG.GLYCAN', 'KEGG.DRUG', 'KEGG', 'KEGG.ENVIRON', 'UMLS', 'ncats.drug'], definition_uri='https://w3id.org/biolink/vocab/MolecularMixture', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['translator_minimal'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='chemical mixture', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'trade name', 'available from', 'max tolerated dose', 'is toxic', 'has chemical role', 'is supplement', 'highest FDA approval status', 'drug regulatory status world wide', 'routes of delivery'], slot_usage={}, attributes={}, class_uri='biolink:MolecularMixture', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'complex molecular mixture': ClassDefinition(name='complex molecular mixture', id_prefixes=['PUBCHEM.COMPOUND', 'CHEMBL.COMPOUND', 'UNII', 'CHEBI', 'DRUGBANK', 'MESH', 'CAS', 'DrugCentral', 'GTOPDB', 'HMDB', 'KEGG.COMPOUND', 'ChemBank', 'PUBCHEM.SUBSTANCE', 'SIDER.DRUG', 'INCHI', 'INCHIKEY', 'KEGG.GLYCAN', 'KEGG.DRUG', 'KEGG', 'KEGG.ENVIRON', 'UMLS'], definition_uri='https://w3id.org/biolink/vocab/ComplexMolecularMixture', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['translator_minimal'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='chemical mixture', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'trade name', 'available from', 'max tolerated dose', 'is toxic', 'has chemical role', 'is supplement', 'highest FDA approval status', 'drug regulatory status world wide', 'routes of delivery'], slot_usage={}, attributes={}, class_uri='biolink:ComplexMolecularMixture', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'biological process or activity': ClassDefinition(name='biological process or activity', id_prefixes=['GO', 'REACT'], definition_uri='https://w3id.org/biolink/vocab/BiologicalProcessOrActivity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='biological entity', abstract=None, mixin=None, mixins=['occurrent', 'ontology class'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon', 'has input', 'has output', 'enabled by'], slot_usage={}, attributes={}, class_uri='biolink:BiologicalProcessOrActivity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'molecular activity': ClassDefinition(name='molecular activity', id_prefixes=['GO', 'REACT', 'RHEA', 'metacyc.reaction', 'EC', 'TCDB', 'KEGG.REACTION', 'KEGG', 'KEGG.ORTHOLOGY', 'UMLS', 'BIGG.REACTION', 'SEED.REACTION', 'METANETX.REACTION'], definition_uri='https://w3id.org/biolink/vocab/MolecularActivity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An execution of a molecular function carried out by a gene product or macromolecular complex.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['molecular function', 'molecular event', 'reaction'], structured_aliases={}, mappings=[], exact_mappings=['GO:0003674', 'STY:T044'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['STY:T045'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='biological process or activity', abstract=None, mixin=None, mixins=['occurrent', 'ontology class'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon', 'molecular activity_has input', 'molecular activity_has output', 'molecular activity_enabled by'], slot_usage={'has input': SlotDefinition(name='has input', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A chemical entity that is the input for the reaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='molecular entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'has output': SlotDefinition(name='has output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A chemical entity that is the output for the reaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='molecular entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'enabled by': SlotDefinition(name='enabled by', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The gene product, gene, or complex that catalyzes the reaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='macromolecular machine mixin', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:MolecularActivity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'biological process': ClassDefinition(name='biological process', id_prefixes=['GO', 'REACT', 'metacyc.reaction', 'KEGG.MODULE', 'KEGG'], definition_uri='https://w3id.org/biolink/vocab/BiologicalProcess', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='One or more causally connected executions of molecular functions', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['GO:0008150', 'SIO:000006', 'WIKIDATA:Q2996394'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['WIKIDATA:P682'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='biological process or activity', abstract=None, mixin=None, mixins=['occurrent', 'ontology class'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon', 'has input', 'has output', 'enabled by'], slot_usage={}, attributes={}, class_uri='biolink:BiologicalProcess', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'pathway': ClassDefinition(name='pathway', id_prefixes=['GO', 'REACT', 'KEGG', 'SMPDB', 'MSigDB', 'PHARMGKB.PATHWAYS', 'WIKIPATHWAYS', 'FB', 'PANTHER.PATHWAY', 'KEGG.PATHWAY', 'ncats.bioplanet'], definition_uri='https://w3id.org/biolink/vocab/Pathway', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['PW:0000001', 'WIKIDATA:Q4915012'], close_mappings=[], related_mappings=[], narrow_mappings=['SIO:010526', 'GO:0007165'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='biological process', abstract=None, mixin=None, mixins=['ontology class'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon', 'has input', 'has output', 'enabled by'], slot_usage={}, attributes={}, class_uri='biolink:Pathway', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'physiological process': ClassDefinition(name='physiological process', id_prefixes=['GO', 'REACT'], definition_uri='https://w3id.org/biolink/vocab/PhysiologicalProcess', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['physiology'], structured_aliases={}, mappings=[], exact_mappings=['STY:T039', 'WIKIDATA:Q30892994'], close_mappings=[], related_mappings=[], narrow_mappings=['STY:T040', 'STY:T042', 'STY:T043', 'STY:T045'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='biological process', abstract=None, mixin=None, mixins=['ontology class'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon', 'has input', 'has output', 'enabled by'], slot_usage={}, attributes={}, class_uri='biolink:PhysiologicalProcess', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'behavior': ClassDefinition(name='behavior', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Behavior', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['GO:0007610', 'STY:T053'], close_mappings=[], related_mappings=[], narrow_mappings=['STY:T041', 'STY:T054', 'STY:T055'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='biological process', abstract=None, mixin=None, mixins=['ontology class', 'activity and behavior'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon', 'has input', 'has output', 'enabled by'], slot_usage={}, attributes={}, class_uri='biolink:Behavior', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'processed material': ClassDefinition(name='processed material', id_prefixes=['UMLS'], definition_uri='https://w3id.org/biolink/vocab/ProcessedMaterial', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['OBI:0000047'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='chemical mixture', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'trade name', 'available from', 'max tolerated dose', 'is toxic', 'has chemical role', 'is supplement', 'highest FDA approval status', 'drug regulatory status world wide', 'routes of delivery'], slot_usage={}, attributes={}, class_uri='biolink:ProcessedMaterial', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'drug': ClassDefinition(name='drug', id_prefixes=['ncats.drug', 'RXCUI', 'NDC', 'UMLS'], definition_uri='https://w3id.org/biolink/vocab/Drug', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['The CHEBI ID represents a role rather than a substance'], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['WIKIDATA:Q12140', 'CHEBI:23888', 'STY:T200', 'dcid:Drug'], close_mappings=[], related_mappings=[], narrow_mappings=['STY:T195'], broad_mappings=['STY:T121'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='molecular mixture', abstract=None, mixin=None, mixins=['chemical or drug or treatment', 'ontology class'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'trade name', 'available from', 'max tolerated dose', 'is toxic', 'has chemical role', 'is supplement', 'highest FDA approval status', 'drug regulatory status world wide', 'routes of delivery'], slot_usage={}, attributes={}, class_uri='biolink:Drug', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'environmental food contaminant': ClassDefinition(name='environmental food contaminant', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/EnvironmentalFoodContaminant', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=['CHEBI:78299'], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='chemical entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'trade name', 'available from', 'max tolerated dose', 'is toxic', 'has chemical role'], slot_usage={}, attributes={}, class_uri='biolink:EnvironmentalFoodContaminant', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'food additive': ClassDefinition(name='food additive', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/FoodAdditive', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=['CHEBI:64047'], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='chemical entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'trade name', 'available from', 'max tolerated dose', 'is toxic', 'has chemical role'], slot_usage={}, attributes={}, class_uri='biolink:FoodAdditive', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'food': ClassDefinition(name='food', id_prefixes=['foodb.food', 'FOODON', 'UMLS', 'NCIT'], definition_uri='https://w3id.org/biolink/vocab/Food', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A substance consumed by a living organism as a source of nutrition', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['STY:T168'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='chemical mixture', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'trade name', 'available from', 'max tolerated dose', 'is toxic', 'has chemical role', 'is supplement', 'highest FDA approval status', 'drug regulatory status world wide', 'routes of delivery'], slot_usage={}, attributes={}, class_uri='biolink:Food', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'organism attribute': ClassDefinition(name='organism attribute', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/OrganismAttribute', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='describes a characteristic of an organismal entity.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['STY:T032'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='attribute', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has attribute type', 'has quantitative value', 'has qualitative value', 'iri'], slot_usage={}, attributes={}, class_uri='biolink:OrganismAttribute', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'phenotypic quality': ClassDefinition(name='phenotypic quality', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/PhenotypicQuality', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A property of a phenotype', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='weight', description=None, object=None)], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['phenotypic properties'], structured_aliases={}, mappings=['PATO:0000001'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='organism attribute', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has attribute type', 'has quantitative value', 'has qualitative value', 'iri'], slot_usage={}, attributes={}, class_uri='biolink:PhenotypicQuality', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'genetic inheritance': ClassDefinition(name='genetic inheritance', id_prefixes=['HP', 'GENO', 'NCIT'], definition_uri='https://w3id.org/biolink/vocab/GeneticInheritance', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=\"The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc.\", alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['inheritance'], structured_aliases={}, mappings=[], exact_mappings=['HP:0000005', 'GENO:0000141', 'NCIT:C45827'], close_mappings=['STY:T045'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='biological entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon'], slot_usage={}, attributes={}, class_uri='biolink:GeneticInheritance', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'organismal entity': ClassDefinition(name='organismal entity', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/OrganismalEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['WIKIDATA:Q7239', 'UMLSSG:LIVB', 'CARO:0001010'], close_mappings=[], related_mappings=[], narrow_mappings=['STY:T008'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='biological entity', abstract=True, mixin=None, mixins=['subject of investigation'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'provided by', 'xref', 'named thing_category', 'in taxon', 'organismal entity_has attribute'], slot_usage={'has attribute': SlotDefinition(name='has attribute', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='may often be an organism attribute', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:OrganismalEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'bacterium': ClassDefinition(name='bacterium', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Bacterium', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and are often motile.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['NCBITaxon:1869227', 'STY:T007'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='organismal entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'provided by', 'xref', 'named thing_category', 'in taxon', 'organismal entity_has attribute'], slot_usage={}, attributes={}, class_uri='biolink:Bacterium', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'virus': ClassDefinition(name='virus', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Virus', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A virus is a microorganism that replicates itself as a microRNA and infects the host cell.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['NCBITaxon:10239', 'STY:T005'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='organismal entity', abstract=None, mixin=None, mixins=['subject of investigation'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'provided by', 'xref', 'named thing_category', 'in taxon', 'organismal entity_has attribute'], slot_usage={}, attributes={}, class_uri='biolink:Virus', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'cellular organism': ClassDefinition(name='cellular organism', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/CellularOrganism', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['NCBITaxon:131567'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='organismal entity', abstract=None, mixin=None, mixins=['subject of investigation'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'provided by', 'xref', 'named thing_category', 'in taxon', 'organismal entity_has attribute'], slot_usage={}, attributes={}, class_uri='biolink:CellularOrganism', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'mammal': ClassDefinition(name='mammal', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Mammal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A member of the class Mammalia, a clade of endothermic amniotes distinguished from reptiles and birds by the possession of hair, three middle ear bones, mammary glands, and a neocortex', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['NCBITaxon:40674', 'STY:T015', 'NCIT:C14234', 'FOODON:03411134'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='cellular organism', abstract=None, mixin=None, mixins=['subject of investigation'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'provided by', 'xref', 'named thing_category', 'in taxon', 'organismal entity_has attribute'], slot_usage={}, attributes={}, class_uri='biolink:Mammal', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'human': ClassDefinition(name='human', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Human', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A member of the the species Homo sapiens.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['STY:T016', 'NCBITaxon:9606', 'SIO:000485', 'NCIT:C14225'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='mammal', abstract=None, mixin=None, mixins=['subject of investigation'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'provided by', 'xref', 'named thing_category', 'in taxon', 'organismal entity_has attribute'], slot_usage={}, attributes={}, class_uri='biolink:Human', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'plant': ClassDefinition(name='plant', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Plant', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['NCIT:C14258', 'STY:T002', 'PO:0000003', 'NCIT:C79659'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='cellular organism', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'provided by', 'xref', 'named thing_category', 'in taxon', 'organismal entity_has attribute'], slot_usage={}, attributes={}, class_uri='biolink:Plant', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'invertebrate': ClassDefinition(name='invertebrate', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Invertebrate', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An animal lacking a vertebral column. This group consists of 98% of all animal species.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['NCIT:C14228', 'OMIT:0008565', 'FOODON:00002452', 'STY:T011'], close_mappings=[], related_mappings=['NCBITaxon:1767184'], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='cellular organism', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'provided by', 'xref', 'named thing_category', 'in taxon', 'organismal entity_has attribute'], slot_usage={}, attributes={}, class_uri='biolink:Invertebrate', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'vertebrate': ClassDefinition(name='vertebrate', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Vertebrate', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['STY:T010', 'NCBITaxon:7742', 'OMIT:0015545'], close_mappings=[], related_mappings=['NCBITaxon:2662825'], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='cellular organism', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'provided by', 'xref', 'named thing_category', 'in taxon', 'organismal entity_has attribute'], slot_usage={}, attributes={}, class_uri='biolink:Vertebrate', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'fungus': ClassDefinition(name='fungus', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Fungus', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi refer to those that grow as multicellular colonies (mushrooms and molds).', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['STY:T004', 'NCIT:C14209', 'FOODON:03411261'], close_mappings=[], related_mappings=[], narrow_mappings=['FOODON:03315605', 'NCBITaxon:1670606'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='cellular organism', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'provided by', 'xref', 'named thing_category', 'in taxon', 'organismal entity_has attribute'], slot_usage={}, attributes={}, class_uri='biolink:Fungus', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'life stage': ClassDefinition(name='life stage', id_prefixes=['HsapDv', 'MmusDv', 'ZFS', 'FBdv', 'WBls', 'UBERON'], definition_uri='https://w3id.org/biolink/vocab/LifeStage', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A stage of development or growth of an organism, including post-natal adult stages', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['model_organism_database'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['UBERON:0000105'], close_mappings=[], related_mappings=[], narrow_mappings=['HsapDv:0000000'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='organismal entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'provided by', 'xref', 'named thing_category', 'in taxon', 'organismal entity_has attribute'], slot_usage={}, attributes={}, class_uri='biolink:LifeStage', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'individual organism': ClassDefinition(name='individual organism', id_prefixes=['ORCID'], definition_uri='https://w3id.org/biolink/vocab/IndividualOrganism', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['organism'], structured_aliases={}, mappings=[], exact_mappings=['SIO:010000', 'STY:T001'], close_mappings=[], related_mappings=[], narrow_mappings=['WIKIDATA:Q795052', 'foaf:Person'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='organismal entity', abstract=None, mixin=None, mixins=['subject of investigation'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'provided by', 'xref', 'named thing_category', 'in taxon', 'organismal entity_has attribute'], slot_usage={}, attributes={}, class_uri='biolink:IndividualOrganism', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'population of individual organisms': ClassDefinition(name='population of individual organisms', id_prefixes=['HANCESTRO'], definition_uri='https://w3id.org/biolink/vocab/PopulationOfIndividualOrganisms', local_names={'ga4gh': LocalName(local_name_source='ga4gh', local_name_value='population')}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['model_organism_database'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['PCO:0000001', 'SIO:001061', 'STY:T098', 'OBI:0000181'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='organismal entity', abstract=None, mixin=None, mixins=['subject of investigation'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'provided by', 'xref', 'named thing_category', 'in taxon', 'organismal entity_has attribute'], slot_usage={}, attributes={}, class_uri='biolink:PopulationOfIndividualOrganisms', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'disease or phenotypic feature': ClassDefinition(name='disease or phenotypic feature', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeature', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['phenome'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=['STY:T033'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='biological entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon'], slot_usage={}, attributes={}, class_uri='biolink:DiseaseOrPhenotypicFeature', subclass_of=None, union_of=['disease', 'phenotypic feature'], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'disease': ClassDefinition(name='disease', id_prefixes=['MONDO', 'DOID', 'OMIM', 'OMIM.PS', 'orphanet', 'EFO', 'UMLS', 'MESH', 'MEDDRA', 'NCIT', 'SNOMEDCT', 'medgen', 'ICD10', 'ICD9', 'KEGG.DISEASE', 'HP', 'MP', 'PHARMGKB.DISEASE'], definition_uri='https://w3id.org/biolink/vocab/Disease', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['model_organism_database', 'translator_minimal'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['condition', 'disorder', 'medical condition'], structured_aliases={}, mappings=[], exact_mappings=['MONDO:0000001', 'DOID:4', 'NCIT:C2991', 'WIKIDATA:Q12136', 'SIO:010299', 'UMLSSG:DISO', 'STY:T047', 'dcid:Disease'], close_mappings=[], related_mappings=[], narrow_mappings=['STY:T019', 'STY:T020', 'STY:T048', 'STY:T049', 'STY:T190', 'STY:T191', 'MONDO:0042489'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='disease or phenotypic feature', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon'], slot_usage={}, attributes={}, class_uri='biolink:Disease', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'phenotypic feature': ClassDefinition(name='phenotypic feature', id_prefixes=['HP', 'EFO', 'NCIT', 'UMLS', 'MEDDRA', 'MP', 'ZP', 'UPHENO', 'APO', 'FBcv', 'WBPhenotype', 'SNOMEDCT', 'MESH', 'XPO', 'FYPO', 'TO'], definition_uri='https://w3id.org/biolink/vocab/PhenotypicFeature', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='MP:0001262', description='decreased body weight', object=None)], in_subset=['model_organism_database'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['sign', 'symptom', 'phenotype', 'trait', 'endophenotype'], structured_aliases={}, mappings=[], exact_mappings=['UPHENO:0001001', 'SIO:010056', 'WIKIDATA:Q104053', 'UMLS:C4021819', 'NCIT:C16977', 'SNOMEDCT:8116006', 'MESH:D010641'], close_mappings=[], related_mappings=[], narrow_mappings=['STY:T184', 'WIKIDATA:Q169872', 'WIKIDATA:Q25203551', 'ZP:00000000', 'FBcv:0001347', 'HP:0000118', 'MP:0000001', 'WBPhenotype:0000886', 'XPO:00000000', 'FYPO:0000001', 'APO:0000017', 'TO:0000387'], broad_mappings=['BFO:0000019', 'PATO:0000001'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='disease or phenotypic feature', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon'], slot_usage={}, attributes={}, class_uri='biolink:PhenotypicFeature', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'behavioral feature': ClassDefinition(name='behavioral feature', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/BehavioralFeature', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A phenotypic feature which is behavioral in nature.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['NBO:0000243'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='phenotypic feature', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon'], slot_usage={}, attributes={}, class_uri='biolink:BehavioralFeature', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'anatomical entity': ClassDefinition(name='anatomical entity', id_prefixes=['UBERON', 'GO', 'CL', 'UMLS', 'MESH', 'NCIT', 'EMAPA', 'ZFA', 'FBbt', 'WBbt'], definition_uri='https://w3id.org/biolink/vocab/AnatomicalEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A subcellular location, cell type or gross anatomical part', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['model_organism_database'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['UBERON:0001062', 'WIKIDATA:Q4936952', 'UMLSSG:ANAT', 'STY:T017', 'FMA:62955', 'CARO:0000000', 'SIO:001262', 'STY:T029', 'STY:T030'], close_mappings=[], related_mappings=['SNOMEDCT:123037004'], narrow_mappings=['ZFA:0100000', 'FBbt:10000000', 'EMAPA:0', 'MA:0000001', 'XAO:0000000', 'WBbt:0000100', 'NCIT:C12219', 'GO:0110165', 'STY:T031'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='organismal entity', abstract=None, mixin=None, mixins=['physical essence'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'provided by', 'xref', 'named thing_category', 'in taxon', 'organismal entity_has attribute'], slot_usage={}, attributes={}, class_uri='biolink:AnatomicalEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'cellular component': ClassDefinition(name='cellular component', id_prefixes=['GO', 'MESH', 'UMLS', 'NCIT', 'SNOMEDCT', 'CL', 'UBERON'], definition_uri='https://w3id.org/biolink/vocab/CellularComponent', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A location in or around a cell', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['cell component', 'cell part'], structured_aliases={}, mappings=[], exact_mappings=['GO:0005575', 'SIO:001400', 'WIKIDATA:Q5058355', 'STY:T026'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['WIKIDATA:P681'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='anatomical entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'provided by', 'xref', 'named thing_category', 'in taxon', 'organismal entity_has attribute'], slot_usage={}, attributes={}, class_uri='biolink:CellularComponent', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'cell': ClassDefinition(name='cell', id_prefixes=['CL', 'PO', 'UMLS', 'NCIT', 'MESH', 'UBERON', 'SNOMEDCT', 'MESH'], definition_uri='https://w3id.org/biolink/vocab/Cell', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['GO:0005623', 'CL:0000000', 'SIO:010001', 'WIKIDATA:Q7868', 'STY:T025', 'MESH:D002477'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='anatomical entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'provided by', 'xref', 'named thing_category', 'in taxon', 'organismal entity_has attribute'], slot_usage={}, attributes={}, class_uri='biolink:Cell', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'cell line': ClassDefinition(name='cell line', id_prefixes=['CLO'], definition_uri='https://w3id.org/biolink/vocab/CellLine', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['CLO:0000031'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='organismal entity', abstract=None, mixin=None, mixins=['subject of investigation'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'provided by', 'xref', 'named thing_category', 'in taxon', 'organismal entity_has attribute'], slot_usage={}, attributes={}, class_uri='biolink:CellLine', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'gross anatomical structure': ClassDefinition(name='gross anatomical structure', id_prefixes=['UBERON', 'UMLS', 'MESH', 'NCIT', 'PO', 'FAO'], definition_uri='https://w3id.org/biolink/vocab/GrossAnatomicalStructure', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['tissue', 'organ'], structured_aliases={}, mappings=[], exact_mappings=['UBERON:0010000', 'WIKIDATA:Q4936952'], close_mappings=[], related_mappings=[], narrow_mappings=['STY:T023', 'STY:T024', 'STY:T018'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='anatomical entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'provided by', 'xref', 'named thing_category', 'in taxon', 'organismal entity_has attribute'], slot_usage={}, attributes={}, class_uri='biolink:GrossAnatomicalStructure', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'chemical entity or gene or gene product': ClassDefinition(name='chemical entity or gene or gene product', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ChemicalEntityOrGeneOrGeneProduct', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A union of chemical entities and children, and gene or gene product. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='biolink:ChemicalEntityOrGeneOrGeneProduct', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'chemical entity or protein or polypeptide': ClassDefinition(name='chemical entity or protein or polypeptide', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ChemicalEntityOrProteinOrPolypeptide', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A union of chemical entities and children, and protein and polypeptide. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='biolink:ChemicalEntityOrProteinOrPolypeptide', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'macromolecular machine mixin': ClassDefinition(name='macromolecular machine mixin', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/MacromolecularMachineMixin', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A union of gene locus, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['macromolecular machine mixin_name'], slot_usage={'name': SlotDefinition(name='name', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='symbol type', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:MacromolecularMachineMixin', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'gene or gene product': ClassDefinition(name='gene or gene product', id_prefixes=['CHEMBL.TARGET', 'IUPHAR.FAMILY'], definition_uri='https://w3id.org/biolink/vocab/GeneOrGeneProduct', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='macromolecular machine mixin', abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['macromolecular machine mixin_name'], slot_usage={}, attributes={}, class_uri='biolink:GeneOrGeneProduct', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'gene': ClassDefinition(name='gene', id_prefixes=['NCBIGene', 'ENSEMBL', 'HGNC', 'MGI', 'ZFIN', 'dictyBase', 'WB', 'WormBase', 'FB', 'RGD', 'SGD', 'PomBase', 'OMIM', 'KEGG.GENES', 'UMLS', 'Xenbase', 'AspGD', 'PHARMGKB.GENE'], definition_uri='https://w3id.org/biolink/vocab/Gene', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['translator_minimal', 'model_organism_database'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['SO:0000704', 'SIO:010035', 'WIKIDATA:Q7187', 'dcid:Gene'], close_mappings=[], related_mappings=[], narrow_mappings=['bioschemas:gene'], broad_mappings=['NCIT:C45822'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='biological entity', abstract=None, mixin=None, mixins=['gene or gene product', 'genomic entity', 'chemical entity or gene or gene product', 'physical essence', 'ontology class'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'named thing_category', 'in taxon', 'symbol', 'synonym', 'xref', 'has biological sequence'], slot_usage={}, attributes={}, class_uri='biolink:Gene', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'gene product mixin': ClassDefinition(name='gene product mixin', id_prefixes=['UniProtKB', 'gtpo', 'PR'], definition_uri='https://w3id.org/biolink/vocab/GeneProductMixin', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA molecules.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['WIKIDATA:Q424689', 'GENO:0000907', 'NCIT:C26548'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='gene or gene product', abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['macromolecular machine mixin_name', 'synonym', 'xref'], slot_usage={}, attributes={}, class_uri='biolink:GeneProductMixin', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'gene product isoform mixin': ClassDefinition(name='gene product isoform mixin', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GeneProductIsoformMixin', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='gene product mixin', abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['macromolecular machine mixin_name', 'synonym', 'xref'], slot_usage={}, attributes={}, class_uri='biolink:GeneProductIsoformMixin', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'macromolecular complex': ClassDefinition(name='macromolecular complex', id_prefixes=['INTACT', 'GO', 'PR', 'REACT', 'ComplexPortal'], definition_uri='https://w3id.org/biolink/vocab/MacromolecularComplex', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['model_organism_database'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['GO:0032991', 'WIKIDATA:Q22325163'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='biological entity', abstract=None, mixin=None, mixins=['macromolecular machine mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon'], slot_usage={}, attributes={}, class_uri='biolink:MacromolecularComplex', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'nucleosome modification': ClassDefinition(name='nucleosome modification', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/NucleosomeModification', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='biological entity', abstract=None, mixin=None, mixins=['gene product isoform mixin', 'genomic entity', 'epigenomic entity'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon', 'synonym', 'has biological sequence'], slot_usage={}, attributes={}, class_uri='biolink:NucleosomeModification', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'genome': ClassDefinition(name='genome', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Genome', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A genome is the sum of genetic material within a cell or virion.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['model_organism_database'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['SO:0001026', 'SIO:000984', 'WIKIDATA:Q7020'], close_mappings=['dcid:GenomeAssemblyUnit'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='biological entity', abstract=None, mixin=None, mixins=['genomic entity', 'physical essence', 'ontology class'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon', 'has biological sequence'], slot_usage={}, attributes={}, class_uri='biolink:Genome', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'exon': ClassDefinition(name='exon', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Exon', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['SO:0000147', 'SIO:010445', 'WIKIDATA:Q373027'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='nucleic acid entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'trade name', 'available from', 'max tolerated dose', 'is toxic', 'has chemical role', 'is metabolite', 'has biological sequence', 'in taxon'], slot_usage={}, attributes={}, class_uri='biolink:Exon', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'transcript': ClassDefinition(name='transcript', id_prefixes=['ENSEMBL', 'FB'], definition_uri='https://w3id.org/biolink/vocab/Transcript', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An RNA synthesized on a DNA or RNA template by an RNA polymerase.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['model_organism_database'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['SO:0000673', 'SIO:010450', 'WIKIDATA:Q7243183', 'dcid:RNATranscript'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='nucleic acid entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'trade name', 'available from', 'max tolerated dose', 'is toxic', 'has chemical role', 'is metabolite', 'has biological sequence', 'in taxon'], slot_usage={}, attributes={}, class_uri='biolink:Transcript', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'coding sequence': ClassDefinition(name='coding sequence', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/CodingSequence', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['SO:0000316', 'SIO:001390'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='nucleic acid entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'trade name', 'available from', 'max tolerated dose', 'is toxic', 'has chemical role', 'is metabolite', 'has biological sequence', 'in taxon'], slot_usage={}, attributes={}, class_uri='biolink:CodingSequence', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'polypeptide': ClassDefinition(name='polypeptide', id_prefixes=['UniProtKB', 'PR', 'ENSEMBL', 'FB', 'UMLS'], definition_uri='https://w3id.org/biolink/vocab/Polypeptide', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['model_organism_database'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['amino acid entity'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=['SO:0000104', 'STY:T116', 'STY:T087'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='biological entity', abstract=None, mixin=None, mixins=['chemical entity or gene or gene product', 'chemical entity or protein or polypeptide'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon'], slot_usage={}, attributes={}, class_uri='biolink:Polypeptide', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'protein': ClassDefinition(name='protein', id_prefixes=['UniProtKB', 'PR', 'ENSEMBL', 'FB', 'UMLS', 'MESH', 'ncats.drug'], definition_uri='https://w3id.org/biolink/vocab/Protein', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['PR:000000001', 'SIO:010043', 'WIKIDATA:Q8054'], close_mappings=[], related_mappings=[], narrow_mappings=['STY:T126', 'STY:T192'], broad_mappings=['bioschemas:Protein'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='polypeptide', abstract=None, mixin=None, mixins=['gene product mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon', 'synonym'], slot_usage={}, attributes={}, class_uri='biolink:Protein', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'protein isoform': ClassDefinition(name='protein isoform', id_prefixes=['UniProtKB', 'UNIPROT.ISOFORM', 'PR', 'ENSEMBL'], definition_uri='https://w3id.org/biolink/vocab/ProteinIsoform', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['proteoform'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='protein', abstract=None, mixin=None, mixins=['gene product isoform mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon', 'synonym'], slot_usage={}, attributes={}, class_uri='biolink:ProteinIsoform', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'protein domain': ClassDefinition(name='protein domain', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ProteinDomain', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['NCIT:C13379', 'SIO:001379', 'UMLS:C1514562'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='biological entity', abstract=None, mixin=None, mixins=['gene grouping mixin', 'chemical entity or gene or gene product'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon', 'has gene or gene product'], slot_usage={}, attributes={}, class_uri='biolink:ProteinDomain', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'posttranslational modification': ClassDefinition(name='posttranslational modification', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/PosttranslationalModification', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='biological entity', abstract=None, mixin=None, mixins=['gene product isoform mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon', 'synonym'], slot_usage={}, attributes={}, class_uri='biolink:PosttranslationalModification', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'protein family': ClassDefinition(name='protein family', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ProteinFamily', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['NCIT:C26004', 'WIKIDATA:Q2278983'], close_mappings=[], related_mappings=[], narrow_mappings=['SIO:001380', 'NCIT:C20130', 'WIKIDATA:Q417841'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='biological entity', abstract=None, mixin=None, mixins=['gene grouping mixin', 'chemical entity or gene or gene product'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon', 'has gene or gene product'], slot_usage={}, attributes={}, class_uri='biolink:ProteinFamily', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'nucleic acid sequence motif': ClassDefinition(name='nucleic acid sequence motif', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/NucleicAcidSequenceMotif', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['consensus sequence'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='biological entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon'], slot_usage={}, attributes={}, class_uri='biolink:NucleicAcidSequenceMotif', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RNA product': ClassDefinition(name='RNA product', id_prefixes=['RNACENTRAL'], definition_uri='https://w3id.org/biolink/vocab/RNAProduct', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['CHEBI:33697', 'WIKIDATA:Q11053'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='transcript', abstract=None, mixin=None, mixins=['gene product mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'trade name', 'available from', 'max tolerated dose', 'is toxic', 'has chemical role', 'is metabolite', 'has biological sequence', 'in taxon', 'synonym'], slot_usage={}, attributes={}, class_uri='biolink:RNAProduct', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RNA product isoform': ClassDefinition(name='RNA product isoform', id_prefixes=['RNACENTRAL'], definition_uri='https://w3id.org/biolink/vocab/RNAProductIsoform', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Represents a protein that is a specific isoform of the canonical or reference RNA', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='RNA product', abstract=None, mixin=None, mixins=['gene product isoform mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'trade name', 'available from', 'max tolerated dose', 'is toxic', 'has chemical role', 'is metabolite', 'has biological sequence', 'in taxon', 'synonym'], slot_usage={}, attributes={}, class_uri='biolink:RNAProductIsoform', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'noncoding RNA product': ClassDefinition(name='noncoding RNA product', id_prefixes=['RNACENTRAL', 'NCBIGene', 'ENSEMBL'], definition_uri='https://w3id.org/biolink/vocab/NoncodingRNAProduct', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['SO:0000655', 'SIO:001235'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='RNA product', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'trade name', 'available from', 'max tolerated dose', 'is toxic', 'has chemical role', 'is metabolite', 'has biological sequence', 'in taxon', 'synonym'], slot_usage={}, attributes={}, class_uri='biolink:NoncodingRNAProduct', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'microRNA': ClassDefinition(name='microRNA', id_prefixes=['MIR', 'HGNC', 'WormBase'], definition_uri='https://w3id.org/biolink/vocab/MicroRNA', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['model_organism_database'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['SO:0000276', 'SIO:001397', 'WIKIDATA:Q310899'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='noncoding RNA product', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'trade name', 'available from', 'max tolerated dose', 'is toxic', 'has chemical role', 'is metabolite', 'has biological sequence', 'in taxon', 'synonym'], slot_usage={}, attributes={}, class_uri='biolink:MicroRNA', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'siRNA': ClassDefinition(name='siRNA', id_prefixes=['MIR', 'HGNC', 'WormBase'], definition_uri='https://w3id.org/biolink/vocab/SiRNA', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['model_organism_database'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['small interfering RNA', 'RNAi'], structured_aliases={}, mappings=[], exact_mappings=['SO:0000646', 'WIKIDATA:Q203221'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='noncoding RNA product', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'trade name', 'available from', 'max tolerated dose', 'is toxic', 'has chemical role', 'is metabolite', 'has biological sequence', 'in taxon', 'synonym'], slot_usage={}, attributes={}, class_uri='biolink:SiRNA', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'gene grouping mixin': ClassDefinition(name='gene grouping mixin', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GeneGroupingMixin', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='any grouping of multiple genes or gene products', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['has gene or gene product'], slot_usage={}, attributes={}, class_uri='biolink:GeneGroupingMixin', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'gene family': ClassDefinition(name='gene family', id_prefixes=['PANTHER.FAMILY', 'HGNC.FAMILY', 'FB', 'interpro', 'CATH', 'CDD', 'HAMAP', 'PFAM', 'PIRSF', 'PRINTS', 'PRODOM', 'PROSITE', 'SMART', 'SUPFAM', 'TIGRFAM', 'CATH.SUPERFAMILY', 'RFAM', 'KEGG.ORTHOLOGY', 'EGGNOG', 'COG'], definition_uri='https://w3id.org/biolink/vocab/GeneFamily', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='any grouping of multiple genes or gene products related by common descent', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['model_organism_database'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['orthogroup', 'protein family'], structured_aliases={}, mappings=[], exact_mappings=['NCIT:C26004', 'WIKIDATA:Q2278983'], close_mappings=[], related_mappings=[], narrow_mappings=['SIO:001380', 'NCIT:C20130', 'WIKIDATA:Q417841'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='biological entity', abstract=None, mixin=None, mixins=['gene grouping mixin', 'chemical entity or gene or gene product'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon', 'has gene or gene product'], slot_usage={}, attributes={}, class_uri='biolink:GeneFamily', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'zygosity': ClassDefinition(name='zygosity', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Zygosity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['GENO:0000133'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='attribute', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has attribute type', 'has quantitative value', 'has qualitative value', 'iri'], slot_usage={}, attributes={}, class_uri='biolink:Zygosity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'genotype': ClassDefinition(name='genotype', id_prefixes=['ZFIN', 'FB'], definition_uri='https://w3id.org/biolink/vocab/Genotype', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Consider renaming as genotypic entity'], examples=[], in_subset=['model_organism_database'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['GENO:0000536', 'SIO:001079'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='biological entity', abstract=None, mixin=None, mixins=['physical essence', 'genomic entity', 'ontology class'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon', 'has zygosity', 'has biological sequence'], slot_usage={}, attributes={}, class_uri='biolink:Genotype', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'haplotype': ClassDefinition(name='haplotype', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Haplotype', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A set of zero or more Alleles on a single instance of a Sequence[VMC]', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['GENO:0000871', 'SO:0001024', 'VMC:Haplotype'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='biological entity', abstract=None, mixin=None, mixins=['genomic entity', 'physical essence', 'ontology class'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon', 'has biological sequence'], slot_usage={}, attributes={}, class_uri='biolink:Haplotype', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'sequence variant': ClassDefinition(name='sequence variant', id_prefixes=['CAID', 'CLINVAR', 'WIKIDATA', 'DBSNP', 'MGI', 'ZFIN', 'FB', 'RGD', 'AGRKB', 'SPDI', 'WB', 'WormBase', 'PHARMGKB.VARIANT'], definition_uri='https://w3id.org/biolink/vocab/SequenceVariant', local_names={'agr': LocalName(local_name_source='agr', local_name_value='allele')}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.', alt_descriptions={'AGR': AltDescription(source='AGR', description='An entity that describes a single affected, endogenous allele. These can be of any type that matches that definition'), 'VMC': AltDescription(source='VMC', description='A contiguous change at a Location')}, title=None, deprecated=None, todos=[], notes=[], comments=['This class is for modeling the specific state at a locus. A single DBSNP rs ID could correspond to more than one sequence variants (e.g CIViC:1252 and CIViC:1253, two distinct BRCA2 alleles for rs28897743)'], examples=[], in_subset=['model_organism_database'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['allele'], structured_aliases={}, mappings=[], exact_mappings=['WIKIDATA:Q15304597'], close_mappings=['dcid:Allele', 'SO:0001060', 'VMC:Allele', 'GENO:0000002', 'SIO:010277', 'SO:0001060'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='biological entity', abstract=None, mixin=None, mixins=['genomic entity', 'physical essence', 'ontology class'], apply_to=[], values_from=[], string_serialization=None, slots=['iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon', 'sequence variant_has gene', 'sequence variant_has biological sequence', 'sequence variant_id'], slot_usage={'has gene': SlotDefinition(name='has gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Each allele can be associated with any number of genes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'has biological sequence': SlotDefinition(name='has biological sequence', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The state of the sequence w.r.t a reference sequence', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='ZFIN:ZDB-ALT-980203-1091', description='ti282a allele from ZFIN', object=None), Example(value='CLINVAR:17681', description='NM_007294.3(BRCA1):c.2521C>T (p.Arg841Trp)', object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:SequenceVariant', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'snv': ClassDefinition(name='snv', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Snv', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['single nucleotide variant', 'single nucleotide polymorphism', 'snp'], structured_aliases={}, mappings=[], exact_mappings=['SO:0001483'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='sequence variant', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon', 'sequence variant_has gene', 'sequence variant_has biological sequence', 'sequence variant_id'], slot_usage={}, attributes={}, class_uri='biolink:Snv', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'reagent targeted gene': ClassDefinition(name='reagent targeted gene', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ReagentTargetedGene', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['model_organism_database'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['sequence targeting reagent'], structured_aliases={}, mappings=[], exact_mappings=['GENO:0000504'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='biological entity', abstract=None, mixin=None, mixins=['genomic entity', 'physical essence', 'ontology class'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon', 'has biological sequence'], slot_usage={}, attributes={}, class_uri='biolink:ReagentTargetedGene', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'clinical attribute': ClassDefinition(name='clinical attribute', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ClinicalAttribute', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Attributes relating to a clinical manifestation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['STY:T201'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='attribute', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has attribute type', 'has quantitative value', 'has qualitative value', 'iri'], slot_usage={}, attributes={}, class_uri='biolink:ClinicalAttribute', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'clinical measurement': ClassDefinition(name='clinical measurement', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ClinicalMeasurement', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=\"A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot.\", alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['EFO:0001444'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='clinical attribute', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has quantitative value', 'has qualitative value', 'iri', 'clinical measurement_has attribute type'], slot_usage={'has attribute type': SlotDefinition(name='has attribute type', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=['EFO', 'LOINC'], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=False, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=True, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:ClinicalMeasurement', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'clinical modifier': ClassDefinition(name='clinical modifier', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ClinicalModifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='clinical attribute', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has attribute type', 'has quantitative value', 'has qualitative value', 'iri'], slot_usage={}, attributes={}, class_uri='biolink:ClinicalModifier', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'clinical course': ClassDefinition(name='clinical course', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ClinicalCourse', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['HP:0031797'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='clinical attribute', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has attribute type', 'has quantitative value', 'has qualitative value', 'iri'], slot_usage={}, attributes={}, class_uri='biolink:ClinicalCourse', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'onset': ClassDefinition(name='onset', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Onset', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The age group in which (disease) symptom manifestations appear', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['HP:0003674'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='clinical course', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has attribute type', 'has quantitative value', 'has qualitative value', 'iri'], slot_usage={}, attributes={}, class_uri='biolink:Onset', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'clinical entity': ClassDefinition(name='clinical entity', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ClinicalEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='named thing', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category'], slot_usage={}, attributes={}, class_uri='biolink:ClinicalEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'clinical trial': ClassDefinition(name='clinical trial', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ClinicalTrial', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='clinical entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category'], slot_usage={}, attributes={}, class_uri='biolink:ClinicalTrial', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'clinical intervention': ClassDefinition(name='clinical intervention', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ClinicalIntervention', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='clinical entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category'], slot_usage={}, attributes={}, class_uri='biolink:ClinicalIntervention', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'clinical finding': ClassDefinition(name='clinical finding', id_prefixes=['LOINC', 'NCIT', 'EFO'], definition_uri='https://w3id.org/biolink/vocab/ClinicalFinding', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=\"this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations.\", alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='phenotypic feature', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'provided by', 'xref', 'named thing_category', 'in taxon', 'clinical finding_has attribute'], slot_usage={'has attribute': SlotDefinition(name='has attribute', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='clinical attribute', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:ClinicalFinding', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'hospitalization': ClassDefinition(name='hospitalization', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Hospitalization', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['SNOMEDCT:32485007', 'WIKIDATA:Q3140971'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='clinical intervention', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category'], slot_usage={}, attributes={}, class_uri='biolink:Hospitalization', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'socioeconomic attribute': ClassDefinition(name='socioeconomic attribute', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/SocioeconomicAttribute', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Attributes relating to a socioeconomic manifestation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='attribute', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has attribute type', 'has quantitative value', 'has qualitative value', 'iri'], slot_usage={}, attributes={}, class_uri='biolink:SocioeconomicAttribute', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'case': ClassDefinition(name='case', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Case', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An individual (human) organism that has a patient role in some clinical context.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['patient', 'proband'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='individual organism', abstract=None, mixin=None, mixins=['subject of investigation'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'provided by', 'xref', 'named thing_category', 'in taxon', 'organismal entity_has attribute'], slot_usage={}, attributes={}, class_uri='biolink:Case', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'cohort': ClassDefinition(name='cohort', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Cohort', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=\"A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time.\", alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['WIKIDATA:Q1303415'], close_mappings=[], related_mappings=[], narrow_mappings=['STY:T097', 'STY:T099', 'STY:T100', 'STY:T101'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='study population', abstract=None, mixin=None, mixins=['subject of investigation'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'provided by', 'xref', 'named thing_category', 'in taxon', 'organismal entity_has attribute'], slot_usage={}, attributes={}, class_uri='biolink:Cohort', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'exposure event': ClassDefinition(name='exposure event', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ExposureEvent', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A (possibly time bounded) incidence of a feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['model_organism_database'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['exposure', 'experimental condition'], structured_aliases={}, mappings=[], exact_mappings=['XCO:0000000'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='ontology class', abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'timepoint'], slot_usage={}, attributes={}, class_uri='biolink:ExposureEvent', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'genomic background exposure': ClassDefinition(name='genomic background exposure', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GenomicBackgroundExposure', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=\"A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome.\", alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='attribute', abstract=None, mixin=None, mixins=['exposure event', 'gene grouping mixin', 'physical essence', 'genomic entity', 'thing with taxon', 'ontology class'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has attribute type', 'has quantitative value', 'has qualitative value', 'iri', 'timepoint', 'has gene or gene product', 'has biological sequence', 'in taxon'], slot_usage={}, attributes={}, class_uri='biolink:GenomicBackgroundExposure', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'pathological entity mixin': ClassDefinition(name='pathological entity mixin', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/PathologicalEntityMixin', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A pathological (abnormal) structure or process.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['MPATH:0'], close_mappings=[], related_mappings=[], narrow_mappings=['HP:0000118'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='biolink:PathologicalEntityMixin', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'pathological process': ClassDefinition(name='pathological process', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/PathologicalProcess', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['OBI:1110122', 'NCIT:C16956', 'MPATH:596'], close_mappings=[], related_mappings=[], narrow_mappings=['NCIT:C19151', 'EFO:0009708', 'STY:T046', 'STY:T037'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='biological process', abstract=None, mixin=None, mixins=['pathological entity mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'in taxon', 'has input', 'has output', 'enabled by'], slot_usage={}, attributes={}, class_uri='biolink:PathologicalProcess', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'pathological process exposure': ClassDefinition(name='pathological process exposure', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/PathologicalProcessExposure', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='attribute', abstract=None, mixin=None, mixins=['exposure event'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has attribute type', 'has quantitative value', 'has qualitative value', 'iri', 'timepoint'], slot_usage={}, attributes={}, class_uri='biolink:PathologicalProcessExposure', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'pathological anatomical structure': ClassDefinition(name='pathological anatomical structure', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/PathologicalAnatomicalStructure', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['MPATH:603'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='anatomical entity', abstract=None, mixin=None, mixins=['pathological entity mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'provided by', 'xref', 'named thing_category', 'in taxon', 'organismal entity_has attribute'], slot_usage={}, attributes={}, class_uri='biolink:PathologicalAnatomicalStructure', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'pathological anatomical exposure': ClassDefinition(name='pathological anatomical exposure', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/PathologicalAnatomicalExposure', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='attribute', abstract=None, mixin=None, mixins=['exposure event'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has attribute type', 'has quantitative value', 'has qualitative value', 'iri', 'timepoint'], slot_usage={}, attributes={}, class_uri='biolink:PathologicalAnatomicalExposure', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'disease or phenotypic feature exposure': ClassDefinition(name='disease or phenotypic feature exposure', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeatureExposure', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='attribute', abstract=None, mixin=None, mixins=['exposure event', 'pathological entity mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has attribute type', 'has quantitative value', 'has qualitative value', 'iri', 'timepoint'], slot_usage={}, attributes={}, class_uri='biolink:DiseaseOrPhenotypicFeatureExposure', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'chemical exposure': ClassDefinition(name='chemical exposure', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ChemicalExposure', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A chemical exposure is an intake of a particular chemical entity.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['ECTO:9000000', 'SIO:001399'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='attribute', abstract=None, mixin=None, mixins=['exposure event'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has attribute type', 'has qualitative value', 'iri', 'has quantitative value', 'timepoint'], slot_usage={}, attributes={}, class_uri='biolink:ChemicalExposure', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'complex chemical exposure': ClassDefinition(name='complex chemical exposure', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ComplexChemicalExposure', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='attribute', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has attribute type', 'has quantitative value', 'has qualitative value', 'iri'], slot_usage={}, attributes={}, class_uri='biolink:ComplexChemicalExposure', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'drug exposure': ClassDefinition(name='drug exposure', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/DrugExposure', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A drug exposure is an intake of a particular drug.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['drug intake', 'drug dose', 'medication intake'], structured_aliases={}, mappings=[], exact_mappings=['ECTO:0000509'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['SIO:001005'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='chemical exposure', abstract=None, mixin=None, mixins=['exposure event'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has attribute type', 'has qualitative value', 'iri', 'has quantitative value', 'timepoint'], slot_usage={}, attributes={}, class_uri='biolink:DrugExposure', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'drug to gene interaction exposure': ClassDefinition(name='drug to gene interaction exposure', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/DrugToGeneInteractionExposure', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=\"drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome.\", alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='drug exposure', abstract=None, mixin=None, mixins=['gene grouping mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has attribute type', 'has qualitative value', 'iri', 'has quantitative value', 'timepoint', 'has gene or gene product'], slot_usage={}, attributes={}, class_uri='biolink:DrugToGeneInteractionExposure', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'treatment': ClassDefinition(name='treatment', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Treatment', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=\"A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures\", alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['medical action', 'medical intervention'], structured_aliases={}, mappings=[], exact_mappings=['OGMS:0000090', 'SIO:001398'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['MAXO:0000058'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='named thing', abstract=None, mixin=None, mixins=['exposure event', 'chemical or drug or treatment'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'type', 'name', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'has drug', 'has device', 'has procedure', 'timepoint'], slot_usage={}, attributes={}, class_uri='biolink:Treatment', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'biotic exposure': ClassDefinition(name='biotic exposure', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/BioticExposure', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses).', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['viral exposure', 'bacterial exposure'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='attribute', abstract=None, mixin=None, mixins=['exposure event'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has attribute type', 'has quantitative value', 'has qualitative value', 'iri', 'timepoint'], slot_usage={}, attributes={}, class_uri='biolink:BioticExposure', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'geographic exposure': ClassDefinition(name='geographic exposure', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GeographicExposure', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A geographic exposure is a factor relating to geographic proximity to some impactful entity.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['dcid:GeologicalEvent'], related_mappings=[], narrow_mappings=['dcid:IceStoremEvent', 'dcid:LakeEffectSnowEvent', 'dcid:LandslideEvent', 'dcid:MarineDenseFogEvent', 'dcid:MarineLighteningEvent', 'dcid:MarineStrongWindEvent', 'dcid:MarineThunderstormWindEvent', 'dcid:StormEvent', 'dcid:StormSurgeTideEvent', 'dcid:StrongWindEvent', 'dcid:ThunderstormWindEvent', 'dcid:TornadoEvent', 'dcid:TropicalDepressionEvent', 'dcid:WinterStoremEvent'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='environmental exposure', abstract=None, mixin=None, mixins=['exposure event'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has attribute type', 'has quantitative value', 'has qualitative value', 'iri', 'timepoint'], slot_usage={}, attributes={}, class_uri='biolink:GeographicExposure', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'environmental exposure': ClassDefinition(name='environmental exposure', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/EnvironmentalExposure', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='attribute', abstract=None, mixin=None, mixins=['exposure event'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has attribute type', 'has quantitative value', 'has qualitative value', 'iri', 'timepoint'], slot_usage={}, attributes={}, class_uri='biolink:EnvironmentalExposure', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'behavioral exposure': ClassDefinition(name='behavioral exposure', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/BehavioralExposure', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A behavioral exposure is a factor relating to behavior impacting an individual.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='attribute', abstract=None, mixin=None, mixins=['exposure event'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'has attribute', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has attribute type', 'has quantitative value', 'has qualitative value', 'iri', 'timepoint'], slot_usage={}, attributes={}, class_uri='biolink:BehavioralExposure', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'socioeconomic exposure': ClassDefinition(name='socioeconomic exposure', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/SocioeconomicExposure', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty).', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='attribute', abstract=None, mixin=None, mixins=['exposure event'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'type', 'description', 'provided by', 'xref', 'named thing_category', 'attribute_name', 'has attribute type', 'has quantitative value', 'has qualitative value', 'iri', 'socioeconomic exposure_has attribute', 'timepoint'], slot_usage={'has attribute': SlotDefinition(name='has attribute', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='socioeconomic attribute', range_expression=None, enum_range=None, required=True, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:SocioeconomicExposure', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'outcome': ClassDefinition(name='outcome', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Outcome', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An entity that has the role of being the consequence of an exposure event. This is an abstract mixin grouping of various categories of possible biological or non-biological (e.g. clinical) outcomes.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='biolink:Outcome', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'pathological process outcome': ClassDefinition(name='pathological process outcome', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/PathologicalProcessOutcome', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An outcome resulting from an exposure event which is the manifestation of a pathological process.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=['outcome'], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='biolink:PathologicalProcessOutcome', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'pathological anatomical outcome': ClassDefinition(name='pathological anatomical outcome', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/PathologicalAnatomicalOutcome', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An outcome resulting from an exposure event which is the manifestation of an abnormal anatomical structure.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=['outcome'], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='biolink:PathologicalAnatomicalOutcome', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'disease or phenotypic feature outcome': ClassDefinition(name='disease or phenotypic feature outcome', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeatureOutcome', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Physiological outcomes resulting from an exposure event which is the manifestation of a disease or other characteristic phenotype.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=['outcome'], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='biolink:DiseaseOrPhenotypicFeatureOutcome', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'behavioral outcome': ClassDefinition(name='behavioral outcome', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/BehavioralOutcome', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An outcome resulting from an exposure event which is the manifestation of human behavior.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=['outcome'], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='biolink:BehavioralOutcome', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'hospitalization outcome': ClassDefinition(name='hospitalization outcome', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/HospitalizationOutcome', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An outcome resulting from an exposure event which is the increased manifestation of acute (e.g. emergency room visit) or chronic (inpatient) hospitalization.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=['outcome'], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='biolink:HospitalizationOutcome', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'mortality outcome': ClassDefinition(name='mortality outcome', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/MortalityOutcome', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An outcome of death from resulting from an exposure event.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=['outcome'], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='biolink:MortalityOutcome', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'epidemiological outcome': ClassDefinition(name='epidemiological outcome', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/EpidemiologicalOutcome', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An epidemiological outcome, such as societal disease burden, resulting from an exposure event.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=['NCIT:C19291'], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=['outcome'], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='biolink:EpidemiologicalOutcome', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'socioeconomic outcome': ClassDefinition(name='socioeconomic outcome', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/SocioeconomicOutcome', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An general social or economic outcome, such as healthcare costs, utilization, etc., resulting from an exposure event', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=['outcome'], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='biolink:SocioeconomicOutcome', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'association': ClassDefinition(name='association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Association', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A typed association between two entities, supported by evidence', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['This is roughly the model used by biolink and ontobio at the moment'], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['OBAN:association', 'rdf:Statement', 'owl:Axiom'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='entity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'subject', 'predicate', 'object', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category'], slot_usage={'type': SlotDefinition(name='type', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='rdf:type of biolink:Association should be fixed at rdf:Statement', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'category': SlotDefinition(name='category', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='category type', range_expression=None, enum_range=None, required=False, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:Association', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'chemical entity assesses named thing association': ClassDefinition(name='chemical entity assesses named thing association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ChemicalEntityAssessesNamedThingAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'chemical entity assesses named thing association_subject', 'chemical entity assesses named thing association_object', 'chemical entity assesses named thing association_predicate'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='chemical entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='named thing', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='assesses', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:ChemicalEntityAssessesNamedThingAssociation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'contributor association': ClassDefinition(name='contributor association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ContributorAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Any association between an entity (such as a publication) and various agents that contribute to its realisation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'contributor association_subject', 'contributor association_predicate', 'contributor association_object', 'contributor association_qualifiers'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='information content entity which an agent has helped realise', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='information content entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=\"generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'\", alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='contributor', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='agent helping to realise the given entity (e.g. such as a publication)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='agent', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifiers': SlotDefinition(name='qualifiers', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=\"this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'\", alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:ContributorAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'predicate', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'genotype to genotype part association': ClassDefinition(name='genotype to genotype part association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GenotypeToGenotypePartAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Any association between one genotype and a genotypic entity that is a sub-component of it', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'genotype to genotype part association_predicate', 'genotype to genotype part association_subject', 'genotype to genotype part association_object'], slot_usage={'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='has variant part', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='parent genotype', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='genotype', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='child genotype', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='genotype', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:GenotypeToGenotypePartAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'genotype to gene association': ClassDefinition(name='genotype to gene association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GenotypeToGeneAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'genotype to gene association_predicate', 'genotype to gene association_subject', 'genotype to gene association_object'], slot_usage={'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the relationship type used to connect genotype to gene', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='parent genotype', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='genotype', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='gene implicated in genotype', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:GenotypeToGeneAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'genotype to variant association': ClassDefinition(name='genotype to variant association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GenotypeToVariantAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Any association between a genotype and a sequence variant.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'genotype to variant association_predicate', 'genotype to variant association_subject', 'genotype to variant association_object'], slot_usage={'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the relationship type used to connect genotype to gene', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='parent genotype', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='genotype', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='gene implicated in genotype', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='sequence variant', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:GenotypeToVariantAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'gene to gene association': ClassDefinition(name='gene to gene association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GeneToGeneAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['molecular or genetic interaction'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'gene to gene association_subject', 'gene to gene association_object'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene or gene product', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene or gene product', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:GeneToGeneAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'gene to gene homology association': ClassDefinition(name='gene to gene homology association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GeneToGeneHomologyAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='gene to gene association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'gene to gene homology association_subject', 'gene to gene homology association_predicate', 'gene to gene homology association_object'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene or gene product', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='homology relationship type', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='homologous to', symmetric=True, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene or gene product', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:GeneToGeneHomologyAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'predicate', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'gene to gene family association': ClassDefinition(name='gene to gene family association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GeneToGeneFamilyAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'gene to gene family association_subject', 'gene to gene family association_object', 'gene to gene family association_predicate'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene family', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='membership of the gene in the given gene family.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='member of', symmetric=False, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:GeneToGeneFamilyAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'predicate', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'gene expression mixin': ClassDefinition(name='gene expression mixin', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GeneExpressionMixin', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['gene expression mixin_quantifier qualifier', 'expression site', 'stage qualifier', 'phenotypic state'], slot_usage={'quantifier qualifier': SlotDefinition(name='quantifier qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Optional quantitative value indicating degree of expression.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:GeneExpressionMixin', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'gene to gene coexpression association': ClassDefinition(name='gene to gene coexpression association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GeneToGeneCoexpressionAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Indicates that two genes are co-expressed, generally under the same conditions.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='gene to gene association', abstract=None, mixin=None, mixins=['gene expression mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'gene to gene association_subject', 'gene to gene association_object', 'gene to gene coexpression association_predicate', 'gene expression mixin_quantifier qualifier', 'expression site', 'stage qualifier', 'phenotypic state'], slot_usage={'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='coexpressed with', symmetric=True, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:GeneToGeneCoexpressionAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'predicate', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'pairwise gene to gene interaction': ClassDefinition(name='pairwise gene to gene interaction', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/PairwiseGeneToGeneInteraction', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=['dcid:ProteinProteinInteraction'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='gene to gene association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'gene to gene association_subject', 'gene to gene association_object', 'pairwise gene to gene interaction_predicate'], slot_usage={'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='interaction relationship type', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='interacts with', symmetric=True, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:PairwiseGeneToGeneInteraction', subclass_of=None, union_of=[], defining_slots=['subject', 'predicate', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'pairwise molecular interaction': ClassDefinition(name='pairwise molecular interaction', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/PairwiseMolecularInteraction', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An interaction at the molecular level between two physical entities', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='pairwise gene to gene interaction', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'interacting molecules category', 'pairwise molecular interaction_subject', 'pairwise molecular interaction_id', 'pairwise molecular interaction_predicate', 'pairwise molecular interaction_object'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='molecular entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='identifier for the interaction. This may come from an interaction database such as IMEX.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='WB:WBInteraction000538741', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=['IMEX', 'BioGRID'], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='interaction relationship type', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='RO:0002447', description='the subject molecular phosphorylates the object molecule', object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='interacts with', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='molecular entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:PairwiseMolecularInteraction', subclass_of=None, union_of=[], defining_slots=['subject', 'predicate', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'cell line to entity association mixin': ClassDefinition(name='cell line to entity association mixin', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/CellLineToEntityAssociationMixin', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An relationship between a cell line and another entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['cell line to entity association mixin_subject'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='cell line', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:CellLineToEntityAssociationMixin', subclass_of=None, union_of=[], defining_slots=['subject'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'cell line to disease or phenotypic feature association': ClassDefinition(name='cell line to disease or phenotypic feature association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/CellLineToDiseaseOrPhenotypicFeatureAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=['cell line to entity association mixin', 'entity to disease or phenotypic feature association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'object', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'cell line to disease or phenotypic feature association_subject'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='disease or phenotypic feature', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'chemical entity to entity association mixin': ClassDefinition(name='chemical entity to entity association mixin', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ChemicalEntityToEntityAssociationMixin', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An interaction between a chemical entity and another entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['chemical entity to entity association mixin_subject'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the chemical entity that is an interactor', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='chemical entity or gene or gene product', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:ChemicalEntityToEntityAssociationMixin', subclass_of=None, union_of=[], defining_slots=['subject'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'drug to entity association mixin': ClassDefinition(name='drug to entity association mixin', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/DrugToEntityAssociationMixin', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An interaction between a drug and another entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='chemical entity to entity association mixin', abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['drug to entity association mixin_subject'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the drug that is an interactor', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='drug', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:DrugToEntityAssociationMixin', subclass_of=None, union_of=[], defining_slots=['subject'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'chemical to entity association mixin': ClassDefinition(name='chemical to entity association mixin', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ChemicalToEntityAssociationMixin', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An interaction between a chemical entity and another entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='chemical entity to entity association mixin', abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['chemical to entity association mixin_subject'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the chemical entity or entity that is an interactor', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='chemical entity or gene or gene product', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:ChemicalToEntityAssociationMixin', subclass_of=None, union_of=[], defining_slots=['subject'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'case to entity association mixin': ClassDefinition(name='case to entity association mixin', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/CaseToEntityAssociationMixin', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An abstract association for use where the case is the subject', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['case to entity association mixin_subject'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the case (e.g. patient) that has the property', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='case', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:CaseToEntityAssociationMixin', subclass_of=None, union_of=[], defining_slots=['subject'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'chemical to chemical association': ClassDefinition(name='chemical to chemical association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ChemicalToChemicalAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=['chemical to entity association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'subject', 'predicate', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'chemical to chemical association_object'], slot_usage={'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the chemical element that is the target of the statement', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='chemical entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:ChemicalToChemicalAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'reaction to participant association': ClassDefinition(name='reaction to participant association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ReactionToParticipantAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='chemical to chemical association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'chemical to chemical association_object', 'stoichiometry', 'reaction direction', 'reaction side', 'reaction to participant association_subject'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='molecular entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:ReactionToParticipantAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'predicate', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'reaction to catalyst association': ClassDefinition(name='reaction to catalyst association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ReactionToCatalystAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='reaction to participant association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'stoichiometry', 'reaction direction', 'reaction side', 'reaction to participant association_subject', 'reaction to catalyst association_object'], slot_usage={'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene or gene product', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:ReactionToCatalystAssociation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'chemical to chemical derivation association': ClassDefinition(name='chemical to chemical derivation association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ChemicalToChemicalDerivationAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction:\\n IF\\n R has-input C1 AND\\n R has-output C2 AND\\n R enabled-by P AND\\n R type Reaction\\n THEN\\n C1 derives-into C2 <>', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='chemical to chemical association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'chemical to chemical derivation association_catalyst qualifier', 'chemical to chemical derivation association_subject', 'chemical to chemical derivation association_object', 'chemical to chemical derivation association_predicate'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the upstream chemical entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='chemical entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the downstream chemical entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='chemical entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='derives into', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'catalyst qualifier': SlotDefinition(name='catalyst qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:ChemicalToChemicalDerivationAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'predicate', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'chemical to disease or phenotypic feature association': ClassDefinition(name='chemical to disease or phenotypic feature association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ChemicalToDiseaseOrPhenotypicFeatureAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=['SIO:000993'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=['chemical to entity association mixin', 'entity to disease or phenotypic feature association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'subject', 'predicate', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'chemical to disease or phenotypic feature association_object'], slot_usage={'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the disease or phenotype that is affected by the chemical', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='disease or phenotypic feature', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'chemical or drug or treatment to disease or phenotypic feature association': ClassDefinition(name='chemical or drug or treatment to disease or phenotypic feature association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=['chemical to entity association mixin', 'entity to disease or phenotypic feature association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'subject', 'object', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'FDA adverse event level', 'chemical or drug or treatment to disease or phenotypic feature association_predicate'], slot_usage={'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='has adverse event', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'predicate', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'chemical or drug or treatment side effect disease or phenotypic feature association': ClassDefinition(name='chemical or drug or treatment side effect disease or phenotypic feature association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='chemical or drug or treatment to disease or phenotypic feature association', abstract=None, mixin=None, mixins=['chemical to entity association mixin', 'entity to disease or phenotypic feature association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'subject', 'object', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'FDA adverse event level', 'chemical or drug or treatment side effect disease or phenotypic feature association_predicate'], slot_usage={'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='has side effect', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'predicate', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'gene to pathway association': ClassDefinition(name='gene to pathway association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GeneToPathwayAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An interaction between a gene or gene product and a biological process or pathway.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=['gene to entity association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'gene to pathway association_subject', 'gene to pathway association_object'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the gene or gene product entity that participates or influences the pathway', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene or gene product', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the pathway that includes or is affected by the gene or gene product', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='pathway', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:GeneToPathwayAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'molecular activity to pathway association': ClassDefinition(name='molecular activity to pathway association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/MolecularActivityToPathwayAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Association that holds the relationship between a reaction and the pathway it participates in.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'molecular activity to pathway association_subject', 'molecular activity to pathway association_object', 'molecular activity to pathway association_predicate'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='molecular activity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='pathway', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='part of', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:MolecularActivityToPathwayAssociation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'chemical to pathway association': ClassDefinition(name='chemical to pathway association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ChemicalToPathwayAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An interaction between a chemical entity and a biological process or pathway.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['SIO:001250'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=['chemical to entity association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'chemical to pathway association_subject', 'chemical to pathway association_object'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the chemical entity that is affecting the pathway', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='chemical entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the pathway that is affected by the chemical', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='pathway', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:ChemicalToPathwayAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'named thing associated with likelihood of named thing association': ClassDefinition(name='named thing associated with likelihood of named thing association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/NamedThingAssociatedWithLikelihoodOfNamedThingAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'subject', 'object', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'named thing associated with likelihood of named thing association_predicate', 'named thing associated with likelihood of named thing association_subject aspect qualifier', 'named thing associated with likelihood of named thing association_subject context qualifier', 'named thing associated with likelihood of named thing association_object aspect qualifier', 'named thing associated with likelihood of named thing association_object context qualifier'], slot_usage={'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='associated with', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject aspect qualifier': SlotDefinition(name='subject aspect qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject context qualifier': SlotDefinition(name='subject context qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ontology class', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object aspect qualifier': SlotDefinition(name='object aspect qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object context qualifier': SlotDefinition(name='object context qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ontology class', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'subject aspect qualifier', 'subject context qualifier', 'predicate', 'object', 'object aspect qualifier', 'object context qualifier', 'population context qualifier'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'chemical gene interaction association': ClassDefinition(name='chemical gene interaction association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ChemicalGeneInteractionAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['SIO:001257'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=['chemical to entity association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'chemical gene interaction association_subject form or variant qualifier', 'chemical gene interaction association_subject part qualifier', 'chemical gene interaction association_subject derivative qualifier', 'chemical gene interaction association_subject context qualifier', 'chemical gene interaction association_object form or variant qualifier', 'chemical gene interaction association_object part qualifier', 'chemical gene interaction association_object context qualifier', 'chemical gene interaction association_anatomical context qualifier', 'chemical gene interaction association_subject', 'chemical gene interaction association_object', 'chemical gene interaction association_predicate'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='chemical entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene or gene product', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='physically interacts with', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject form or variant qualifier': SlotDefinition(name='subject form or variant qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalOrGeneOrGeneProductFormOrVariantEnum', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject part qualifier': SlotDefinition(name='subject part qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneOrGeneProductOrChemicalPartQualifierEnum', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject derivative qualifier': SlotDefinition(name='subject derivative qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntityDerivativeEnum', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject context qualifier': SlotDefinition(name='subject context qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='anatomical entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object form or variant qualifier': SlotDefinition(name='object form or variant qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalOrGeneOrGeneProductFormOrVariantEnum', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object part qualifier': SlotDefinition(name='object part qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneOrGeneProductOrChemicalPartQualifierEnum', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object context qualifier': SlotDefinition(name='object context qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='anatomical entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'anatomical context qualifier': SlotDefinition(name='anatomical context qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='anatomical entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:ChemicalGeneInteractionAssociation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'chemical affects gene association': ClassDefinition(name='chemical affects gene association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ChemicalAffectsGeneAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity, localization, processing, expression, etc.)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'chemical affects gene association_subject form or variant qualifier', 'chemical affects gene association_subject part qualifier', 'chemical affects gene association_subject derivative qualifier', 'chemical affects gene association_subject aspect qualifier', 'chemical affects gene association_subject context qualifier', 'chemical affects gene association_subject direction qualifier', 'chemical affects gene association_object form or variant qualifier', 'chemical affects gene association_object part qualifier', 'chemical affects gene association_object aspect qualifier', 'chemical affects gene association_object context qualifier', 'chemical affects gene association_causal mechanism qualifier', 'chemical affects gene association_anatomical context qualifier', 'chemical affects gene association_qualified predicate', 'chemical affects gene association_subject', 'chemical affects gene association_predicate', 'chemical affects gene association_object', 'chemical affects gene association_object direction qualifier', 'chemical affects gene association_species context qualifier'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='chemical entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject form or variant qualifier': SlotDefinition(name='subject form or variant qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalOrGeneOrGeneProductFormOrVariantEnum', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject part qualifier': SlotDefinition(name='subject part qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneOrGeneProductOrChemicalPartQualifierEnum', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject derivative qualifier': SlotDefinition(name='subject derivative qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntityDerivativeEnum', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject aspect qualifier': SlotDefinition(name='subject aspect qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneOrGeneProductOrChemicalPartQualifierEnum', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject context qualifier': SlotDefinition(name='subject context qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='anatomical entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject direction qualifier': SlotDefinition(name='subject direction qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='DirectionQualifierEnum', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='affects', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualified predicate': SlotDefinition(name='qualified predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='causes', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene or gene product', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object form or variant qualifier': SlotDefinition(name='object form or variant qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalOrGeneOrGeneProductFormOrVariantEnum', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object part qualifier': SlotDefinition(name='object part qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneOrGeneProductOrChemicalPartQualifierEnum', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object aspect qualifier': SlotDefinition(name='object aspect qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneOrGeneProductOrChemicalPartQualifierEnum', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object context qualifier': SlotDefinition(name='object context qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='anatomical entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object direction qualifier': SlotDefinition(name='object direction qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='DirectionQualifierEnum', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'causal mechanism qualifier': SlotDefinition(name='causal mechanism qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='CausalMechanismQualifierEnum', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'anatomical context qualifier': SlotDefinition(name='anatomical context qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='anatomical entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'species context qualifier': SlotDefinition(name='species context qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='organism taxon', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:ChemicalAffectsGeneAssociation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'drug to gene association': ClassDefinition(name='drug to gene association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/DrugToGeneAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An interaction between a drug and a gene or gene product.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=['SIO:001257'], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=['drug to entity association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'subject', 'predicate', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'drug to gene association_object'], slot_usage={'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the gene or gene product that is affected by the drug', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene or gene product', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:DrugToGeneAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'material sample to entity association mixin': ClassDefinition(name='material sample to entity association mixin', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/MaterialSampleToEntityAssociationMixin', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An association between a material sample and something.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['material sample to entity association mixin_subject'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the material sample being described', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='material sample', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:MaterialSampleToEntityAssociationMixin', subclass_of=None, union_of=[], defining_slots=['subject'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'material sample derivation association': ClassDefinition(name='material sample derivation association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/MaterialSampleDerivationAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An association between a material sample and the material entity from which it is derived.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'material sample derivation association_subject', 'material sample derivation association_object', 'material sample derivation association_predicate'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the material sample being described', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='material sample', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='derivation relationship', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='derives from', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:MaterialSampleDerivationAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'predicate'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'material sample to disease or phenotypic feature association': ClassDefinition(name='material sample to disease or phenotypic feature association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/MaterialSampleToDiseaseOrPhenotypicFeatureAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An association between a material sample and a disease or phenotype.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=['material sample to entity association mixin', 'entity to disease or phenotypic feature association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'subject', 'predicate', 'object', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category'], slot_usage={}, attributes={}, class_uri='biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'disease to entity association mixin': ClassDefinition(name='disease to entity association mixin', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/DiseaseToEntityAssociationMixin', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['disease to entity association mixin_subject'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='disease class', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='MONDO:0017314', description='Ehlers-Danlos syndrome, vascular type', object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=['mondo', 'omim', 'orphanet', 'ncit', 'doid'], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='disease', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:DiseaseToEntityAssociationMixin', subclass_of=None, union_of=[], defining_slots=['subject'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'entity to exposure event association mixin': ClassDefinition(name='entity to exposure event association mixin', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/EntityToExposureEventAssociationMixin', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An association between some entity and an exposure event.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['entity to exposure event association mixin_object'], slot_usage={'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='exposure event', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:EntityToExposureEventAssociationMixin', subclass_of=None, union_of=[], defining_slots=['object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'disease to exposure event association': ClassDefinition(name='disease to exposure event association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/DiseaseToExposureEventAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An association between an exposure event and a disease.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=['disease to entity association mixin', 'entity to exposure event association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'subject', 'predicate', 'object', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category'], slot_usage={}, attributes={}, class_uri='biolink:DiseaseToExposureEventAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'entity to outcome association mixin': ClassDefinition(name='entity to outcome association mixin', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/EntityToOutcomeAssociationMixin', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An association between some entity and an outcome', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['entity to outcome association mixin_object'], slot_usage={'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='outcome', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:EntityToOutcomeAssociationMixin', subclass_of=None, union_of=[], defining_slots=['object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'exposure event to outcome association': ClassDefinition(name='exposure event to outcome association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ExposureEventToOutcomeAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An association between an exposure event and an outcome.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=['entity to outcome association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'subject', 'predicate', 'object', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'population context qualifier', 'temporal context qualifier'], slot_usage={}, attributes={}, class_uri='biolink:ExposureEventToOutcomeAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'frequency qualifier mixin': ClassDefinition(name='frequency qualifier mixin', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/FrequencyQualifierMixin', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Qualifier for frequency type associations', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['frequency qualifier'], slot_usage={}, attributes={}, class_uri='biolink:FrequencyQualifierMixin', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'entity to feature or disease qualifiers mixin': ClassDefinition(name='entity to feature or disease qualifiers mixin', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/EntityToFeatureOrDiseaseQualifiersMixin', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Qualifiers for entity to disease or phenotype associations.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='frequency qualifier mixin', abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['frequency qualifier', 'severity qualifier', 'onset qualifier'], slot_usage={}, attributes={}, class_uri='biolink:EntityToFeatureOrDiseaseQualifiersMixin', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'entity to phenotypic feature association mixin': ClassDefinition(name='entity to phenotypic feature association mixin', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/EntityToPhenotypicFeatureAssociationMixin', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='entity to feature or disease qualifiers mixin', abstract=None, mixin=True, mixins=['frequency quantifier'], apply_to=[], values_from=[], string_serialization=None, slots=['frequency qualifier', 'severity qualifier', 'onset qualifier', 'sex qualifier', 'entity to phenotypic feature association mixin_object', 'has count', 'has total', 'has quotient', 'has percentage'], slot_usage={'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='HP:0002487', description='Hyperkinesis', object=None), Example(value='WBPhenotype:0000180', description='axon morphology variant', object=None), Example(value='MP:0001569', description='abnormal circulating bilirubin level', object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=['upheno', 'hp', 'mp', 'wbphenotype'], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='phenotypic feature', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:EntityToPhenotypicFeatureAssociationMixin', subclass_of=None, union_of=[], defining_slots=['object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'information content entity to named thing association': ClassDefinition(name='information content entity to named thing association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/InformationContentEntityToNamedThingAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=\"association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property).\", alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['model_organism_database'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'information content entity to named thing association_subject', 'information content entity to named thing association_object', 'information content entity to named thing association_predicate'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain='publication', slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='named thing', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='mentions', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:InformationContentEntityToNamedThingAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'entity to disease association mixin': ClassDefinition(name='entity to disease association mixin', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/EntityToDiseaseAssociationMixin', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='mixin class for any association whose object (target node) is a disease', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='entity to feature or disease qualifiers mixin', abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['frequency qualifier', 'severity qualifier', 'onset qualifier', 'entity to disease association mixin_object'], slot_usage={'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='disease', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='MONDO:0020066', description='Ehlers-Danlos syndrome', object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='disease', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:EntityToDiseaseAssociationMixin', subclass_of=None, union_of=[], defining_slots=['object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'disease or phenotypic feature to entity association mixin': ClassDefinition(name='disease or phenotypic feature to entity association mixin', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeatureToEntityAssociationMixin', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['disease or phenotypic feature to entity association mixin_subject'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='disease or phenotype', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='MONDO:0017314', description='Ehlers-Danlos syndrome, vascular type', object=None), Example(value='MP:0013229', description='abnormal brain ventricle size', object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='disease or phenotypic feature', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin', subclass_of=None, union_of=[], defining_slots=['subject'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'disease or phenotypic feature to location association': ClassDefinition(name='disease or phenotypic feature to location association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeatureToLocationAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=['disease or phenotypic feature to entity association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'subject', 'predicate', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'disease or phenotypic feature to location association_object'], slot_usage={'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='anatomical entity in which the disease or feature is found.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='UBERON:0002048', description='lung', object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='anatomical entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:DiseaseOrPhenotypicFeatureToLocationAssociation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'disease or phenotypic feature to genetic inheritance association': ClassDefinition(name='disease or phenotypic feature to genetic inheritance association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=['disease or phenotypic feature to entity association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'subject', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'disease or phenotypic feature to genetic inheritance association_predicate', 'disease or phenotypic feature to genetic inheritance association_object'], slot_usage={'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='has mode of inheritance', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='genetic inheritance associated with the specified disease or phenotypic feature.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='HP:0001417', description='X-linked inheritance', object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='genetic inheritance', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'entity to disease or phenotypic feature association mixin': ClassDefinition(name='entity to disease or phenotypic feature association mixin', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/EntityToDiseaseOrPhenotypicFeatureAssociationMixin', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['entity to disease or phenotypic feature association mixin_object'], slot_usage={'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='disease or phenotype', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='MONDO:0017314', description='Ehlers-Danlos syndrome, vascular type', object=None), Example(value='MP:0013229', description='abnormal brain ventricle size', object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='disease or phenotypic feature', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin', subclass_of=None, union_of=[], defining_slots=['object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'genotype to entity association mixin': ClassDefinition(name='genotype to entity association mixin', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GenotypeToEntityAssociationMixin', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['genotype to entity association mixin_subject'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='genotype that is the subject of the association', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='genotype', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:GenotypeToEntityAssociationMixin', subclass_of=None, union_of=[], defining_slots=['subject'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'genotype to phenotypic feature association': ClassDefinition(name='genotype to phenotypic feature association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GenotypeToPhenotypicFeatureAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=['entity to phenotypic feature association mixin', 'genotype to entity association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'object', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'genotype to phenotypic feature association_predicate', 'genotype to phenotypic feature association_subject', 'frequency qualifier', 'severity qualifier', 'onset qualifier', 'sex qualifier', 'has count', 'has total', 'has quotient', 'has percentage'], slot_usage={'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='has phenotype', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='genotype that is associated with the phenotypic feature', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='genotype', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:GenotypeToPhenotypicFeatureAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'exposure event to phenotypic feature association': ClassDefinition(name='exposure event to phenotypic feature association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ExposureEventToPhenotypicFeatureAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=['entity to phenotypic feature association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'object', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'exposure event to phenotypic feature association_subject', 'frequency qualifier', 'severity qualifier', 'onset qualifier', 'sex qualifier', 'has count', 'has total', 'has quotient', 'has percentage'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='exposure event', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:ExposureEventToPhenotypicFeatureAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'disease to phenotypic feature association': ClassDefinition(name='disease to phenotypic feature association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/DiseaseToPhenotypicFeatureAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['dcid:DiseaseSymptomAssociation'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=['entity to phenotypic feature association mixin', 'disease to entity association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'disease to phenotypic feature association_subject', 'disease to phenotypic feature association_object', 'frequency qualifier', 'severity qualifier', 'onset qualifier', 'sex qualifier', 'has count', 'has total', 'has quotient', 'has percentage'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='disease', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='phenotypic feature', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:DiseaseToPhenotypicFeatureAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'case to phenotypic feature association': ClassDefinition(name='case to phenotypic feature association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/CaseToPhenotypicFeatureAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=['entity to phenotypic feature association mixin', 'case to entity association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'subject', 'predicate', 'object', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'frequency qualifier', 'severity qualifier', 'onset qualifier', 'sex qualifier', 'has count', 'has total', 'has quotient', 'has percentage'], slot_usage={}, attributes={}, class_uri='biolink:CaseToPhenotypicFeatureAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'behavior to behavioral feature association': ClassDefinition(name='behavior to behavioral feature association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/BehaviorToBehavioralFeatureAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=['entity to phenotypic feature association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'behavior to behavioral feature association_subject', 'behavior to behavioral feature association_object', 'frequency qualifier', 'severity qualifier', 'onset qualifier', 'sex qualifier', 'has count', 'has total', 'has quotient', 'has percentage'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='behavior that is the subject of the association', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='behavior', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='behavioral feature that is the object of the association', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='behavioral feature', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:BehaviorToBehavioralFeatureAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'gene to entity association mixin': ClassDefinition(name='gene to entity association mixin', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GeneToEntityAssociationMixin', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['gene to entity association mixin_subject'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='gene that is the subject of the association', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene or gene product', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:GeneToEntityAssociationMixin', subclass_of=None, union_of=[], defining_slots=['subject'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'variant to entity association mixin': ClassDefinition(name='variant to entity association mixin', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/VariantToEntityAssociationMixin', local_names={'ga4gh': LocalName(local_name_source='ga4gh', local_name_value='variant annotation')}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['variant to entity association mixin_subject'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a sequence variant in which the allele state is associated with some other entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='CLINVAR:38077', description='CLINVAR representation of NM_000059.3(BRCA2):c.7007G>A (p.Arg2336His)', object=None), Example(value='ClinGen:CA024716', description='chr13:g.32921033G>C (hg19) in ClinGen', object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='sequence variant', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:VariantToEntityAssociationMixin', subclass_of=None, union_of=[], defining_slots=['subject'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'gene to disease or phenotypic feature association': ClassDefinition(name='gene to disease or phenotypic feature association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GeneToDiseaseOrPhenotypicFeatureAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['NCIT:R176 refers to the inverse relationship', 'for use in describing the affect that the loss of function of a gene can have on exacerbating or ameliorating a symptom/phenotype', 'if the relationship of the statement using this predicate is statistical in nature, please use `associated with likelihood` or one of its children.'], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=['WBVocab:Gene-Phenotype-Association', 'dcid:DiseaseGeneAssociation', 'SIO:000983'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=['entity to phenotypic feature association mixin', 'gene to entity association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'gene to disease or phenotypic feature association_subject aspect qualifier', 'gene to disease or phenotypic feature association_object direction qualifier', 'gene to disease or phenotypic feature association_subject', 'gene to disease or phenotypic feature association_object', 'gene to disease or phenotypic feature association_predicate', 'frequency qualifier', 'severity qualifier', 'onset qualifier', 'sex qualifier', 'has count', 'has total', 'has quotient', 'has percentage'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='gene in which variation is correlated with the phenotypic feature', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='HGNC:2197', description='COL1A1 (Human)', object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene or gene product', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject aspect qualifier': SlotDefinition(name='subject aspect qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneOrGeneProductOrChemicalEntityAspectEnum', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='disease or phenotypic feature', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object direction qualifier': SlotDefinition(name='object direction qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='DirectionQualifierEnum', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='affects', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:GeneToDiseaseOrPhenotypicFeatureAssociation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'gene to phenotype association': ClassDefinition(name='gene to phenotype association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GeneToPhenotypeAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['WBVocab:Gene-Phenotype-Association'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='gene to disease or phenotypic feature association', abstract=None, mixin=None, mixins=['entity to phenotypic feature association mixin', 'gene to entity association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'gene to disease or phenotypic feature association_subject aspect qualifier', 'gene to disease or phenotypic feature association_object direction qualifier', 'gene to disease or phenotypic feature association_predicate', 'frequency qualifier', 'severity qualifier', 'onset qualifier', 'sex qualifier', 'has count', 'has total', 'has quotient', 'has percentage', 'gene to phenotype association_subject', 'gene to phenotype association_object'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='gene in which variation is correlated with the phenotypic feature', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='HGNC:2197', description='COL1A1 (Human)', object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene or gene product', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='phenotypic feature', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:GeneToPhenotypeAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'gene to disease association': ClassDefinition(name='gene to disease association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GeneToDiseaseAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['NCIT:R176 refers to the inverse relationship'], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['SIO:000983'], close_mappings=['dcid:DiseaseGeneAssociation'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='gene to disease or phenotypic feature association', abstract=None, mixin=None, mixins=['entity to disease association mixin', 'gene to entity association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'gene to disease or phenotypic feature association_subject aspect qualifier', 'gene to disease or phenotypic feature association_object direction qualifier', 'gene to disease or phenotypic feature association_predicate', 'frequency qualifier', 'severity qualifier', 'onset qualifier', 'sex qualifier', 'has count', 'has total', 'has quotient', 'has percentage', 'gene to disease association_subject', 'gene to disease association_object'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene or gene product', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='disease', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:GeneToDiseaseAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'causal gene to disease association': ClassDefinition(name='causal gene to disease association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/CausalGeneToDiseaseAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='gene to disease association', abstract=None, mixin=None, mixins=['entity to disease association mixin', 'gene to entity association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'gene to disease or phenotypic feature association_subject aspect qualifier', 'gene to disease or phenotypic feature association_object direction qualifier', 'gene to disease or phenotypic feature association_predicate', 'frequency qualifier', 'severity qualifier', 'onset qualifier', 'sex qualifier', 'has count', 'has total', 'has quotient', 'has percentage', 'causal gene to disease association_subject', 'causal gene to disease association_object'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='gene in which variation is shown to cause the disease.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene or gene product', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='disease', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:CausalGeneToDiseaseAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'correlated gene to disease association': ClassDefinition(name='correlated gene to disease association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/CorrelatedGeneToDiseaseAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='gene to disease association', abstract=None, mixin=None, mixins=['entity to disease association mixin', 'gene to entity association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'gene to disease or phenotypic feature association_subject aspect qualifier', 'gene to disease or phenotypic feature association_object direction qualifier', 'gene to disease or phenotypic feature association_predicate', 'frequency qualifier', 'severity qualifier', 'onset qualifier', 'sex qualifier', 'has count', 'has total', 'has quotient', 'has percentage', 'correlated gene to disease association_subject', 'correlated gene to disease association_object'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='gene in which variation is shown to correlate with the disease.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene or gene product', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='disease', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:CorrelatedGeneToDiseaseAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'druggable gene to disease association': ClassDefinition(name='druggable gene to disease association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/DruggableGeneToDiseaseAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='gene to disease association', abstract=None, mixin=None, mixins=['entity to disease association mixin', 'gene to entity association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'gene to disease or phenotypic feature association_subject aspect qualifier', 'gene to disease or phenotypic feature association_object direction qualifier', 'frequency qualifier', 'severity qualifier', 'onset qualifier', 'sex qualifier', 'has count', 'has total', 'has quotient', 'has percentage', 'gene to disease association_object', 'druggable gene to disease association_subject', 'druggable gene to disease association_predicate', 'druggable gene to disease association_has evidence'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene or gene product', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='target for', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'has evidence': SlotDefinition(name='has evidence', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='DruggableGeneCategoryEnum', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:DruggableGeneToDiseaseAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object', 'predicate'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'variant to gene association': ClassDefinition(name='variant to gene association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/VariantToGeneAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=['variant to entity association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'subject', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'variant to gene association_object', 'variant to gene association_predicate'], slot_usage={'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='genetically associated with', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:VariantToGeneAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'predicate', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'variant to gene expression association': ClassDefinition(name='variant to gene expression association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/VariantToGeneExpressionAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An association between a variant and expression of a gene (i.e. e-QTL)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='variant to gene association', abstract=None, mixin=None, mixins=['gene expression mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'subject', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'variant to gene association_object', 'variant to gene expression association_predicate', 'gene expression mixin_quantifier qualifier', 'expression site', 'stage qualifier', 'phenotypic state'], slot_usage={'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='affects', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:VariantToGeneExpressionAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'predicate', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'variant to population association': ClassDefinition(name='variant to population association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/VariantToPopulationAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An association between a variant and a population, where the variant has particular frequency in the population', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=['variant to entity association mixin', 'frequency quantifier', 'frequency qualifier mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'variant to population association_subject', 'variant to population association_object', 'variant to population association_has quotient', 'variant to population association_has count', 'variant to population association_has total', 'has percentage', 'frequency qualifier'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='an allele that has a certain frequency in a given population', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='NC_000017.11:g.43051071A>T', description='17:41203088 A/C in gnomad', object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='sequence variant', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the population that is observed to have the frequency', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='HANCESTRO:0010', description='African', object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='population of individual organisms', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'has quotient': SlotDefinition(name='has quotient', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='0.0001666', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'has count': SlotDefinition(name='has count', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='number in object population that carry a particular allele, aka allele count', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='4', description='4 individuals in gnomad set', object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'has total': SlotDefinition(name='has total', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='number all populations that carry a particular allele, aka allele number', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='24014', description='24014 individuals in gnomad set', object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:VariantToPopulationAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'population to population association': ClassDefinition(name='population to population association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/PopulationToPopulationAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An association between a two populations', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'population to population association_subject', 'population to population association_object', 'population to population association_predicate'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the population that form the subject of the association', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='population of individual organisms', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the population that form the object of the association', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='population of individual organisms', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:PopulationToPopulationAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'variant to phenotypic feature association': ClassDefinition(name='variant to phenotypic feature association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/VariantToPhenotypicFeatureAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=['variant to entity association mixin', 'entity to phenotypic feature association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'object', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'variant to phenotypic feature association_subject', 'frequency qualifier', 'severity qualifier', 'onset qualifier', 'sex qualifier', 'has count', 'has total', 'has quotient', 'has percentage'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a sequence variant in which the allele state is associated in some way with the phenotype state', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='sequence variant', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:VariantToPhenotypicFeatureAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'variant to disease association': ClassDefinition(name='variant to disease association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/VariantToDiseaseAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['TODO decide no how to model pathogenicity'], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=['variant to entity association mixin', 'entity to disease association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'variant to disease association_subject', 'variant to disease association_predicate', 'variant to disease association_object', 'frequency qualifier', 'severity qualifier', 'onset qualifier'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a sequence variant in which the allele state is associated in some way with the disease state', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='CLINVAR:52241', description='NM_000059.3(BRCA2):c.7007G>C (p.Arg2336Pro)', object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='E.g. is pathogenic for', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='related condition', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a disease that is associated with that variant', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='MONDO:0016419', description='hereditary breast cancer', object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:VariantToDiseaseAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'genotype to disease association': ClassDefinition(name='genotype to disease association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GenotypeToDiseaseAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['TODO decide no how to model pathogenicity'], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=['genotype to entity association mixin', 'entity to disease association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'genotype to disease association_subject', 'genotype to disease association_predicate', 'genotype to disease association_object', 'frequency qualifier', 'severity qualifier', 'onset qualifier'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a genotype that is associated in some way with a disease state', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='E.g. is pathogenic for', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='related condition', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a disease that is associated with that genotype', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='MONDO:0016419', description='hereditary breast cancer', object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:GenotypeToDiseaseAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'model to disease association mixin': ClassDefinition(name='model to disease association mixin', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ModelToDiseaseAssociationMixin', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=\"This mixin is used for any association class for which the subject (source node) plays the role of a 'model', in that it recapitulates some features of the disease in a way that is useful for studying the disease outside a patient carrying the disease\", alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['model to disease association mixin_subject', 'model to disease association mixin_predicate'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The entity that serves as the model of the disease. This may be an organism, a strain of organism, a genotype or variant that exhibits similar features, or a gene that when mutated exhibits features of the disease', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The relationship to the disease', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='model of', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:ModelToDiseaseAssociationMixin', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'gene as a model of disease association': ClassDefinition(name='gene as a model of disease association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GeneAsAModelOfDiseaseAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='gene to disease association', abstract=None, mixin=None, mixins=['model to disease association mixin', 'entity to disease association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'gene to disease or phenotypic feature association_subject aspect qualifier', 'gene to disease or phenotypic feature association_object direction qualifier', 'gene to disease or phenotypic feature association_predicate', 'frequency qualifier', 'severity qualifier', 'onset qualifier', 'sex qualifier', 'has count', 'has total', 'has quotient', 'has percentage', 'gene to disease association_object', 'gene as a model of disease association_subject'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene or gene product', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:GeneAsAModelOfDiseaseAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'predicate', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'variant as a model of disease association': ClassDefinition(name='variant as a model of disease association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/VariantAsAModelOfDiseaseAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='variant to disease association', abstract=None, mixin=None, mixins=['model to disease association mixin', 'entity to disease association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'variant to disease association_predicate', 'variant to disease association_object', 'frequency qualifier', 'severity qualifier', 'onset qualifier', 'variant as a model of disease association_subject'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A variant that has a role in modeling the disease.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='sequence variant', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:VariantAsAModelOfDiseaseAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'predicate', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'genotype as a model of disease association': ClassDefinition(name='genotype as a model of disease association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GenotypeAsAModelOfDiseaseAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='genotype to disease association', abstract=None, mixin=None, mixins=['model to disease association mixin', 'entity to disease association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'genotype to disease association_predicate', 'genotype to disease association_object', 'frequency qualifier', 'severity qualifier', 'onset qualifier', 'genotype as a model of disease association_subject'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A genotype that has a role in modeling the disease.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='genotype', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:GenotypeAsAModelOfDiseaseAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'predicate', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'cell line as a model of disease association': ClassDefinition(name='cell line as a model of disease association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/CellLineAsAModelOfDiseaseAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='cell line to disease or phenotypic feature association', abstract=None, mixin=None, mixins=['model to disease association mixin', 'entity to disease association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'object', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'cell line as a model of disease association_subject', 'frequency qualifier', 'severity qualifier', 'onset qualifier'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A cell line derived from an organismal entity with a disease state that is used as a model of that disease.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='cell line', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:CellLineAsAModelOfDiseaseAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'predicate', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'organismal entity as a model of disease association': ClassDefinition(name='organismal entity as a model of disease association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/OrganismalEntityAsAModelOfDiseaseAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=['model to disease association mixin', 'entity to disease association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'object', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'organismal entity as a model of disease association_subject', 'frequency qualifier', 'severity qualifier', 'onset qualifier'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='organismal entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:OrganismalEntityAsAModelOfDiseaseAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'predicate', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'organism to organism association': ClassDefinition(name='organism to organism association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/OrganismToOrganismAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'organism to organism association_subject', 'organism to organism association_object'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='individual organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An association between two individual organisms.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='individual organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:OrganismToOrganismAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'predicate', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'taxon to taxon association': ClassDefinition(name='taxon to taxon association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/TaxonToTaxonAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'taxon to taxon association_subject', 'taxon to taxon association_object'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='organism taxon', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An association between individuals of different taxa.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='organism taxon', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:TaxonToTaxonAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'predicate', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'gene has variant that contributes to disease association': ClassDefinition(name='gene has variant that contributes to disease association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GeneHasVariantThatContributesToDiseaseAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='gene to disease association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'gene to disease or phenotypic feature association_subject aspect qualifier', 'gene to disease or phenotypic feature association_object direction qualifier', 'frequency qualifier', 'severity qualifier', 'onset qualifier', 'sex qualifier', 'has count', 'has total', 'has quotient', 'has percentage', 'subject form or variant qualifier', 'gene has variant that contributes to disease association_subject', 'gene has variant that contributes to disease association_object', 'gene has variant that contributes to disease association_predicate'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene or gene product', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='disease', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='contributes to', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:GeneHasVariantThatContributesToDiseaseAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'predicate', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'gene to expression site association': ClassDefinition(name='gene to expression site association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GeneToExpressionSiteAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An association between a gene and a gene expression site, possibly qualified by stage/timing info.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['TBD: introduce subclasses for distinction between wild-type and experimental conditions?'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=['https://github.com/monarch-initiative/ingest-artifacts/tree/master/sources/BGee'], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'gene to expression site association_stage qualifier', 'gene to expression site association_quantifier qualifier', 'gene to expression site association_subject', 'gene to expression site association_object', 'gene to expression site association_predicate'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene or gene product', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='location in which the gene is expressed', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='UBERON:0002037', description='cerebellum', object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='anatomical entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='expression relationship', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='expressed in', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'stage qualifier': SlotDefinition(name='stage qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='stage at which the gene is expressed in the site', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='UBERON:0000069', description='larval stage', object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='life stage', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'quantifier qualifier': SlotDefinition(name='quantifier qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='can be used to indicate magnitude, or also ranking', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:GeneToExpressionSiteAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'predicate', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'sequence variant modulates treatment association': ClassDefinition(name='sequence variant modulates treatment association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/SequenceVariantModulatesTreatmentAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['An alternate way to model the same information could be via a qualifier'], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'sequence variant modulates treatment association_subject', 'sequence variant modulates treatment association_object'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='variant that modulates the treatment of some disease', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='sequence variant', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='treatment whose efficacy is modulated by the subject variant', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:SequenceVariantModulatesTreatmentAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'functional association': ClassDefinition(name='functional association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/FunctionalAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'functional association_subject', 'functional association_object'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='gene, product or macromolecular complex that has the function associated with the GO term', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='ZFIN:ZDB-GENE-050417-357', description='twist1b', object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='macromolecular machine mixin', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='class describing the activity, process or localization of the gene product', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='GO:0016301', description='kinase activity', object=None), Example(value='GO:0045211', description='postsynaptic membrane', object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=['go'], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ontology class', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:FunctionalAssociation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'macromolecular machine to entity association mixin': ClassDefinition(name='macromolecular machine to entity association mixin', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/MacromolecularMachineToEntityAssociationMixin', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='an association which has a macromolecular machine mixin as a subject', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['macromolecular machine to entity association mixin_subject'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain='macromolecular machine mixin', slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:MacromolecularMachineToEntityAssociationMixin', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'macromolecular machine to molecular activity association': ClassDefinition(name='macromolecular machine to molecular activity association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/MacromolecularMachineToMolecularActivityAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='functional association', abstract=None, mixin=None, mixins=['macromolecular machine to entity association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'functional association_subject', 'macromolecular machine to molecular activity association_object'], slot_usage={'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='molecular activity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:MacromolecularMachineToMolecularActivityAssociation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'macromolecular machine to biological process association': ClassDefinition(name='macromolecular machine to biological process association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/MacromolecularMachineToBiologicalProcessAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='functional association', abstract=None, mixin=None, mixins=['macromolecular machine to entity association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'functional association_subject', 'macromolecular machine to biological process association_object'], slot_usage={'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='biological process', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:MacromolecularMachineToBiologicalProcessAssociation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'macromolecular machine to cellular component association': ClassDefinition(name='macromolecular machine to cellular component association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/MacromolecularMachineToCellularComponentAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='functional association', abstract=None, mixin=None, mixins=['macromolecular machine to entity association mixin'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'functional association_subject', 'macromolecular machine to cellular component association_object'], slot_usage={'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='cellular component', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:MacromolecularMachineToCellularComponentAssociation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'molecular activity to chemical entity association': ClassDefinition(name='molecular activity to chemical entity association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/MolecularActivityToChemicalEntityAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'molecular activity to chemical entity association_subject', 'molecular activity to chemical entity association_object'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='molecular activity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='chemical entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:MolecularActivityToChemicalEntityAssociation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'molecular activity to molecular activity association': ClassDefinition(name='molecular activity to molecular activity association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/MolecularActivityToMolecularActivityAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'molecular activity to molecular activity association_subject', 'molecular activity to molecular activity association_object'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='molecular activity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='molecular activity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:MolecularActivityToMolecularActivityAssociation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'gene to go term association': ClassDefinition(name='gene to go term association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GeneToGoTermAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['functional association'], structured_aliases={}, mappings=[], exact_mappings=['WBVocab:Gene-GO-Association'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='functional association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'gene to go term association_subject', 'gene to go term association_object'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='gene, product or macromolecular complex that has the function associated with the GO term', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='ZFIN:ZDB-GENE-050417-357', description='twist1b', object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='class describing the activity, process or localization of the gene product', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='GO:0016301', description='kinase activity', object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=['go'], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ontology class', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:GeneToGoTermAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'entity to disease association': ClassDefinition(name='entity to disease association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/EntityToDiseaseAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'subject', 'predicate', 'object', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'FDA approval status'], slot_usage={}, attributes={}, class_uri='biolink:EntityToDiseaseAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'entity to phenotypic feature association': ClassDefinition(name='entity to phenotypic feature association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/EntityToPhenotypicFeatureAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'subject', 'predicate', 'object', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'FDA approval status'], slot_usage={}, attributes={}, class_uri='biolink:EntityToPhenotypicFeatureAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'sequence association': ClassDefinition(name='sequence association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/SequenceAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An association between a sequence feature and a nucleic acid entity it is localized to.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'subject', 'predicate', 'object', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category'], slot_usage={}, attributes={}, class_uri='biolink:SequenceAssociation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'genomic sequence localization': ClassDefinition(name='genomic sequence localization', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GenomicSequenceLocalization', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['dcid:GenomeAnnotation'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['dcid:Chromosome'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='sequence association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'start interbase coordinate', 'end interbase coordinate', 'genome build', 'strand', 'phase', 'genomic sequence localization_subject', 'genomic sequence localization_object', 'genomic sequence localization_predicate'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['sequence feature'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='nucleic acid entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['reference'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='nucleic acid entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='has sequence location', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:GenomicSequenceLocalization', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'sequence feature relationship': ClassDefinition(name='sequence feature relationship', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/SequenceFeatureRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='For example, a particular exon is part of a particular transcript or gene', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['CHADO:feature_relationship'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'sequence feature relationship_subject', 'sequence feature relationship_object'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='nucleic acid entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='nucleic acid entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:SequenceFeatureRelationship', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'transcript to gene relationship': ClassDefinition(name='transcript to gene relationship', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/TranscriptToGeneRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A gene is a collection of transcripts', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='sequence feature relationship', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'transcript to gene relationship_subject', 'transcript to gene relationship_object'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='transcript', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:TranscriptToGeneRelationship', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'gene to gene product relationship': ClassDefinition(name='gene to gene product relationship', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GeneToGeneProductRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A gene is transcribed and potentially translated to a gene product', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='sequence feature relationship', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'gene to gene product relationship_subject', 'gene to gene product relationship_object', 'gene to gene product relationship_predicate'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene product mixin', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='has gene product', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:GeneToGeneProductRelationship', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'exon to transcript relationship': ClassDefinition(name='exon to transcript relationship', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ExonToTranscriptRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A transcript is formed from multiple exons', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='sequence feature relationship', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'exon to transcript relationship_subject', 'exon to transcript relationship_object'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='exon', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='transcript', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:ExonToTranscriptRelationship', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'chemical entity or gene or gene product regulates gene association': ClassDefinition(name='chemical entity or gene or gene product regulates gene association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A regulatory relationship between two genes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'chemical entity or gene or gene product regulates gene association_object direction qualifier', 'chemical entity or gene or gene product regulates gene association_predicate', 'chemical entity or gene or gene product regulates gene association_subject', 'chemical entity or gene or gene product regulates gene association_object'], slot_usage={'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the direction is always from regulator to regulated', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='regulates', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role='regulatory gene', is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='chemical entity or gene or gene product', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role='regulated gene', is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='gene or gene product', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object direction qualifier': SlotDefinition(name='object direction qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='DirectionQualifierEnum', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'anatomical entity to anatomical entity association': ClassDefinition(name='anatomical entity to anatomical entity association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/AnatomicalEntityToAnatomicalEntityAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'anatomical entity to anatomical entity association_subject', 'anatomical entity to anatomical entity association_object'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='anatomical entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='anatomical entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:AnatomicalEntityToAnatomicalEntityAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'anatomical entity to anatomical entity part of association': ClassDefinition(name='anatomical entity to anatomical entity part of association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/AnatomicalEntityToAnatomicalEntityPartOfAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='anatomical entity to anatomical entity association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'anatomical entity to anatomical entity part of association_subject', 'anatomical entity to anatomical entity part of association_object', 'anatomical entity to anatomical entity part of association_predicate'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the part', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='anatomical entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the whole', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='anatomical entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='part of', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation', subclass_of=None, union_of=[], defining_slots=['predicate'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'anatomical entity to anatomical entity ontogenic association': ClassDefinition(name='anatomical entity to anatomical entity ontogenic association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/AnatomicalEntityToAnatomicalEntityOntogenicAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='anatomical entity to anatomical entity association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'anatomical entity to anatomical entity ontogenic association_subject', 'anatomical entity to anatomical entity ontogenic association_object', 'anatomical entity to anatomical entity ontogenic association_predicate'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the structure at a later time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='anatomical entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the structure at an earlier time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='anatomical entity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='develops from', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation', subclass_of=None, union_of=[], defining_slots=['predicate'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'organism taxon to entity association': ClassDefinition(name='organism taxon to entity association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/OrganismTaxonToEntityAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An association between an organism taxon and another entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=True, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['organism taxon to entity association_subject'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='organism taxon that is the subject of the association', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='organism taxon', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:OrganismTaxonToEntityAssociation', subclass_of=None, union_of=[], defining_slots=['subject'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'organism taxon to organism taxon association': ClassDefinition(name='organism taxon to organism taxon association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/OrganismTaxonToOrganismTaxonAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A relationship between two organism taxon nodes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=True, mixin=None, mixins=['organism taxon to entity association'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'predicate', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'organism taxon to organism taxon association_subject', 'organism taxon to organism taxon association_object'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='organism taxon', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='organism taxon', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:OrganismTaxonToOrganismTaxonAssociation', subclass_of=None, union_of=[], defining_slots=['subject', 'object'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'organism taxon to organism taxon specialization': ClassDefinition(name='organism taxon to organism taxon specialization', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/OrganismTaxonToOrganismTaxonSpecialization', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='organism taxon to organism taxon association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'organism taxon to organism taxon specialization_subject', 'organism taxon to organism taxon specialization_object', 'organism taxon to organism taxon specialization_predicate'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the more specific taxon', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role='child taxon', is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='organism taxon', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the more general taxon', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role='parent taxon', is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='organism taxon', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='subclass of', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:OrganismTaxonToOrganismTaxonSpecialization', subclass_of=None, union_of=[], defining_slots=['predicate'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'organism taxon to organism taxon interaction': ClassDefinition(name='organism taxon to organism taxon interaction', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/OrganismTaxonToOrganismTaxonInteraction', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='organism taxon to organism taxon association', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'organism taxon to organism taxon interaction_associated environmental context', 'organism taxon to organism taxon interaction_subject', 'organism taxon to organism taxon interaction_object', 'organism taxon to organism taxon interaction_predicate'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the taxon that is the subject of the association', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role='interactor taxon', is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='organism taxon', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the taxon that is the subject of the association', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role='interactee taxon', is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='organism taxon', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of='interacts with', symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'associated environmental context': SlotDefinition(name='associated environmental context', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the environment in which the two taxa interact', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:OrganismTaxonToOrganismTaxonInteraction', subclass_of=None, union_of=[], defining_slots=['predicate'], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'organism taxon to environment association': ClassDefinition(name='organism taxon to environment association', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/OrganismTaxonToEnvironmentAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='association', abstract=True, mixin=None, mixins=['organism taxon to entity association'], apply_to=[], values_from=[], string_serialization=None, slots=['id', 'iri', 'name', 'description', 'has attribute', 'negated', 'qualifiers', 'publications', 'has evidence', 'knowledge source', 'primary knowledge source', 'aggregator knowledge source', 'timepoint', 'original subject', 'original predicate', 'original object', 'subject category', 'object category', 'subject closure', 'object closure', 'subject category closure', 'object category closure', 'subject namespace', 'object namespace', 'subject label closure', 'object label closure', 'retrieval source ids', 'association_type', 'association_category', 'organism taxon to environment association_subject', 'organism taxon to environment association_object', 'organism taxon to environment association_predicate'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the taxon that is the subject of the association', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role='interactor taxon', is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='organism taxon', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the environment in which the organism occurs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role='environmental context', is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='predicate describing the relationship between the taxon and the environment', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='biolink:OrganismTaxonToEnvironmentAssociation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; + linkml:enums "{'DirectionQualifierEnum': EnumDefinition(name='DirectionQualifierEnum', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/DirectionQualifierEnum', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'increased': PermissibleValue(text='increased', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'upregulated': PermissibleValue(text='upregulated', description=None, meaning=None, unit=None, is_a='increased', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['RO:0002213'], close_mappings=['RO:0002336'], related_mappings=[], narrow_mappings=['RO:0004032', 'RO:0004034', 'RO:0002629'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'decreased': PermissibleValue(text='decreased', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'downregulated': PermissibleValue(text='downregulated', description=None, meaning=None, unit=None, is_a='decreased', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['RO:0004035', 'RO:0002212'], close_mappings=['RO:0002335'], related_mappings=[], narrow_mappings=[], broad_mappings=['RO:0004033'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[]), 'ChemicalEntityDerivativeEnum': EnumDefinition(name='ChemicalEntityDerivativeEnum', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ChemicalEntityDerivativeEnum', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'metabolite': PermissibleValue(text='metabolite', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[]), 'ChemicalOrGeneOrGeneProductFormOrVariantEnum': EnumDefinition(name='ChemicalOrGeneOrGeneProductFormOrVariantEnum', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ChemicalOrGeneOrGeneProductFormOrVariantEnum', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'genetic_variant_form': PermissibleValue(text='genetic_variant_form', description=None, meaning=None, unit=None, is_a='modified_form', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'modified_form': PermissibleValue(text='modified_form', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'loss_of_function_variant_form': PermissibleValue(text='loss_of_function_variant_form', description=None, meaning=None, unit=None, is_a='genetic_variant_form', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'gain_of_function_variant_form': PermissibleValue(text='gain_of_function_variant_form', description=None, meaning=None, unit=None, is_a='genetic_variant_form', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'polymorphic_form': PermissibleValue(text='polymorphic_form', description=None, meaning=None, unit=None, is_a='genetic_variant_form', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'snp_form': PermissibleValue(text='snp_form', description=None, meaning=None, unit=None, is_a='polymorphic_form', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'analog_form': PermissibleValue(text='analog_form', description=None, meaning=None, unit=None, is_a='modified_form', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[]), 'GeneOrGeneProductOrChemicalPartQualifierEnum': EnumDefinition(name='GeneOrGeneProductOrChemicalPartQualifierEnum', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GeneOrGeneProductOrChemicalPartQualifierEnum', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'3_prime_utr': PermissibleValue(text='3_prime_utr', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), '5_prime_utr': PermissibleValue(text='5_prime_utr', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'polya_tail': PermissibleValue(text='polya_tail', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'promoter': PermissibleValue(text='promoter', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'enhancer': PermissibleValue(text='enhancer', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'exon': PermissibleValue(text='exon', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'intron': PermissibleValue(text='intron', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[]), 'GeneOrGeneProductOrChemicalEntityAspectEnum': EnumDefinition(name='GeneOrGeneProductOrChemicalEntityAspectEnum', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/GeneOrGeneProductOrChemicalEntityAspectEnum', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'activity_or_abundance': PermissibleValue(text='activity_or_abundance', description='Used in cases where the specificity of the relationship can not be determined to be either activity or abundance. In general, a more specific value from this enumeration should be used.', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'abundance': PermissibleValue(text='abundance', description=None, meaning=None, unit=None, is_a='activity_or_abundance', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'activity': PermissibleValue(text='activity', description=None, meaning=None, unit=None, is_a='activity_or_abundance', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'expression': PermissibleValue(text='expression', description=None, meaning=None, unit=None, is_a='abundance', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'synthesis': PermissibleValue(text='synthesis', description=None, meaning=None, unit=None, is_a='abundance', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'degradation': PermissibleValue(text='degradation', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'cleavage': PermissibleValue(text='cleavage', description=None, meaning=None, unit=None, is_a='degradation', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'hydrolysis': PermissibleValue(text='hydrolysis', description=None, meaning=None, unit=None, is_a='degradation', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'metabolic_processing': PermissibleValue(text='metabolic_processing', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'mutation_rate': PermissibleValue(text='mutation_rate', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'stability': PermissibleValue(text='stability', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'folding': PermissibleValue(text='folding', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'localization': PermissibleValue(text='localization', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'transport': PermissibleValue(text='transport', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'secretion': PermissibleValue(text='secretion', description=None, meaning=None, unit=None, is_a='transport', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'uptake': PermissibleValue(text='uptake', description=None, meaning=None, unit=None, is_a='transport', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'molecular_modification': PermissibleValue(text='molecular_modification', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'acetylation': PermissibleValue(text='acetylation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'acylation': PermissibleValue(text='acylation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'alkylation': PermissibleValue(text='alkylation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'amination': PermissibleValue(text='amination', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'carbamoylation': PermissibleValue(text='carbamoylation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'ethylation': PermissibleValue(text='ethylation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'glutathionylation': PermissibleValue(text='glutathionylation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'glycation': PermissibleValue(text='glycation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'glycosylation': PermissibleValue(text='glycosylation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'glucuronidation': PermissibleValue(text='glucuronidation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'n_linked_glycosylation': PermissibleValue(text='n_linked_glycosylation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'o_linked_glycosylation': PermissibleValue(text='o_linked_glycosylation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'hydroxylation': PermissibleValue(text='hydroxylation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'lipidation': PermissibleValue(text='lipidation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'farnesylation': PermissibleValue(text='farnesylation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'geranoylation': PermissibleValue(text='geranoylation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'myristoylation': PermissibleValue(text='myristoylation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'palmitoylation': PermissibleValue(text='palmitoylation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'prenylation': PermissibleValue(text='prenylation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'methylation': PermissibleValue(text='methylation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'nitrosation': PermissibleValue(text='nitrosation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'nucleotidylation': PermissibleValue(text='nucleotidylation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'phosphorylation': PermissibleValue(text='phosphorylation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'ribosylation': PermissibleValue(text='ribosylation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'ADP-ribosylation': PermissibleValue(text='ADP-ribosylation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'sulfation': PermissibleValue(text='sulfation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'sumoylation': PermissibleValue(text='sumoylation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'ubiquitination': PermissibleValue(text='ubiquitination', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'oxidation': PermissibleValue(text='oxidation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'reduction': PermissibleValue(text='reduction', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'carboxylation': PermissibleValue(text='carboxylation', description=None, meaning=None, unit=None, is_a='molecular_modification', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[]), 'CausalMechanismQualifierEnum': EnumDefinition(name='CausalMechanismQualifierEnum', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/CausalMechanismQualifierEnum', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'binding': PermissibleValue(text='binding', description='A causal mechanism mediated by the direct contact between effector and target chemical or biomolecular entity, which form a stable physical interaction.', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'inhibition': PermissibleValue(text='inhibition', description='A causal mechanism in which the effector binds to the target and negatively effects its normal function, e.g. prevention of enzymatic reaction or activation of downstream pathway.', meaning=None, unit=None, is_a='binding', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['DGIdb:inhibitor', 'SEMMEDDB:INHIBITS'], related_mappings=[], narrow_mappings=['DGIdb:blocker', 'DGIdb:channel_blocker', 'DGIdb:gating_inhibitor', 'CHEMBL.MECHANISM:antisense_inhibitor', 'CHEMBL.MECHANISM:blocker', 'CHEMBL.MECHANISM:inhibitor', 'CHEMBL.MECHANISM:negative_allosteric_modulator', 'CHEMBL.MECHANISM:negative_modulator', 'DGIdb:negative_modulator'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'antibody_inhibition': PermissibleValue(text='antibody_inhibition', description='A causal mechanism in which an antibody specifically binds to and interferes with the target.', meaning=None, unit=None, is_a='inhibition', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'antagonism': PermissibleValue(text='antagonism', description='A causal mechanism in which the effector binds to a receptor and prevents activation by an agonist through competing for the binding site.', meaning=None, unit=None, is_a='inhibition', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['DGIdb:antagonist', 'CHEMBL.MECHANISM:antagonist'], related_mappings=[], narrow_mappings=['CHEMBL.MECHANISM:allosteric_antagonist'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'molecular_channel_blockage': PermissibleValue(text='molecular_channel_blockage', description='A causal mechanism in which the effector binds to a molecular channel and prevents or reduces transport of ions through it.', meaning=None, unit=None, is_a='inhibition', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'inverse_agonism': PermissibleValue(text='inverse_agonism', description='A causal mechanism in which the effector binds to the same receptor-binding site as an agonist and antagonizes its effects, often exerting the opposite effect of the agonist by suppressing spontaneous receptor signaling.', meaning=None, unit=None, is_a='inhibition', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['CHEMBL.MECHANISM:inverse_agonist', 'DGIdb:inverse_agonist'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'negative_allosteric_modulation': PermissibleValue(text='negative_allosteric_modulation', description='A causal mechanism in which the effector reduces or prevents the action of the endogenous ligand of a receptor by binding to a site distinct from that ligand (i.e. non-competitive inhibition)', meaning=None, unit=None, is_a='inhibition', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['CHEMBL.MECHANISM:negative_allosteric_modulator', 'DGIdb:inhibitory_allosteric_modulator'], related_mappings=[], narrow_mappings=['DGIdb:negative_modulator'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'agonism': PermissibleValue(text='agonism', description='A causal mechanism in which the effector binds and activates a receptor to mimic the effect of an endogenous ligand.', meaning=None, unit=None, is_a='activation', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['CHEMBL.MECHANISM:agonist', 'DGIdb:agonist'], related_mappings=[], narrow_mappings=['CHEMBL.MECHANISM:partial_agonist', 'DGIdb:partial_agonist'], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'molecular_channel_opening': PermissibleValue(text='molecular_channel_opening', description='A causal mechanism in which the effector binds to a molecular channel and facilitates transport of ions through it.', meaning=None, unit=None, is_a='activation', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['CHEMBL.MECHANISM:opener'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'positive_allosteric_modulation': PermissibleValue(text='positive_allosteric_modulation', description='A causal mechanism in which the effector enhances the action of the endogenous ligand of a receptor by binding to a site distinct from that ligand (i.e. non-competitive inhibition)', meaning=None, unit=None, is_a='activation', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['CHEMBL.MECHANISM:positive_allosteric_modulator', 'CHEMBL.MECHANISM:positive_modulator', 'DGIdb:positive_allosteric_modulator'], related_mappings=[], narrow_mappings=[], broad_mappings=['DGIdb:modulator', 'DGIdb:allosteric_modulator'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'potentiation': PermissibleValue(text='potentiation', description='A causal mechanism in which the effector binds to and enhances or intensifies the effect of some other chemical or drug on its target.', meaning=None, unit=None, is_a='binding', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'activation': PermissibleValue(text='activation', description='A causal mechanism in which the effector binds to and positively affects the normal functioning of its target.', meaning=None, unit=None, is_a='binding', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['CHEMBL.MECHANISM:activator', 'DGIdb:activator'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'inducer': PermissibleValue(text='inducer', description='A causal mechanism in which the effector binds to and increases the activity/rate of an enzyme that processes drugs in the body.', meaning=None, unit=None, is_a='binding', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['DGIdb:inducer'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'transcriptional_regulation': PermissibleValue(text='transcriptional_regulation', description='A causal mechanism mediated by through the control of target gene transcription', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'signaling_mediated_control': PermissibleValue(text='signaling_mediated_control', description='A causal mechanism mediated by the activation or control of signaling events that influence the some aspect of the target entity (e.g. its activity, processing, transport, etc)', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'stabilization': PermissibleValue(text='stabilization', description=None, meaning=None, unit=None, is_a='activation', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['CHEMBL.MECHANISM:stabiliser'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'stimulation': PermissibleValue(text='stimulation', description=None, meaning=None, unit=None, is_a='activation', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['DGIdb:stimulator', 'SEMMEDDB:STIMULATES', 'DGIdb:stimulator'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'releasing_activity': PermissibleValue(text='releasing_activity', description=None, meaning=None, unit=None, is_a='activation', mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['CHEMBL:MECHANISM:releasing_agent'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[]), 'LogicalInterpretationEnum': EnumDefinition(name='LogicalInterpretationEnum', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/LogicalInterpretationEnum', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'some_some': PermissibleValue(text='some_some', description='A modifier on a triple that causes the triple to be interpreted as a some-some statement', meaning='os:SomeSomeInterpretation', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'all_some': PermissibleValue(text='all_some', description='A modifier on a triple that causes the triple to be interpreted as an all-some statement.', meaning='os:AllSomeInterpretation', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'inverse_all_some': PermissibleValue(text='inverse_all_some', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[]), 'ReactionDirectionEnum': EnumDefinition(name='ReactionDirectionEnum', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ReactionDirectionEnum', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'left_to_right': PermissibleValue(text='left_to_right', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'right_to_left': PermissibleValue(text='right_to_left', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'bidirectional': PermissibleValue(text='bidirectional', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'neutral': PermissibleValue(text='neutral', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[]), 'ReactionSideEnum': EnumDefinition(name='ReactionSideEnum', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ReactionSideEnum', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'left': PermissibleValue(text='left', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'right': PermissibleValue(text='right', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[]), 'PhaseEnum': EnumDefinition(name='PhaseEnum', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/PhaseEnum', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='phase', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'0': PermissibleValue(text='0', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), '1': PermissibleValue(text='1', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), '2': PermissibleValue(text='2', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[]), 'StrandEnum': EnumDefinition(name='StrandEnum', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/StrandEnum', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='strand', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'+': PermissibleValue(text='+', description='Positive', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), '-': PermissibleValue(text='-', description='Negative', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), '.': PermissibleValue(text='.', description='Unstranded', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), '?': PermissibleValue(text='?', description='Unknown', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[]), 'SequenceEnum': EnumDefinition(name='SequenceEnum', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/SequenceEnum', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='type of sequence', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'na': PermissibleValue(text='na', description='nucleic acid', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'aa': PermissibleValue(text='aa', description='amino acid', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[]), 'DruggableGeneCategoryEnum': EnumDefinition(name='DruggableGeneCategoryEnum', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/DruggableGeneCategoryEnum', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'tclin': PermissibleValue(text='tclin', description='These targets have activities in DrugCentral (ie. approved drugs) with known mechanism of action.', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'tbio': PermissibleValue(text='tbio', description='These targets have activities in ChEMBL, Guide to Pharmacology or DrugCentral that satisfy the activity thresholds detailed below.', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'tchem': PermissibleValue(text='tchem', description='These targets do not have known drug or small molecule activities that satisfy the activity thresholds detailed below AND satisfy one or more of the following criteria: target is above the cutoff criteria for Tdark target is annotated with a Gene Ontology Molecular Function or Biological Process leaf term(s) with an Experimental Evidence code', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'tdark': PermissibleValue(text='tdark', description='These are targets about which virtually nothing is known. They do not have known drug or small molecule activities that satisfy the activity thresholds detailed below AND satisfy two or more of the following criteria: A PubMed text-mining score from Jensen Lab less than 5, greater than or equal TO 3 Gene RIFs, or less than or equal to 50 Antibodies available according to http://antibodypedia.com.', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[]), 'DrugAvailabilityEnum': EnumDefinition(name='DrugAvailabilityEnum', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/DrugAvailabilityEnum', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'over_the_counter': PermissibleValue(text='over_the_counter', description='chemical entity is available over the counter without a prescription.', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'prescription': PermissibleValue(text='prescription', description='chemical entity is available by prescription.', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[]), 'DrugDeliveryEnum': EnumDefinition(name='DrugDeliveryEnum', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/DrugDeliveryEnum', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'inhalation': PermissibleValue(text='inhalation', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'oral': PermissibleValue(text='oral', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'absorption_through_the_skin': PermissibleValue(text='absorption_through_the_skin', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'intravenous_injection': PermissibleValue(text='intravenous_injection', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[]), 'ResourceRoleEnum': EnumDefinition(name='ResourceRoleEnum', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ResourceRoleEnum', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=\"The role played by the information reource in serving as a source for an edge in a TRAPI message. Note that a given Edge should have one and only one 'primary' source, and may have any number of 'aggregator' or 'supporting data' sources. This enumeration is found in Biolink Model, but is repeated here for convenience.\", alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=['translator_minimal'], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'primary_knowledge_source': PermissibleValue(text='primary_knowledge_source', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'aggregator_knowledge_source': PermissibleValue(text='aggregator_knowledge_source', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'supporting_data_source': PermissibleValue(text='supporting_data_source', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[]), 'FDAApprovalStatusEnum': EnumDefinition(name='FDAApprovalStatusEnum', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/FDAApprovalStatusEnum', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'discovery_and_development_phase': PermissibleValue(text='discovery_and_development_phase', description='Discovery & Development Phase. Discovery involves researchers finding new possibilities for medication through testing molecular compounds, noting unexpected effects from existing treatments, or the creation of new technology that allows novel ways of targeting medical products to sites in the body. Drug development occurs after researchers identify potential compounds for experiments.', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'preclinical_research_phase': PermissibleValue(text='preclinical_research_phase', description='Preclinical Research Phase. Once researchers have examined the possibilities a new drug may contain, they must do preliminary research to determine its potential for harm (toxicity). This is categorized as preclinical research and can be one of two types: in vitro or in vivo.', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'fda_clinical_research_phase': PermissibleValue(text='fda_clinical_research_phase', description='Clinical Research Phase. Clinical research involves trials of the drug on people, and it is one of the most involved stages in the drug development and approval process. Clinical trials must answer specific questions and follow a protocol determined by the drug researcher or manufacturer.', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'fda_review_phase_4': PermissibleValue(text='fda_review_phase_4', description='FDA Review', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'fda_post_market_safety_review': PermissibleValue(text='fda_post_market_safety_review', description='FDA Post-Market Safety Monitoring. The last phase of drug approval is an ongoing one while the drug is on the marketplace. If a developer wants to change anything about the drug formulation or approve it for a new use, they must apply with the FDA. The FDA also frequently reviews the drug’s advertising and its manufacturing facility to make sure everything involved in its creation and marketing is in compliance with regulations.', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'fda_clinical_research_phase_1': PermissibleValue(text='fda_clinical_research_phase_1', description='In the FDA Clinical Research Phase, the Clinical Research Phase 1 involves 20 – 100 study participants and lasts several months. This phase is used to determine the safety and dosage of the drug, and about 70% of these drugs move on to the next clinical research phase.', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'fda_clinical_research_phase_2': PermissibleValue(text='fda_clinical_research_phase_2', description='In the FDA Clinical Research Phase, the Clinical Research Phase 2 involves up to several hundred people, who must have the disease or condition the drug supposes to treat. This phase can last from a few months to two years, and its purpose is to monitor the efficacy of the drug, as well as note side effects that may occur.', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'fda_clinical_research_phase_3': PermissibleValue(text='fda_clinical_research_phase_3', description='In the FDA Clinical Research Phase, the Clinical Research Phase 3 involves 300 – 3000 volunteers and can last up to four years. It is used to continue monitoring the efficacy of the drug, as well as exploring any longer-term adverse reactions.', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'fda_clinical_research_phase_4': PermissibleValue(text='fda_clinical_research_phase_4', description='In the FDA Clinical Research Phase, the Clinical Research Phase 4 involves several thousands of volunteers who have the disease or condition and continues to monitor safety and efficacy. If a drug passes this phase, it goes on to FDA review.', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'fda_fast_track': PermissibleValue(text='fda_fast_track', description='Fast track is a process designed to facilitate the development, and expedite the review of drugs to treat serious conditions and fill an unmet medical need. The purpose is to get important new drugs to the patient earlier. Fast Track addresses a broad range of serious conditions. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/fast-track', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'fda_breakthrough_therapy': PermissibleValue(text='fda_breakthrough_therapy', description='Breakthrough Therapy designation is a process designed to expedite the development and review of drugs that are intended to treat a serious condition and preliminary clinical evidence indicates that the drug may demonstrate substantial improvement over available therapy on a clinically significant endpoint(s). For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/breakthrough-therapy', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'fda_accelerated_approval': PermissibleValue(text='fda_accelerated_approval', description='When studying a new drug, it can sometimes take many years to learn whether a drug actually provides a real effect on how a patient survives, feels, or functions. A positive therapeutic effect that is clinically meaningful in the context of a given disease is known as “clinical benefit”. Mindful of the fact that it may take an extended period of time to measure a drug’s intended clinical benefit, in 1992 FDA instituted the Accelerated Approval regulations. These regulations allowed drugs for serious conditions that filled an unmet medical need to be approved based on a surrogate endpoint. Using a surrogate endpoint enabled the FDA to approve these drugs faster. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/accelerated-approval', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'fda_priority_review': PermissibleValue(text='fda_priority_review', description='Prior to approval, each drug marketed in the United States must go through a detailed FDA review process. In 1992, under the Prescription Drug User Act (PDUFA), FDA agreed to specific goals for improving the drug review time and created a two-tiered system of review times – Standard Review and Priority Review. A Priority Review designation means FDA’s goal is to take action on an application within 6 months (compared to 10 months under standard review). For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/priority-review', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'regular_fda_approval': PermissibleValue(text='regular_fda_approval', description='Regular FDA Approval. The last phase of drug approval is an ongoing one while the drug is on the marketplace. If a developer wants to change anything about the drug formulation or approve it for a new use, they must apply with the FDA. The FDA also frequently reviews the drug’s advertising and its manufacturing facility to make sure everything involved in its creation and marketing is in compliance with regulations.', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'post_approval_withdrawal': PermissibleValue(text='post_approval_withdrawal', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[]), 'FDAIDAAdverseEventEnum': EnumDefinition(name='FDAIDAAdverseEventEnum', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/FDAIDAAdverseEventEnum', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='please consult with the FDA guidelines as proposed in this document: https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm?fr=312.32', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'life_threatening_adverse_event': PermissibleValue(text='life_threatening_adverse_event', description=\"An adverse event or suspected adverse reaction is considered 'life-threatening' if, in the view of either the investigator or sponsor, its occurrence places the patient or subject at immediate risk of death. It does not include an adverse event or suspected adverse reaction that, had it occurred in a more severe form, might have caused death.\", meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'serious_adverse_event': PermissibleValue(text='serious_adverse_event', description=\"An adverse event or suspected adverse reaction is considered 'serious' if, in the view of either the investigator or sponsor, it results in any of the following outcomes: Death, a life-threatening adverse event, inpatient hospitalization or prolongation of existing hospitalization, a persistent or significant incapacity or substantial disruption of the ability to conduct normal life functions, or a congenital anomaly/birth defect. Important medical events that may not result in death, be life-threatening, or require hospitalization may be considered serious when, based upon appropriate medical judgment, they may jeopardize the patient or subject and may require medical or surgical intervention to prevent one of the outcomes listed in this definition. Examples of such medical events include allergic bronchospasm requiring intensive treatment in an emergency room or at home, blood dyscrasias or convulsions that do not result in inpatient hospitalization, or the development of drug dependency or drug abuse.\", meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'suspected_adverse_reaction': PermissibleValue(text='suspected_adverse_reaction', description=\"means any adverse event for which there is a reasonable possibility that the drug caused the adverse event. For the purposes of IND safety reporting, 'reasonable possibility' means there is evidence to suggest a causal relationship between the drug and the adverse event. Suspected adverse reaction implies a lesser degree of certainty about causality than adverse reaction, which means any adverse event caused by a drug.\", meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'unexpected_adverse_event': PermissibleValue(text='unexpected_adverse_event', description=\"An adverse event or suspected adverse reaction is considered 'unexpected' if it is not listed in the investigator brochure or is not listed at the specificity or severity that has been observed; or, if an investigator brochure is not required or available, is not consistent with the risk information described in the general investigational plan or elsewhere in the current application, as amended. For example, under this definition, hepatic necrosis would be unexpected (by virtue of greater severity) if the investigator brochure referred only to elevated hepatic enzymes or hepatitis. Similarly, cerebral thromboembolism and cerebral vasculitis would be unexpected (by virtue of greater specificity) if the investigator brochure listed only cerebral vascular accidents. 'Unexpected', as used in this definition, also refers to adverse events or suspected adverse reactions that are mentioned in the investigator brochure as occurring with a class of drugs or as anticipated from the pharmacological properties of the drug, but are not specifically mentioned as occurring with the particular drug under investigation.\", meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; + linkml:id "https://w3id.org/biolink/biolink-model" ; + linkml:imports "information-resource", + "linkml:types" ; + linkml:types "{'chemical formula value': TypeDefinition(name='chemical formula value', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/ChemicalFormulaValue', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A chemical formula', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['Should be implemented as a stronger type'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'category type': TypeDefinition(name='category type', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/CategoryType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A primitive type in which the value denotes a class within the biolink model. The value must be a URI or a CURIE. In a Neo4j representation, the value should be the CURIE for the biolink class, for example biolink:Gene. For an RDF representation, the value should be a URI such as https://w3id.org/biolink/vocab/Gene', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof='uriorcurie', base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'iri type': TypeDefinition(name='iri type', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/IriType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An IRI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof='uriorcurie', base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label type': TypeDefinition(name='label type', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/LabelType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A string that provides a human-readable name for an entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof='string', base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate type': TypeDefinition(name='predicate type', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/PredicateType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A CURIE from the biolink related_to hierarchy. For example, biolink:related_to, biolink:causes, biolink:treats.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof='uriorcurie', base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'narrative text': TypeDefinition(name='narrative text', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/NarrativeText', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A string that provides a human-readable description of something', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof='string', base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'symbol type': TypeDefinition(name='symbol type', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/SymbolType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof='string', base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'frequency value': TypeDefinition(name='frequency value', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/FrequencyValue', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof='string', base='str', uri='UO:0000105', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'percentage frequency value': TypeDefinition(name='percentage frequency value', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/PercentageFrequencyValue', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof='double', base='float', uri='UO:0000187', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'quotient': TypeDefinition(name='quotient', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/Quotient', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['ratio'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof='double', base='float', uri='UO:0010006', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'unit': TypeDefinition(name='unit', id_prefixes=['UO'], definition_uri='https://w3id.org/biolink/vocab/Unit', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['qud:Unit'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof='string', base='str', uri='UO:0000000', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time type': TypeDefinition(name='time type', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/TimeType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof='time', base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'biological sequence': TypeDefinition(name='biological sequence', id_prefixes=[], definition_uri='https://w3id.org/biolink/vocab/BiologicalSequence', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/biolink/biolink-model', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof='string', base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritence and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . biolink:AccessibleDnaRegion a owl:Class ; rdfs:label "accessible dna region" ; @@ -127,15 +125,17 @@ biolink:AccessibleDnaRegion a owl:Class ; skos:altLabel "atac-seq accessible region", "dnase-seq accessible region" ; skos:definition "A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose" ; - skos:exactMatch . + skos:exactMatch ; + linkml:attributes "{}" ; + linkml:is_a "regulatory region" ; + linkml:mixins "chemical entity or gene or gene product", + "genomic entity", + "ontology class", + "physical essence" . biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity ontogenic association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], @@ -143,8 +143,14 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:AnatomicalEntityToAnatomicalEntityAssociation ; - skos:definition "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." . + skos:definition "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." ; + linkml:attributes "{}" ; + linkml:is_a "anatomical entity to anatomical entity association" . biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity part of association" ; @@ -161,25 +167,29 @@ biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a owl:Class ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], biolink:AnatomicalEntityToAnatomicalEntityAssociation ; - skos:definition "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" . + skos:definition "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" ; + linkml:attributes "{}" ; + linkml:is_a "anatomical entity to anatomical entity association" . biolink:Bacterium a owl:Class ; rdfs:label "bacterium" ; rdfs:subClassOf biolink:OrganismalEntity ; skos:definition "A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and are often motile." ; skos:exactMatch STY:T007, - . + ; + linkml:attributes "{}" ; + linkml:is_a "organismal entity" . biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; rdfs:label "behavior to behavioral feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; @@ -189,32 +199,35 @@ biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; - owl:onClass biolink:Behavior ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:onClass biolink:BehavioralFeature ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], + owl:onClass biolink:Behavior ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; owl:onProperty biolink:has_percentage ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin ; - skos:definition "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." . + skos:definition "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." ; + linkml:attributes "{}" ; + linkml:is_a "association" ; + linkml:mixins "entity to phenotypic feature association mixin" . biolink:BehavioralExposure a owl:Class ; rdfs:label "behavioral exposure" ; @@ -224,12 +237,17 @@ biolink:BehavioralExposure a owl:Class ; owl:onProperty biolink:timepoint ], biolink:Attribute, biolink:ExposureEvent ; - skos:definition "A behavioral exposure is a factor relating to behavior impacting an individual." . + skos:definition "A behavioral exposure is a factor relating to behavior impacting an individual." ; + linkml:attributes "{}" ; + linkml:is_a "attribute" ; + linkml:mixins "exposure event" . biolink:BehavioralOutcome a owl:Class ; rdfs:label "behavioral outcome" ; rdfs:subClassOf biolink:Outcome ; - skos:definition "An outcome resulting from an exposure event which is the manifestation of human behavior." . + skos:definition "An outcome resulting from an exposure event which is the manifestation of human behavior." ; + linkml:attributes "{}" ; + linkml:mixins "outcome" . biolink:BioticExposure a owl:Class ; rdfs:label "biotic exposure" ; @@ -241,19 +259,24 @@ biolink:BioticExposure a owl:Class ; biolink:ExposureEvent ; skos:altLabel "bacterial exposure", "viral exposure" ; - skos:definition "An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses)." . + skos:definition "An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses)." ; + linkml:attributes "{}" ; + linkml:is_a "attribute" ; + linkml:mixins "exposure event" . biolink:Book a owl:Class ; rdfs:label "book" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty rdf:type ], - [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty biolink:id ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty rdf:type ], biolink:Publication ; - skos:definition "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." . + skos:definition "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; + linkml:attributes "{}" ; + linkml:is_a "publication" . biolink:CaseToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "case to phenotypic feature association" ; @@ -261,10 +284,6 @@ biolink:CaseToPhenotypicFeatureAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; @@ -273,26 +292,52 @@ biolink:CaseToPhenotypicFeatureAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:has_total ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], biolink:Association, biolink:CaseToEntityAssociationMixin, biolink:EntityToPhenotypicFeatureAssociationMixin ; - skos:definition "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype." . + skos:definition "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype." ; + linkml:attributes "{}" ; + linkml:is_a "association" ; + linkml:mixins "case to entity association mixin", + "entity to phenotypic feature association mixin" . + +biolink:CausalGeneToDiseaseAssociation a owl:Class ; + rdfs:label "causal gene to disease association" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:Disease ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:GeneOrGeneProduct ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], + biolink:EntityToDiseaseAssociationMixin, + biolink:GeneToDiseaseAssociation, + biolink:GeneToEntityAssociationMixin ; + linkml:attributes "{}" ; + linkml:is_a "gene to disease association" ; + linkml:mixins "entity to disease association mixin", + "gene to entity association mixin" . biolink:Cell a owl:Class ; rdfs:label "cell" ; @@ -302,114 +347,118 @@ biolink:Cell a owl:Class ; , , SIO:010001, - WIKIDATA:Q7868 . + WIKIDATA:Q7868 ; + linkml:attributes "{}" ; + linkml:is_a "anatomical entity" . biolink:CellLineAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "cell line as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], + [ a owl:Restriction ; owl:onClass biolink:CellLine ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation, biolink:EntityToDiseaseAssociationMixin, - biolink:ModelToDiseaseAssociationMixin . + biolink:ModelToDiseaseAssociationMixin ; + linkml:attributes "{}" ; + linkml:is_a "cell line to disease or phenotypic feature association" ; + linkml:mixins "entity to disease association mixin", + "model to disease association mixin" . biolink:ChemicalAffectsGeneAssociation a owl:Class ; rdfs:label "chemical affects gene association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ChemicalEntityDerivativeEnum ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onClass biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:ChemicalEntityDerivativeEnum ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:ChemicalEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:onClass linkml:String ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], + owl:onClass biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:qualified_predicate ], + owl:onClass biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onClass biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:ChemicalEntity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], biolink:Association ; - skos:definition "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity, localization, processing, expression, etc.)" . + skos:definition "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity, localization, processing, expression, etc.)" ; + linkml:attributes "{}" ; + linkml:is_a "association" . biolink:ChemicalEntityAssessesNamedThingAssociation a owl:Class ; rdfs:label "chemical entity assesses named thing association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:ChemicalEntity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], @@ -417,7 +466,13 @@ biolink:ChemicalEntityAssessesNamedThingAssociation a owl:Class ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], - biolink:Association . + [ a owl:Restriction ; + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], + biolink:Association ; + linkml:attributes "{}" ; + linkml:is_a "association" . biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a owl:Class ; rdfs:label "chemical entity or gene or gene product regulates gene association" ; @@ -425,10 +480,6 @@ biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a owl:Class ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:ChemicalEntityOrGeneOrGeneProduct ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DirectionQualifierEnum ; @@ -437,59 +488,68 @@ biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a owl:Class ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:Association ; - skos:definition "A regulatory relationship between two genes" . + skos:definition "A regulatory relationship between two genes" ; + linkml:attributes "{}" ; + linkml:is_a "association" . biolink:ChemicalGeneInteractionAssociation a owl:Class ; rdfs:label "chemical gene interaction association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; owl:onProperty biolink:subject_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:object_context_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:object ; + owl:onClass biolink:ChemicalEntity ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:ChemicalEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ChemicalEntityDerivativeEnum ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:anatomical_context_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:GeneOrGeneProduct ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; owl:onProperty biolink:object_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:ChemicalEntityDerivativeEnum ; + owl:onProperty biolink:subject_derivative_qualifier ], biolink:Association, biolink:ChemicalToEntityAssociationMixin ; skos:definition "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; - skos:exactMatch SIO:001257 . + skos:exactMatch SIO:001257 ; + linkml:attributes "{}" ; + linkml:is_a "association" ; + linkml:mixins "chemical to entity association mixin" . biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "chemical or drug or treatment side effect disease or phenotypic feature association" ; @@ -500,25 +560,29 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation, biolink:ChemicalToEntityAssociationMixin, biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ; - skos:definition "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect." . + skos:definition "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect." ; + linkml:attributes "{}" ; + linkml:is_a "chemical or drug or treatment to disease or phenotypic feature association" ; + linkml:mixins "chemical to entity association mixin", + "entity to disease or phenotypic feature association mixin" . biolink:ChemicalToChemicalDerivationAssociation a owl:Class ; rdfs:label "chemical to chemical derivation association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:ChemicalEntity ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:ChemicalEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:allValuesFrom biolink:MacromolecularMachineMixin ; owl:onProperty biolink:catalyst_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:ChemicalEntity ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:ChemicalToChemicalAssociation ; skos:definition """A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF @@ -527,7 +591,9 @@ biolink:ChemicalToChemicalDerivationAssociation a owl:Class ; R enabled-by P AND R type Reaction THEN - C1 derives-into C2 <>""" . + C1 derives-into C2 <>""" ; + linkml:attributes "{}" ; + linkml:is_a "chemical to chemical association" . biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "chemical to disease or phenotypic feature association" ; @@ -539,27 +605,36 @@ biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; biolink:ChemicalToEntityAssociationMixin, biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ; skos:definition "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype." ; - skos:narrowMatch SIO:000993 . + skos:narrowMatch SIO:000993 ; + linkml:attributes "{}" ; + linkml:is_a "association" ; + linkml:mixins "chemical to entity association mixin", + "entity to disease or phenotypic feature association mixin" . biolink:ChemicalToPathwayAssociation a owl:Class ; rdfs:label "chemical to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:Pathway ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:ChemicalEntity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:Pathway ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:Association, biolink:ChemicalToEntityAssociationMixin ; skos:definition "An interaction between a chemical entity and a biological process or pathway." ; - skos:exactMatch SIO:001250 . + skos:exactMatch SIO:001250 ; + linkml:attributes "{}" ; + linkml:is_a "association" ; + linkml:mixins "chemical to entity association mixin" . biolink:ChiSquaredAnalysisResult a owl:Class ; rdfs:label "chi squared analysis result" ; rdfs:subClassOf biolink:StudyResult ; - skos:definition "A result of a chi squared analysis." . + skos:definition "A result of a chi squared analysis." ; + linkml:attributes "{}" ; + linkml:is_a "study result" . biolink:ClinicalFinding a owl:Class ; rdfs:label "clinical finding" ; @@ -567,7 +642,9 @@ biolink:ClinicalFinding a owl:Class ; owl:allValuesFrom biolink:ClinicalAttribute ; owl:onProperty biolink:has_attribute ], biolink:PhenotypicFeature ; - skos:definition "this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations." . + skos:definition "this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations." ; + linkml:attributes "{}" ; + linkml:is_a "phenotypic feature" . biolink:ClinicalMeasurement a owl:Class ; rdfs:label "clinical measurement" ; @@ -577,11 +654,15 @@ biolink:ClinicalMeasurement a owl:Class ; owl:qualifiedCardinality 1 ], biolink:ClinicalAttribute ; skos:definition "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot." ; - skos:exactMatch EFO:0001444 . + skos:exactMatch EFO:0001444 ; + linkml:attributes "{}" ; + linkml:is_a "clinical attribute" . biolink:ClinicalTrial a owl:Class ; rdfs:label "clinical trial" ; - rdfs:subClassOf biolink:ClinicalEntity . + rdfs:subClassOf biolink:ClinicalEntity ; + linkml:attributes "{}" ; + linkml:is_a "clinical entity" . biolink:Cohort a owl:Class ; rdfs:label "cohort" ; @@ -592,48 +673,79 @@ biolink:Cohort a owl:Class ; skos:narrowMatch STY:T097, STY:T099, STY:T100, - STY:T101 . + STY:T101 ; + linkml:attributes "{}" ; + linkml:is_a "study population" ; + linkml:mixins "subject of investigation" . biolink:CommonDataElement a owl:Class ; rdfs:label "common data element" ; rdfs:subClassOf biolink:InformationContentEntity ; skos:closeMatch ; - skos:definition "A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. (https://cde.nlm.nih.gov/home)" . + skos:definition "A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. (https://cde.nlm.nih.gov/home)" ; + linkml:attributes "{}" ; + linkml:is_a "information content entity" . biolink:ComplexChemicalExposure a owl:Class ; rdfs:label "complex chemical exposure" ; rdfs:subClassOf biolink:Attribute ; - skos:definition "A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug." . + skos:definition "A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug." ; + linkml:attributes "{}" ; + linkml:is_a "attribute" . biolink:ComplexMolecularMixture a owl:Class ; rdfs:label "complex molecular mixture" ; rdfs:subClassOf biolink:ChemicalMixture ; - skos:definition "A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry." . + skos:definition "A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry." ; + linkml:attributes "{}" ; + linkml:is_a "chemical mixture" . biolink:ConceptCountAnalysisResult a owl:Class ; rdfs:label "concept count analysis result" ; rdfs:subClassOf biolink:StudyResult ; - skos:definition "A result of a concept count analysis." . + skos:definition "A result of a concept count analysis." ; + linkml:attributes "{}" ; + linkml:is_a "study result" . biolink:ContributorAssociation a owl:Class ; rdfs:label "contributor association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:qualifiers ], - [ a owl:Restriction ; - owl:onClass biolink:InformationContentEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:Agent ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + owl:onClass biolink:InformationContentEntity ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:Association ; - skos:definition "Any association between an entity (such as a publication) and various agents that contribute to its realisation" . + skos:definition "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ; + linkml:attributes "{}" ; + linkml:is_a "association" . + +biolink:CorrelatedGeneToDiseaseAssociation a owl:Class ; + rdfs:label "correlated gene to disease association" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:GeneOrGeneProduct ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:Disease ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], + biolink:EntityToDiseaseAssociationMixin, + biolink:GeneToDiseaseAssociation, + biolink:GeneToEntityAssociationMixin ; + linkml:attributes "{}" ; + linkml:is_a "gene to disease association" ; + linkml:mixins "entity to disease association mixin", + "gene to entity association mixin" . biolink:DiseaseOrPhenotypicFeatureExposure a owl:Class ; rdfs:label "disease or phenotypic feature exposure" ; @@ -644,26 +756,35 @@ biolink:DiseaseOrPhenotypicFeatureExposure a owl:Class ; biolink:Attribute, biolink:ExposureEvent, biolink:PathologicalEntityMixin ; - skos:definition "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer." . + skos:definition "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer." ; + linkml:attributes "{}" ; + linkml:is_a "attribute" ; + linkml:mixins "exposure event", + "pathological entity mixin" . biolink:DiseaseOrPhenotypicFeatureOutcome a owl:Class ; rdfs:label "disease or phenotypic feature outcome" ; rdfs:subClassOf biolink:Outcome ; - skos:definition "Physiological outcomes resulting from an exposure event which is the manifestation of a disease or other characteristic phenotype." . + skos:definition "Physiological outcomes resulting from an exposure event which is the manifestation of a disease or other characteristic phenotype." ; + linkml:attributes "{}" ; + linkml:mixins "outcome" . biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a owl:Class ; rdfs:label "disease or phenotypic feature to genetic inheritance association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:GeneticInheritance ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:GeneticInheritance ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:Association, biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ; - skos:definition "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance." . + skos:definition "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance." ; + linkml:attributes "{}" ; + linkml:is_a "association" ; + linkml:mixins "disease or phenotypic feature to entity association mixin" . biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a owl:Class ; rdfs:label "disease or phenotypic feature to location association" ; @@ -673,14 +794,21 @@ biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a owl:Class ; owl:qualifiedCardinality 1 ], biolink:Association, biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ; - skos:definition "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site." . + skos:definition "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site." ; + linkml:attributes "{}" ; + linkml:is_a "association" ; + linkml:mixins "disease or phenotypic feature to entity association mixin" . biolink:DiseaseToExposureEventAssociation a owl:Class ; rdfs:label "disease to exposure event association" ; rdfs:subClassOf biolink:Association, biolink:DiseaseToEntityAssociationMixin, biolink:EntityToExposureEventAssociationMixin ; - skos:definition "An association between an exposure event and a disease." . + skos:definition "An association between an exposure event and a disease." ; + linkml:attributes "{}" ; + linkml:is_a "association" ; + linkml:mixins "disease to entity association mixin", + "entity to exposure event association mixin" . biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "disease to phenotypic feature association" ; @@ -691,50 +819,56 @@ biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:PhenotypicFeature ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSex ; owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:onClass biolink:Disease ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:PhenotypicFeature ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:Association, biolink:DiseaseToEntityAssociationMixin, biolink:EntityToPhenotypicFeatureAssociationMixin ; skos:closeMatch dcid:DiseaseSymptomAssociation ; - skos:definition "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." . + skos:definition "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; + linkml:attributes "{}" ; + linkml:is_a "association" ; + linkml:mixins "disease to entity association mixin", + "entity to phenotypic feature association mixin" . biolink:DrugLabel a owl:Class ; rdfs:label "drug label" ; rdfs:subClassOf biolink:Publication ; skos:broadMatch NCIT-OBO:C41203 ; - skos:definition "a document accompanying a drug or its container that provides written, printed or graphic information about the drug, including drug contents, specific instructions or warnings for administration, storage and disposal instructions, etc. " . + skos:definition "a document accompanying a drug or its container that provides written, printed or graphic information about the drug, including drug contents, specific instructions or warnings for administration, storage and disposal instructions, etc. " ; + linkml:attributes "{}" ; + linkml:is_a "publication" . biolink:DrugToGeneAssociation a owl:Class ; rdfs:label "drug to gene association" ; @@ -745,7 +879,10 @@ biolink:DrugToGeneAssociation a owl:Class ; biolink:Association, biolink:DrugToEntityAssociationMixin ; skos:definition "An interaction between a drug and a gene or gene product." ; - skos:relatedMatch SIO:001257 . + skos:relatedMatch SIO:001257 ; + linkml:attributes "{}" ; + linkml:is_a "association" ; + linkml:mixins "drug to entity association mixin" . biolink:DrugToGeneInteractionExposure a owl:Class ; rdfs:label "drug to gene interaction exposure" ; @@ -754,36 +891,31 @@ biolink:DrugToGeneInteractionExposure a owl:Class ; owl:onProperty biolink:has_gene_or_gene_product ], biolink:DrugExposure, biolink:GeneGroupingMixin ; - skos:definition "drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome." . + skos:definition "drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome." ; + linkml:attributes "{}" ; + linkml:is_a "drug exposure" ; + linkml:mixins "gene grouping mixin" . biolink:DruggableGeneToDiseaseAssociation a owl:Class ; rdfs:label "druggable gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + owl:onClass biolink:GeneOrGeneProduct ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:allValuesFrom biolink:DruggableGeneCategoryEnum ; owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:subject ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], biolink:EntityToDiseaseAssociationMixin, biolink:GeneToDiseaseAssociation, - biolink:GeneToEntityAssociationMixin . + biolink:GeneToEntityAssociationMixin ; + linkml:attributes "{}" ; + linkml:is_a "gene to disease association" ; + linkml:mixins "entity to disease association mixin", + "gene to entity association mixin" . biolink:EntityToDiseaseAssociation a owl:Class ; rdfs:label "entity to disease association" ; @@ -791,7 +923,9 @@ biolink:EntityToDiseaseAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FDAApprovalStatusEnum ; owl:onProperty biolink:FDA_approval_status ], - biolink:Association . + biolink:Association ; + linkml:attributes "{}" ; + linkml:is_a "association" . biolink:EntityToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "entity to phenotypic feature association" ; @@ -799,49 +933,64 @@ biolink:EntityToPhenotypicFeatureAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FDAApprovalStatusEnum ; owl:onProperty biolink:FDA_approval_status ], - biolink:Association . + biolink:Association ; + linkml:attributes "{}" ; + linkml:is_a "association" . biolink:EnvironmentalFeature a owl:Class ; rdfs:label "environmental feature" ; rdfs:subClassOf biolink:PlanetaryEntity ; - skos:exactMatch . + skos:exactMatch ; + linkml:attributes "{}" ; + linkml:is_a "planetary entity" . biolink:EnvironmentalFoodContaminant a owl:Class ; rdfs:label "environmental food contaminant" ; rdfs:subClassOf biolink:ChemicalEntity ; - skos:relatedMatch . + skos:relatedMatch ; + linkml:attributes "{}" ; + linkml:is_a "chemical entity" . biolink:EnvironmentalProcess a owl:Class ; rdfs:label "environmental process" ; rdfs:subClassOf biolink:Occurrent, biolink:PlanetaryEntity ; - skos:exactMatch . + skos:exactMatch ; + linkml:attributes "{}" ; + linkml:is_a "planetary entity" ; + linkml:mixins "occurrent" . biolink:EpidemiologicalOutcome a owl:Class ; rdfs:label "epidemiological outcome" ; rdfs:subClassOf biolink:Outcome ; skos:definition "An epidemiological outcome, such as societal disease burden, resulting from an exposure event." ; - skos:relatedMatch . + skos:relatedMatch ; + linkml:attributes "{}" ; + linkml:mixins "outcome" . biolink:Event a owl:Class ; rdfs:label "event" ; rdfs:subClassOf biolink:NamedThing ; skos:definition "Something that happens at a given place and time." ; skos:exactMatch STY:T051, - . + ; + linkml:attributes "{}" ; + linkml:is_a "named thing" . biolink:ExonToTranscriptRelationship a owl:Class ; rdfs:label "exon to transcript relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:Transcript ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:Exon ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:Transcript ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:SequenceFeatureRelationship ; - skos:definition "A transcript is formed from multiple exons" . + skos:definition "A transcript is formed from multiple exons" ; + linkml:attributes "{}" ; + linkml:is_a "sequence feature relationship" . biolink:ExposureEventToOutcomeAssociation a owl:Class ; rdfs:label "exposure event to outcome association" ; @@ -855,30 +1004,37 @@ biolink:ExposureEventToOutcomeAssociation a owl:Class ; owl:onProperty biolink:population_context_qualifier ], biolink:Association, biolink:EntityToOutcomeAssociationMixin ; - skos:definition "An association between an exposure event and an outcome." . + skos:definition "An association between an exposure event and an outcome." ; + linkml:attributes "{}" ; + linkml:is_a "association" ; + linkml:mixins "entity to outcome association mixin" . biolink:ExposureEventToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "exposure event to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; - owl:onClass biolink:ExposureEvent ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:onClass biolink:ExposureEvent ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; @@ -886,29 +1042,32 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; owl:onProperty biolink:has_percentage ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin ; - skos:definition "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." . + skos:definition "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ; + linkml:attributes "{}" ; + linkml:is_a "association" ; + linkml:mixins "entity to phenotypic feature association mixin" . biolink:Food a owl:Class ; rdfs:label "food" ; rdfs:subClassOf biolink:ChemicalMixture ; skos:definition "A substance consumed by a living organism as a source of nutrition" ; - skos:exactMatch STY:T168 . + skos:exactMatch STY:T168 ; + linkml:attributes "{}" ; + linkml:is_a "chemical mixture" . biolink:FoodAdditive a owl:Class ; rdfs:label "food additive" ; rdfs:subClassOf biolink:ChemicalEntity ; - skos:relatedMatch . + skos:relatedMatch ; + linkml:attributes "{}" ; + linkml:is_a "chemical entity" . biolink:Fungus a owl:Class ; rdfs:label "fungus" ; @@ -918,37 +1077,27 @@ biolink:Fungus a owl:Class ; , ; skos:narrowMatch , - . + ; + linkml:attributes "{}" ; + linkml:is_a "cellular organism" . biolink:GeneAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "gene as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], - [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], biolink:EntityToDiseaseAssociationMixin, biolink:GeneToDiseaseAssociation, - biolink:ModelToDiseaseAssociationMixin . + biolink:ModelToDiseaseAssociationMixin ; + linkml:attributes "{}" ; + linkml:is_a "gene to disease association" ; + linkml:mixins "entity to disease association mixin", + "model to disease association mixin" . biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; rdfs:label "gene has variant that contributes to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], @@ -960,141 +1109,88 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - biolink:GeneToDiseaseAssociation . + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], + biolink:GeneToDiseaseAssociation ; + linkml:attributes "{}" ; + linkml:is_a "gene to disease association" . -biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; - rdfs:label "gene to disease or phenotypic feature association" ; +biolink:GeneToExpressionSiteAssociation a owl:Class ; + rdfs:label "gene to expression site association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], - biolink:Association, - biolink:EntityToPhenotypicFeatureAssociationMixin, - biolink:GeneToEntityAssociationMixin ; - skos:narrowMatch WBVocab:Gene-Phenotype-Association, - SIO:000983, - dcid:DiseaseGeneAssociation ; - skos:note "NCIT:R176 refers to the inverse relationship", - "for use in describing the affect that the loss of function of a gene can have on exacerbating or ameliorating a symptom/phenotype", - "if the relationship of the statement using this predicate is statistical in nature, please use `associated with likelihood` or one of its children." . - -biolink:GeneToExpressionSiteAssociation a owl:Class ; - rdfs:label "gene to expression site association" ; - rdfs:seeAlso "https://github.com/monarch-initiative/ingest-artifacts/tree/master/sources/BGee" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:onClass biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], + owl:onClass biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ], biolink:Association ; skos:definition "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; - skos:editorialNote "TBD: introduce subclasses for distinction between wild-type and experimental conditions?" . + linkml:attributes "{}" ; + linkml:is_a "association" . biolink:GeneToGeneCoexpressionAssociation a owl:Class ; rdfs:label "gene to gene coexpression association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:expression_site ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ], + owl:onClass biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:phenotypic_state ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:expression_site ], biolink:GeneExpressionMixin, biolink:GeneToGeneAssociation ; - skos:definition "Indicates that two genes are co-expressed, generally under the same conditions." . + skos:definition "Indicates that two genes are co-expressed, generally under the same conditions." ; + linkml:attributes "{}" ; + linkml:is_a "gene to gene association" ; + linkml:mixins "gene expression mixin" . biolink:GeneToGeneFamilyAssociation a owl:Class ; rdfs:label "gene to gene family association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:GeneFamily ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:Gene ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:GeneFamily ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], biolink:Association ; - skos:definition "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." . + skos:definition "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; + linkml:attributes "{}" ; + linkml:is_a "association" . biolink:GeneToGeneHomologyAssociation a owl:Class ; rdfs:label "gene to gene homology association" ; @@ -1102,16 +1198,18 @@ biolink:GeneToGeneHomologyAssociation a owl:Class ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], biolink:GeneToGeneAssociation ; - skos:definition "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" . + skos:definition "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; + linkml:attributes "{}" ; + linkml:is_a "gene to gene association" . biolink:GeneToGeneProductRelationship a owl:Class ; rdfs:label "gene to gene product relationship" ; @@ -1128,21 +1226,25 @@ biolink:GeneToGeneProductRelationship a owl:Class ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], biolink:SequenceFeatureRelationship ; - skos:definition "A gene is transcribed and potentially translated to a gene product" . + skos:definition "A gene is transcribed and potentially translated to a gene product" ; + linkml:attributes "{}" ; + linkml:is_a "sequence feature relationship" . biolink:GeneToGoTermAssociation a owl:Class ; rdfs:label "gene to go term association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:OntologyClass ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:Gene ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:OntologyClass ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:FunctionalAssociation ; skos:altLabel "functional association" ; - skos:exactMatch WBVocab:Gene-GO-Association . + skos:exactMatch WBVocab:Gene-GO-Association ; + linkml:attributes "{}" ; + linkml:is_a "functional association" . biolink:GeneToPathwayAssociation a owl:Class ; rdfs:label "gene to pathway association" ; @@ -1156,11 +1258,29 @@ biolink:GeneToPathwayAssociation a owl:Class ; owl:qualifiedCardinality 1 ], biolink:Association, biolink:GeneToEntityAssociationMixin ; - skos:definition "An interaction between a gene or gene product and a biological process or pathway." . + skos:definition "An interaction between a gene or gene product and a biological process or pathway." ; + linkml:attributes "{}" ; + linkml:is_a "association" ; + linkml:mixins "gene to entity association mixin" . biolink:GeneToPhenotypeAssociation a owl:Class ; rdfs:label "gene to phenotype association" ; - rdfs:subClassOf biolink:Association . + rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:PhenotypicFeature ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:GeneOrGeneProduct ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], + biolink:EntityToPhenotypicFeatureAssociationMixin, + biolink:GeneToDiseaseOrPhenotypicFeatureAssociation, + biolink:GeneToEntityAssociationMixin ; + skos:exactMatch WBVocab:Gene-Phenotype-Association ; + linkml:attributes "{}" ; + linkml:is_a "gene to disease or phenotypic feature association" ; + linkml:mixins "entity to phenotypic feature association mixin", + "gene to entity association mixin" . biolink:Genome a owl:Class ; rdfs:label "genome" ; @@ -1176,11 +1296,20 @@ biolink:Genome a owl:Class ; skos:definition "A genome is the sum of genetic material within a cell or virion." ; skos:exactMatch , SIO:000984, - WIKIDATA:Q7020 . + WIKIDATA:Q7020 ; + linkml:attributes "{}" ; + linkml:is_a "biological entity" ; + linkml:mixins "genomic entity", + "ontology class", + "physical essence" . biolink:GenomicBackgroundExposure a owl:Class ; rdfs:label "genomic background exposure" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:TimeType ; + owl:onProperty biolink:timepoint ], + [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:in_taxon ], [ a owl:Restriction ; @@ -1190,10 +1319,6 @@ biolink:GenomicBackgroundExposure a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSequence ; owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:TimeType ; - owl:onProperty biolink:timepoint ], biolink:Attribute, biolink:ExposureEvent, biolink:GeneGroupingMixin, @@ -1201,7 +1326,15 @@ biolink:GenomicBackgroundExposure a owl:Class ; biolink:OntologyClass, biolink:PhysicalEssence, biolink:ThingWithTaxon ; - skos:definition "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome." . + skos:definition "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome." ; + linkml:attributes "{}" ; + linkml:is_a "attribute" ; + linkml:mixins "exposure event", + "gene grouping mixin", + "genomic entity", + "ontology class", + "physical essence", + "thing with taxon" . biolink:GenotypeAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "genotype as a model of disease association" ; @@ -1211,7 +1344,11 @@ biolink:GenotypeAsAModelOfDiseaseAssociation a owl:Class ; owl:qualifiedCardinality 1 ], biolink:EntityToDiseaseAssociationMixin, biolink:GenotypeToDiseaseAssociation, - biolink:ModelToDiseaseAssociationMixin . + biolink:ModelToDiseaseAssociationMixin ; + linkml:attributes "{}" ; + linkml:is_a "genotype to disease association" ; + linkml:mixins "entity to disease association mixin", + "model to disease association mixin" . biolink:GenotypeToGeneAssociation a owl:Class ; rdfs:label "genotype to gene association" ; @@ -1219,22 +1356,24 @@ biolink:GenotypeToGeneAssociation a owl:Class ; owl:onClass biolink:Gene ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:Genotype ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], biolink:Association ; - skos:definition "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" . + skos:definition "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" ; + linkml:attributes "{}" ; + linkml:is_a "association" . biolink:GenotypeToGenotypePartAssociation a owl:Class ; rdfs:label "genotype to genotype part association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:Genotype ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; @@ -1242,25 +1381,39 @@ biolink:GenotypeToGenotypePartAssociation a owl:Class ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:Genotype ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:Association ; - skos:definition "Any association between one genotype and a genotypic entity that is a sub-component of it" . + skos:definition "Any association between one genotype and a genotypic entity that is a sub-component of it" ; + linkml:attributes "{}" ; + linkml:is_a "association" . biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "genotype to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty biolink:has_percentage ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_total ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; @@ -1269,38 +1422,26 @@ biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; owl:onClass biolink:Genotype ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin, biolink:GenotypeToEntityAssociationMixin ; - skos:definition "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" . + skos:definition "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ; + linkml:attributes "{}" ; + linkml:is_a "association" ; + linkml:mixins "entity to phenotypic feature association mixin", + "genotype to entity association mixin" . biolink:GenotypeToVariantAssociation a owl:Class ; rdfs:label "genotype to variant association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:Genotype ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], @@ -1308,14 +1449,22 @@ biolink:GenotypeToVariantAssociation a owl:Class ; owl:onClass biolink:SequenceVariant ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], biolink:Association ; - skos:definition "Any association between a genotype and a sequence variant." . + skos:definition "Any association between a genotype and a sequence variant." ; + linkml:attributes "{}" ; + linkml:is_a "association" . biolink:GenotypicSex a owl:Class ; rdfs:label "genotypic sex" ; rdfs:subClassOf biolink:BiologicalSex ; skos:definition "An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes." ; - skos:exactMatch . + skos:exactMatch ; + linkml:attributes "{}" ; + linkml:is_a "biological sex" . biolink:GeographicExposure a owl:Class ; rdfs:label "geographic exposure" ; @@ -1336,7 +1485,10 @@ biolink:GeographicExposure a owl:Class ; dcid:ThunderstormWindEvent, dcid:TornadoEvent, dcid:TropicalDepressionEvent, - dcid:WinterStoremEvent . + dcid:WinterStoremEvent ; + linkml:attributes "{}" ; + linkml:is_a "environmental exposure" ; + linkml:mixins "exposure event" . biolink:GeographicLocationAtTime a owl:Class ; rdfs:label "geographic location at time" ; @@ -1345,7 +1497,9 @@ biolink:GeographicLocationAtTime a owl:Class ; owl:onClass biolink:TimeType ; owl:onProperty biolink:timepoint ], biolink:GeographicLocation ; - skos:definition "a location that can be described in lat/long coordinates, for a particular time" . + skos:definition "a location that can be described in lat/long coordinates, for a particular time" ; + linkml:attributes "{}" ; + linkml:is_a "geographic location" . biolink:GrossAnatomicalStructure a owl:Class ; rdfs:label "gross anatomical structure" ; @@ -1356,7 +1510,9 @@ biolink:GrossAnatomicalStructure a owl:Class ; WIKIDATA:Q4936952 ; skos:narrowMatch STY:T018, STY:T023, - STY:T024 . + STY:T024 ; + linkml:attributes "{}" ; + linkml:is_a "anatomical entity" . biolink:Haplotype a owl:Class ; rdfs:label "haplotype" ; @@ -1371,18 +1527,27 @@ biolink:Haplotype a owl:Class ; skos:definition "A set of zero or more Alleles on a single instance of a Sequence[VMC]" ; skos:exactMatch , , - VMC:Haplotype . + VMC:Haplotype ; + linkml:attributes "{}" ; + linkml:is_a "biological entity" ; + linkml:mixins "genomic entity", + "ontology class", + "physical essence" . biolink:Hospitalization a owl:Class ; rdfs:label "hospitalization" ; rdfs:subClassOf biolink:ClinicalIntervention ; skos:exactMatch SNOMEDCT:32485007, - WIKIDATA:Q3140971 . + WIKIDATA:Q3140971 ; + linkml:attributes "{}" ; + linkml:is_a "clinical intervention" . biolink:HospitalizationOutcome a owl:Class ; rdfs:label "hospitalization outcome" ; rdfs:subClassOf biolink:Outcome ; - skos:definition "An outcome resulting from an exposure event which is the increased manifestation of acute (e.g. emergency room visit) or chronic (inpatient) hospitalization." . + skos:definition "An outcome resulting from an exposure event which is the increased manifestation of acute (e.g. emergency room visit) or chronic (inpatient) hospitalization." ; + linkml:attributes "{}" ; + linkml:mixins "outcome" . biolink:Human a owl:Class ; rdfs:label "human" ; @@ -1392,15 +1557,14 @@ biolink:Human a owl:Class ; skos:exactMatch STY:T016, , , - SIO:000485 . + SIO:000485 ; + linkml:attributes "{}" ; + linkml:is_a "mammal" ; + linkml:mixins "subject of investigation" . biolink:InformationContentEntityToNamedThingAssociation a owl:Class ; rdfs:label "information content entity to named thing association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], @@ -1408,8 +1572,14 @@ biolink:InformationContentEntityToNamedThingAssociation a owl:Class ; owl:onClass biolink:NamedThing ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:Association ; - skos:definition "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." . + skos:definition "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." ; + linkml:attributes "{}" ; + linkml:is_a "association" . biolink:Invertebrate a owl:Class ; rdfs:label "invertebrate" ; @@ -1419,14 +1589,25 @@ biolink:Invertebrate a owl:Class ; , , ; - skos:relatedMatch . + skos:relatedMatch ; + linkml:attributes "{}" ; + linkml:is_a "cellular organism" . biolink:JournalArticle a owl:Class ; rdfs:label "journal article" ; rdfs:subClassOf biolink:Article ; skos:definition "an article, typically presenting results of research, that is published in an issue of a scientific journal." ; skos:exactMatch IAO:0000013, - fabio:JournalArticle . + fabio:JournalArticle ; + linkml:attributes "{}" ; + linkml:is_a "article" . + +biolink:LogOddsAnalysisResult a owl:Class ; + rdfs:label "log odds analysis result" ; + rdfs:subClassOf biolink:StudyResult ; + skos:definition "A result of a log odds ratio analysis." ; + linkml:attributes "{}" ; + linkml:is_a "study result" . biolink:MacromolecularComplex a owl:Class ; rdfs:label "macromolecular complex" ; @@ -1434,7 +1615,10 @@ biolink:MacromolecularComplex a owl:Class ; biolink:MacromolecularMachineMixin ; skos:definition "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." ; skos:exactMatch , - WIKIDATA:Q22325163 . + WIKIDATA:Q22325163 ; + linkml:attributes "{}" ; + linkml:is_a "biological entity" ; + linkml:mixins "macromolecular machine mixin" . biolink:MacromolecularMachineToBiologicalProcessAssociation a owl:Class ; rdfs:label "macromolecular machine to biological process association" ; @@ -1444,7 +1628,10 @@ biolink:MacromolecularMachineToBiologicalProcessAssociation a owl:Class ; owl:qualifiedCardinality 1 ], biolink:FunctionalAssociation, biolink:MacromolecularMachineToEntityAssociationMixin ; - skos:definition "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it." . + skos:definition "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it." ; + linkml:attributes "{}" ; + linkml:is_a "functional association" ; + linkml:mixins "macromolecular machine to entity association mixin" . biolink:MacromolecularMachineToCellularComponentAssociation a owl:Class ; rdfs:label "macromolecular machine to cellular component association" ; @@ -1454,7 +1641,10 @@ biolink:MacromolecularMachineToCellularComponentAssociation a owl:Class ; owl:qualifiedCardinality 1 ], biolink:FunctionalAssociation, biolink:MacromolecularMachineToEntityAssociationMixin ; - skos:definition "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component." . + skos:definition "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component." ; + linkml:attributes "{}" ; + linkml:is_a "functional association" ; + linkml:mixins "macromolecular machine to entity association mixin" . biolink:MacromolecularMachineToMolecularActivityAssociation a owl:Class ; rdfs:label "macromolecular machine to molecular activity association" ; @@ -1464,11 +1654,18 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a owl:Class ; owl:qualifiedCardinality 1 ], biolink:FunctionalAssociation, biolink:MacromolecularMachineToEntityAssociationMixin ; - skos:definition "A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution." . + skos:definition "A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution." ; + linkml:attributes "{}" ; + linkml:is_a "functional association" ; + linkml:mixins "macromolecular machine to entity association mixin" . biolink:MaterialSampleDerivationAssociation a owl:Class ; rdfs:label "material sample derivation association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass biolink:MaterialSample ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], @@ -1476,26 +1673,30 @@ biolink:MaterialSampleDerivationAssociation a owl:Class ; owl:onClass biolink:NamedThing ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], biolink:Association ; - skos:definition "An association between a material sample and the material entity from which it is derived." . + skos:definition "An association between a material sample and the material entity from which it is derived." ; + linkml:attributes "{}" ; + linkml:is_a "association" . biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "material sample to disease or phenotypic feature association" ; rdfs:subClassOf biolink:Association, biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin, biolink:MaterialSampleToEntityAssociationMixin ; - skos:definition "An association between a material sample and a disease or phenotype." . + skos:definition "An association between a material sample and a disease or phenotype." ; + linkml:attributes "{}" ; + linkml:is_a "association" ; + linkml:mixins "entity to disease or phenotypic feature association mixin", + "material sample to entity association mixin" . biolink:MicroRNA a owl:Class ; rdfs:label "microRNA" ; rdfs:subClassOf biolink:NoncodingRNAProduct ; skos:exactMatch , SIO:001397, - WIKIDATA:Q310899 . + WIKIDATA:Q310899 ; + linkml:attributes "{}" ; + linkml:is_a "noncoding RNA product" . biolink:MolecularActivityToChemicalEntityAssociation a owl:Class ; rdfs:label "molecular activity to chemical entity association" ; @@ -1508,42 +1709,50 @@ biolink:MolecularActivityToChemicalEntityAssociation a owl:Class ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:Association ; - skos:definition "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" . + skos:definition "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; + linkml:attributes "{}" ; + linkml:is_a "association" . biolink:MolecularActivityToMolecularActivityAssociation a owl:Class ; rdfs:label "molecular activity to molecular activity association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:MolecularActivity ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:MolecularActivity ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:Association ; - skos:definition "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" . + skos:definition "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; + linkml:attributes "{}" ; + linkml:is_a "association" . biolink:MolecularActivityToPathwayAssociation a owl:Class ; rdfs:label "molecular activity to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + owl:onClass biolink:Pathway ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:MolecularActivity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:Pathway ; - owl:onProperty rdf:object ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], biolink:Association ; - skos:definition "Association that holds the relationship between a reaction and the pathway it participates in." . + skos:definition "Association that holds the relationship between a reaction and the pathway it participates in." ; + linkml:attributes "{}" ; + linkml:is_a "association" . biolink:MortalityOutcome a owl:Class ; rdfs:label "mortality outcome" ; rdfs:subClassOf biolink:Outcome ; - skos:definition "An outcome of death from resulting from an exposure event." . + skos:definition "An outcome of death from resulting from an exposure event." ; + linkml:attributes "{}" ; + linkml:mixins "outcome" . biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a owl:Class ; rdfs:label "named thing associated with likelihood of named thing association" ; @@ -1551,30 +1760,34 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:object_context_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OntologyClass ; - owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:OntologyClass ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], biolink:Association ; - skos:definition "" . + skos:definition "" ; + linkml:attributes "{}" ; + linkml:is_a "association" . biolink:NucleicAcidSequenceMotif a owl:Class ; rdfs:label "nucleic acid sequence motif" ; rdfs:subClassOf biolink:BiologicalEntity ; skos:altLabel "consensus sequence" ; - skos:definition "A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences." . + skos:definition "A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences." ; + linkml:attributes "{}" ; + linkml:is_a "biological entity" . biolink:NucleosomeModification a owl:Class ; rdfs:label "nucleosome modification" ; @@ -1589,12 +1802,19 @@ biolink:NucleosomeModification a owl:Class ; biolink:EpigenomicEntity, biolink:GeneProductIsoformMixin, biolink:GenomicEntity ; - skos:definition "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A." . + skos:definition "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A." ; + linkml:attributes "{}" ; + linkml:is_a "biological entity" ; + linkml:mixins "epigenomic entity", + "gene product isoform mixin", + "genomic entity" . biolink:ObservedExpectedFrequencyAnalysisResult a owl:Class ; rdfs:label "observed expected frequency analysis result" ; rdfs:subClassOf biolink:StudyResult ; - skos:definition "A result of a observed expected frequency analysis." . + skos:definition "A result of a observed expected frequency analysis." ; + linkml:attributes "{}" ; + linkml:is_a "study result" . biolink:OrganismTaxonToEnvironmentAssociation a owl:Class ; rdfs:label "organism taxon to environment association" ; @@ -1602,54 +1822,61 @@ biolink:OrganismTaxonToEnvironmentAssociation a owl:Class ; owl:onClass biolink:NamedThing ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], biolink:Association, - biolink:OrganismTaxonToEntityAssociation . + biolink:OrganismTaxonToEntityAssociation ; + linkml:attributes "{}" ; + linkml:is_a "association" ; + linkml:mixins "organism taxon to entity association" . biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; rdfs:label "organism taxon to organism taxon interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:associated_environmental_context ], - [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:associated_environmental_context ], [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:OrganismTaxonToOrganismTaxonAssociation ; - skos:definition "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" . + skos:definition "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; + linkml:attributes "{}" ; + linkml:is_a "organism taxon to organism taxon association" . biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; rdfs:label "organism taxon to organism taxon specialization" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:OrganismTaxon ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:OrganismTaxonToOrganismTaxonAssociation ; - skos:definition "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" . + skos:definition "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; + linkml:attributes "{}" ; + linkml:is_a "organism taxon to organism taxon association" . biolink:OrganismToOrganismAssociation a owl:Class ; rdfs:label "organism to organism association" ; @@ -1661,44 +1888,42 @@ biolink:OrganismToOrganismAssociation a owl:Class ; owl:onClass biolink:IndividualOrganism ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - biolink:Association . + biolink:Association ; + linkml:attributes "{}" ; + linkml:is_a "association" . biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "organismal entity as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:OrganismalEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; owl:onProperty biolink:severity_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:OrganismalEntity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, - biolink:ModelToDiseaseAssociationMixin . + biolink:ModelToDiseaseAssociationMixin ; + linkml:attributes "{}" ; + linkml:is_a "association" ; + linkml:mixins "entity to disease association mixin", + "model to disease association mixin" . biolink:PairwiseMolecularInteraction a owl:Class ; rdfs:label "pairwise molecular interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty biolink:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:MolecularEntity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:MolecularEntity ; owl:onProperty rdf:object ; @@ -1707,8 +1932,18 @@ biolink:PairwiseMolecularInteraction a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:interacting_molecules_category ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass linkml:String ; + owl:onProperty biolink:id ; + owl:qualifiedCardinality 1 ], biolink:PairwiseGeneToGeneInteraction ; - skos:definition "An interaction at the molecular level between two physical entities" . + skos:definition "An interaction at the molecular level between two physical entities" ; + linkml:attributes "{}" ; + linkml:is_a "pairwise gene to gene interaction" . biolink:Patent a owl:Class ; rdfs:label "patent" ; @@ -1716,13 +1951,17 @@ biolink:Patent a owl:Class ; skos:definition "a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time. " ; skos:exactMatch IAO:0000313, fabio:Patent, - SIO:000153 . + SIO:000153 ; + linkml:attributes "{}" ; + linkml:is_a "publication" . biolink:PathognomonicityQuantifier a owl:Class ; rdfs:label "pathognomonicity quantifier" ; rdfs:subClassOf biolink:SpecificityQuantifier, linkml:mixin ; - skos:definition "A relationship quantifier between a variant or symptom and a disease, which is high when the presence of the feature implies the existence of the disease" . + skos:definition "A relationship quantifier between a variant or symptom and a disease, which is high when the presence of the feature implies the existence of the disease" ; + linkml:attributes "{}" ; + linkml:is_a "specificity quantifier" . biolink:PathologicalAnatomicalExposure a owl:Class ; rdfs:label "pathological anatomical exposure" ; @@ -1732,19 +1971,27 @@ biolink:PathologicalAnatomicalExposure a owl:Class ; owl:onProperty biolink:timepoint ], biolink:Attribute, biolink:ExposureEvent ; - skos:definition "An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome." . + skos:definition "An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome." ; + linkml:attributes "{}" ; + linkml:is_a "attribute" ; + linkml:mixins "exposure event" . biolink:PathologicalAnatomicalOutcome a owl:Class ; rdfs:label "pathological anatomical outcome" ; rdfs:subClassOf biolink:Outcome ; - skos:definition "An outcome resulting from an exposure event which is the manifestation of an abnormal anatomical structure." . + skos:definition "An outcome resulting from an exposure event which is the manifestation of an abnormal anatomical structure." ; + linkml:attributes "{}" ; + linkml:mixins "outcome" . biolink:PathologicalAnatomicalStructure a owl:Class ; rdfs:label "pathological anatomical structure" ; rdfs:subClassOf biolink:AnatomicalEntity, biolink:PathologicalEntityMixin ; skos:definition "An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level." ; - skos:exactMatch . + skos:exactMatch ; + linkml:attributes "{}" ; + linkml:is_a "anatomical entity" ; + linkml:mixins "pathological entity mixin" . biolink:PathologicalProcess a owl:Class ; rdfs:label "pathological process" ; @@ -1757,7 +2004,10 @@ biolink:PathologicalProcess a owl:Class ; skos:narrowMatch STY:T037, STY:T046, , - EFO:0009708 . + EFO:0009708 ; + linkml:attributes "{}" ; + linkml:is_a "biological process" ; + linkml:mixins "pathological entity mixin" . biolink:PathologicalProcessExposure a owl:Class ; rdfs:label "pathological process exposure" ; @@ -1767,12 +2017,17 @@ biolink:PathologicalProcessExposure a owl:Class ; owl:onProperty biolink:timepoint ], biolink:Attribute, biolink:ExposureEvent ; - skos:definition "A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease." . + skos:definition "A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease." ; + linkml:attributes "{}" ; + linkml:is_a "attribute" ; + linkml:mixins "exposure event" . biolink:PathologicalProcessOutcome a owl:Class ; rdfs:label "pathological process outcome" ; rdfs:subClassOf biolink:Outcome ; - skos:definition "An outcome resulting from an exposure event which is the manifestation of a pathological process." . + skos:definition "An outcome resulting from an exposure event which is the manifestation of a pathological process." ; + linkml:attributes "{}" ; + linkml:mixins "outcome" . biolink:PercentageFrequencyValue a owl:Class ; rdfs:label "percentage frequency value" ; @@ -1789,7 +2044,10 @@ biolink:Phenomenon a owl:Class ; skos:exactMatch UMLSSG:PHEN ; skos:narrowMatch STY:T034, STY:T038, - STY:T069 . + STY:T069 ; + linkml:attributes "{}" ; + linkml:is_a "named thing" ; + linkml:mixins "occurrent" . biolink:PhenotypicQuality a owl:Class ; rdfs:label "phenotypic quality" ; @@ -1797,13 +2055,16 @@ biolink:PhenotypicQuality a owl:Class ; skos:altLabel "phenotypic properties" ; skos:definition "A property of a phenotype" ; skos:exactMatch ; - linkml:examples "Example(value='weight', description=None)" . + linkml:attributes "{}" ; + linkml:is_a "organism attribute" . biolink:PhenotypicSex a owl:Class ; rdfs:label "phenotypic sex" ; rdfs:subClassOf biolink:BiologicalSex ; skos:definition "An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present." ; - skos:exactMatch . + skos:exactMatch ; + linkml:attributes "{}" ; + linkml:is_a "biological sex" . biolink:PhysiologicalProcess a owl:Class ; rdfs:label "physiological process" ; @@ -1815,7 +2076,10 @@ biolink:PhysiologicalProcess a owl:Class ; skos:narrowMatch STY:T040, STY:T042, STY:T043, - STY:T045 . + STY:T045 ; + linkml:attributes "{}" ; + linkml:is_a "biological process" ; + linkml:mixins "ontology class" . biolink:Plant a owl:Class ; rdfs:label "plant" ; @@ -1824,7 +2088,9 @@ biolink:Plant a owl:Class ; skos:exactMatch STY:T002, , , - . + ; + linkml:attributes "{}" ; + linkml:is_a "cellular organism" . biolink:PopulationToPopulationAssociation a owl:Class ; rdfs:label "population to population association" ; @@ -1832,16 +2098,18 @@ biolink:PopulationToPopulationAssociation a owl:Class ; owl:onClass biolink:PopulationOfIndividualOrganisms ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PopulationOfIndividualOrganisms ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], biolink:Association ; - skos:definition "An association between a two populations" . + skos:definition "An association between a two populations" ; + linkml:attributes "{}" ; + linkml:is_a "association" . biolink:PosttranslationalModification a owl:Class ; rdfs:label "posttranslational modification" ; @@ -1850,20 +2118,27 @@ biolink:PosttranslationalModification a owl:Class ; owl:onProperty biolink:synonym ], biolink:BiologicalEntity, biolink:GeneProductIsoformMixin ; - skos:definition "A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination." . + skos:definition "A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination." ; + linkml:attributes "{}" ; + linkml:is_a "biological entity" ; + linkml:mixins "gene product isoform mixin" . biolink:PreprintPublication a owl:Class ; rdfs:label "preprint publication" ; rdfs:subClassOf biolink:Publication ; skos:definition "a document reresenting an early version of an author's original scholarly work, such as a research paper or a review, prior to formal peer review and publication in a peer-reviewed scholarly or scientific journal." ; skos:exactMatch fabio:Preprint, - EFO:0010558 . + EFO:0010558 ; + linkml:attributes "{}" ; + linkml:is_a "publication" . biolink:ProcessedMaterial a owl:Class ; rdfs:label "processed material" ; rdfs:subClassOf biolink:ChemicalMixture ; skos:definition "A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing." ; - skos:exactMatch . + skos:exactMatch ; + linkml:attributes "{}" ; + linkml:is_a "chemical mixture" . biolink:ProteinDomain a owl:Class ; rdfs:label "protein domain" ; @@ -1876,7 +2151,11 @@ biolink:ProteinDomain a owl:Class ; skos:definition "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain." ; skos:exactMatch , , - SIO:001379 . + SIO:001379 ; + linkml:attributes "{}" ; + linkml:is_a "biological entity" ; + linkml:mixins "chemical entity or gene or gene product", + "gene grouping mixin" . biolink:ProteinFamily a owl:Class ; rdfs:label "protein family" ; @@ -1890,14 +2169,21 @@ biolink:ProteinFamily a owl:Class ; WIKIDATA:Q2278983 ; skos:narrowMatch , SIO:001380, - WIKIDATA:Q417841 . + WIKIDATA:Q417841 ; + linkml:attributes "{}" ; + linkml:is_a "biological entity" ; + linkml:mixins "chemical entity or gene or gene product", + "gene grouping mixin" . biolink:ProteinIsoform a owl:Class ; rdfs:label "protein isoform" ; rdfs:subClassOf biolink:GeneProductIsoformMixin, biolink:Protein ; skos:altLabel "proteoform" ; - skos:definition "Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/" . + skos:definition "Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/" ; + linkml:attributes "{}" ; + linkml:is_a "protein" ; + linkml:mixins "gene product isoform mixin" . biolink:Quotient a owl:Class ; rdfs:label "quotient" ; @@ -1907,7 +2193,10 @@ biolink:RNAProductIsoform a owl:Class ; rdfs:label "RNA product isoform" ; rdfs:subClassOf biolink:GeneProductIsoformMixin, biolink:RNAProduct ; - skos:definition "Represents a protein that is a specific isoform of the canonical or reference RNA" . + skos:definition "Represents a protein that is a specific isoform of the canonical or reference RNA" ; + linkml:attributes "{}" ; + linkml:is_a "RNA product" ; + linkml:mixins "gene product isoform mixin" . biolink:ReactionToCatalystAssociation a owl:Class ; rdfs:label "reaction to catalyst association" ; @@ -1915,7 +2204,9 @@ biolink:ReactionToCatalystAssociation a owl:Class ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - biolink:ReactionToParticipantAssociation . + biolink:ReactionToParticipantAssociation ; + linkml:attributes "{}" ; + linkml:is_a "reaction to participant association" . biolink:ReagentTargetedGene a owl:Class ; rdfs:label "reagent targeted gene" ; @@ -1929,22 +2220,33 @@ biolink:ReagentTargetedGene a owl:Class ; biolink:PhysicalEssence ; skos:altLabel "sequence targeting reagent" ; skos:definition "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi." ; - skos:exactMatch . + skos:exactMatch ; + linkml:attributes "{}" ; + linkml:is_a "biological entity" ; + linkml:mixins "genomic entity", + "ontology class", + "physical essence" . biolink:RelationshipType a owl:Class ; rdfs:label "relationship type" ; rdfs:subClassOf biolink:OntologyClass ; - skos:definition "An OWL property used as an edge label" . + skos:definition "An OWL property used as an edge label" ; + linkml:attributes "{}" ; + linkml:is_a "ontology class" . biolink:RelativeFrequencyAnalysisResult a owl:Class ; rdfs:label "relative frequency analysis result" ; rdfs:subClassOf biolink:StudyResult ; - skos:definition "A result of a relative frequency analysis." . + skos:definition "A result of a relative frequency analysis." ; + linkml:attributes "{}" ; + linkml:is_a "study result" . biolink:SensitivityQuantifier a owl:Class ; rdfs:label "sensitivity quantifier" ; rdfs:subClassOf biolink:RelationshipQuantifier, - linkml:mixin . + linkml:mixin ; + linkml:attributes "{}" ; + linkml:is_a "relationship quantifier" . biolink:SequenceEnum a owl:Class ; rdfs:label "SequenceEnum" ; @@ -1955,16 +2257,17 @@ biolink:SequenceEnum a owl:Class ; biolink:SequenceVariantModulatesTreatmentAssociation a owl:Class ; rdfs:label "sequence variant modulates treatment association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:SequenceVariant ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:Treatment ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:SequenceVariant ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; - skos:note "An alternate way to model the same information could be via a qualifier" . + linkml:attributes "{}" ; + linkml:is_a "association" . biolink:Serial a owl:Class ; rdfs:label "serial" ; @@ -1972,24 +2275,26 @@ biolink:Serial a owl:Class ; owl:allValuesFrom linkml:String ; owl:onProperty rdf:type ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:issue ], + owl:onProperty biolink:id ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:iso_abbreviation ], + owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:volume ], + owl:onProperty biolink:issue ], [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:id ; - owl:qualifiedCardinality 1 ], + owl:onProperty biolink:iso_abbreviation ], biolink:Publication ; skos:altLabel "journal" ; - skos:definition "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." . + skos:definition "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; + linkml:attributes "{}" ; + linkml:is_a "publication" . biolink:SiRNA a owl:Class ; rdfs:label "siRNA" ; @@ -1998,7 +2303,9 @@ biolink:SiRNA a owl:Class ; "small interfering RNA" ; skos:definition "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." ; skos:exactMatch , - WIKIDATA:Q203221 . + WIKIDATA:Q203221 ; + linkml:attributes "{}" ; + linkml:is_a "noncoding RNA product" . biolink:SmallMolecule a owl:Class ; rdfs:label "small molecule" ; @@ -2023,7 +2330,9 @@ biolink:SmallMolecule a owl:Class ; STY:T196, STY:T197, , - bioschemas:ChemicalSubstance . + bioschemas:ChemicalSubstance ; + linkml:attributes "{}" ; + linkml:is_a "molecular entity" . biolink:Snv a owl:Class ; rdfs:label "snv" ; @@ -2032,28 +2341,35 @@ biolink:Snv a owl:Class ; "single nucleotide variant", "snp" ; skos:definition "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist" ; - skos:exactMatch . + skos:exactMatch ; + linkml:attributes "{}" ; + linkml:is_a "sequence variant" . biolink:SocioeconomicExposure a owl:Class ; rdfs:label "socioeconomic exposure" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:TimeType ; - owl:onProperty biolink:timepoint ], - [ a owl:Class ; + rdfs:subClassOf [ a owl:Class ; owl:intersectionOf ( [ a owl:Restriction ; owl:allValuesFrom biolink:SocioeconomicAttribute ; owl:onProperty biolink:has_attribute ] [ a owl:Restriction ; owl:onProperty biolink:has_attribute ; owl:someValuesFrom biolink:SocioeconomicAttribute ] ) ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:TimeType ; + owl:onProperty biolink:timepoint ], biolink:Attribute, biolink:ExposureEvent ; - skos:definition "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." . + skos:definition "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." ; + linkml:attributes "{}" ; + linkml:is_a "attribute" ; + linkml:mixins "exposure event" . biolink:SocioeconomicOutcome a owl:Class ; rdfs:label "socioeconomic outcome" ; rdfs:subClassOf biolink:Outcome ; - skos:definition "An general social or economic outcome, such as healthcare costs, utilization, etc., resulting from an exposure event" . + skos:definition "An general social or economic outcome, such as healthcare costs, utilization, etc., resulting from an exposure event" ; + linkml:attributes "{}" ; + linkml:mixins "outcome" . biolink:Study a owl:Class ; rdfs:label "study" ; @@ -2062,7 +2378,9 @@ biolink:Study a owl:Class ; SIO:001066 ; skos:definition "a detailed investigation and/or analysis" ; skos:exactMatch ; - skos:narrowMatch SIO:000994 . + skos:narrowMatch SIO:000994 ; + linkml:attributes "{}" ; + linkml:is_a "activity" . biolink:StudyVariable a owl:Class ; rdfs:label "study variable" ; @@ -2070,24 +2388,30 @@ biolink:StudyVariable a owl:Class ; skos:closeMatch , SIO:000367 ; skos:definition "a variable that is used as a measure in the investigation of a study" ; - skos:narrowMatch . + skos:narrowMatch ; + linkml:attributes "{}" ; + linkml:is_a "information content entity" . biolink:TaxonToTaxonAssociation a owl:Class ; rdfs:label "taxon to taxon association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - biolink:Association . + biolink:Association ; + linkml:attributes "{}" ; + linkml:is_a "association" . biolink:TextMiningResult a owl:Class ; rdfs:label "text mining result" ; rdfs:subClassOf biolink:StudyResult ; - skos:definition "A result of text mining." . + skos:definition "A result of text mining." ; + linkml:attributes "{}" ; + linkml:is_a "study result" . biolink:TranscriptToGeneRelationship a owl:Class ; rdfs:label "transcript to gene relationship" ; @@ -2100,7 +2424,9 @@ biolink:TranscriptToGeneRelationship a owl:Class ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:SequenceFeatureRelationship ; - skos:definition "A gene is a collection of transcripts" . + skos:definition "A gene is a collection of transcripts" ; + linkml:attributes "{}" ; + linkml:is_a "sequence feature relationship" . biolink:TranscriptionFactorBindingSite a owl:Class ; rdfs:label "transcription factor binding site" ; @@ -2112,7 +2438,13 @@ biolink:TranscriptionFactorBindingSite a owl:Class ; skos:altLabel "binding site", "tf binding site" ; skos:definition "A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription" ; - skos:exactMatch . + skos:exactMatch ; + linkml:attributes "{}" ; + linkml:is_a "regulatory region" ; + linkml:mixins "chemical entity or gene or gene product", + "genomic entity", + "ontology class", + "physical essence" . biolink:VariantAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "variant as a model of disease association" ; @@ -2122,18 +2454,26 @@ biolink:VariantAsAModelOfDiseaseAssociation a owl:Class ; owl:qualifiedCardinality 1 ], biolink:EntityToDiseaseAssociationMixin, biolink:ModelToDiseaseAssociationMixin, - biolink:VariantToDiseaseAssociation . + biolink:VariantToDiseaseAssociation ; + linkml:attributes "{}" ; + linkml:is_a "variant to disease association" ; + linkml:mixins "entity to disease association mixin", + "model to disease association mixin" . biolink:VariantToGeneExpressionAssociation a owl:Class ; rdfs:label "variant to gene expression association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:phenotypic_state ], - [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:expression_site ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:phenotypic_state ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; @@ -2142,74 +2482,81 @@ biolink:VariantToGeneExpressionAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:LifeStage ; owl:onProperty biolink:stage_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:expression_site ], biolink:GeneExpressionMixin, biolink:VariantToGeneAssociation ; - skos:definition "An association between a variant and expression of a gene (i.e. e-QTL)" . + skos:definition "An association between a variant and expression of a gene (i.e. e-QTL)" ; + linkml:attributes "{}" ; + linkml:is_a "variant to gene association" ; + linkml:mixins "gene expression mixin" . biolink:VariantToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "variant to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass biolink:SequenceVariant ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:onClass biolink:SequenceVariant ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; owl:onProperty biolink:severity_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin, - biolink:VariantToEntityAssociationMixin . + biolink:VariantToEntityAssociationMixin ; + linkml:attributes "{}" ; + linkml:is_a "association" ; + linkml:mixins "entity to phenotypic feature association mixin", + "variant to entity association mixin" . biolink:VariantToPopulationAssociation a owl:Class ; rdfs:label "variant to population association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:onClass biolink:PopulationOfIndividualOrganisms ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:onClass biolink:SequenceVariant ; owl:onProperty rdf:subject ; @@ -2217,16 +2564,17 @@ biolink:VariantToPopulationAssociation a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], + owl:onProperty biolink:has_count ], biolink:Association, biolink:FrequencyQualifierMixin, biolink:FrequencyQuantifier, biolink:VariantToEntityAssociationMixin ; - skos:definition "An association between a variant and a population, where the variant has particular frequency in the population" . + skos:definition "An association between a variant and a population, where the variant has particular frequency in the population" ; + linkml:attributes "{}" ; + linkml:is_a "association" ; + linkml:mixins "frequency qualifier mixin", + "frequency quantifier", + "variant to entity association mixin" . biolink:Vertebrate a owl:Class ; rdfs:label "vertebrate" ; @@ -2235,7 +2583,9 @@ biolink:Vertebrate a owl:Class ; skos:exactMatch STY:T010, , ; - skos:relatedMatch . + skos:relatedMatch ; + linkml:attributes "{}" ; + linkml:is_a "cellular organism" . biolink:Virus a owl:Class ; rdfs:label "virus" ; @@ -2243,7 +2593,10 @@ biolink:Virus a owl:Class ; biolink:SubjectOfInvestigation ; skos:definition "A virus is a microorganism that replicates itself as a microRNA and infects the host cell." ; skos:exactMatch STY:T005, - . + ; + linkml:attributes "{}" ; + linkml:is_a "organismal entity" ; + linkml:mixins "subject of investigation" . biolink:WebPage a owl:Class ; rdfs:label "web page" ; @@ -2251,14 +2604,17 @@ biolink:WebPage a owl:Class ; skos:definition "a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, and/or other features." ; skos:exactMatch NCIT-OBO:C142749, fabio:WebPage, - SIO:000302 . + SIO:000302 ; + linkml:attributes "{}" ; + linkml:is_a "publication" . biolink:animal_model_available_from a owl:ObjectProperty ; rdfs:label "animal model available from" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:DiseaseOrPhenotypicFeature ; rdfs:subPropertyOf biolink:node_property ; - skos:definition "" . + skos:definition "" ; + linkml:is_a "node property" . biolink:binds a owl:ObjectProperty, owl:SymmetricProperty ; @@ -2268,7 +2624,8 @@ biolink:binds a owl:ObjectProperty, rdfs:subPropertyOf biolink:directly_physically_interacts_with ; skos:closeMatch DGIdb:binder ; skos:definition "A causal mechanism mediated by the direct contact between effector and target chemical or biomolecular entity, which form a stable physical interaction." ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "directly physically interacts with" . biolink:biological_role_mixin a owl:ObjectProperty ; rdfs:label "biological role mixin" ; @@ -2282,7 +2639,7 @@ biolink:bonferonni_adjusted_p_value a owl:ObjectProperty ; rdfs:range linkml:Float ; rdfs:subPropertyOf biolink:adjusted_p_value ; skos:definition "The Bonferroni correction is an adjustment made to P values when several dependent or independent statistical tests are being performed simultaneously on a single data set. To perform a Bonferroni correction, divide the critical P value (α) by the number of comparisons being made. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - linkml:examples "Example(value='0.018', description=None)" . + linkml:is_a "adjusted p value" . biolink:broad_matches a owl:ObjectProperty ; rdfs:label "broad matches" ; @@ -2294,7 +2651,8 @@ biolink:broad_synonym a owl:ObjectProperty ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:LabelType ; rdfs:subPropertyOf biolink:synonym ; - skos:exactMatch OIO:hasBroadSynonym . + skos:exactMatch OIO:hasBroadSynonym ; + linkml:is_a "synonym" . biolink:chemical_role_mixin a owl:ObjectProperty ; rdfs:label "chemical role mixin" ; @@ -2316,7 +2674,8 @@ biolink:chemically_similar_to a owl:ObjectProperty, , , ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "similar to" . biolink:chi_squared_statistic a owl:ObjectProperty ; rdfs:label "chi squared statistic" ; @@ -2324,14 +2683,16 @@ biolink:chi_squared_statistic a owl:ObjectProperty ; rdfs:range linkml:Float ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "represents the chi-squared statistic computed from observations" ; - skos:exactMatch . + skos:exactMatch ; + linkml:is_a "association slot" . biolink:clinical_modifier_qualifier a owl:ObjectProperty ; rdfs:label "clinical modifier qualifier" ; rdfs:domain biolink:Association ; rdfs:range biolink:ClinicalModifier ; rdfs:subPropertyOf biolink:association_slot ; - skos:definition "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." . + skos:definition "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + linkml:is_a "association slot" . biolink:coexpressed_with a owl:ObjectProperty, owl:SymmetricProperty ; @@ -2340,7 +2701,8 @@ biolink:coexpressed_with a owl:ObjectProperty, rdfs:range biolink:GeneOrGeneProduct ; rdfs:subPropertyOf biolink:correlated_with ; skos:definition "holds between any two genes or gene products, in which both are generally expressed within a single defined experimental context." ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "correlated with" . biolink:colocalizes_with a owl:ObjectProperty, owl:SymmetricProperty ; @@ -2350,14 +2712,16 @@ biolink:colocalizes_with a owl:ObjectProperty, rdfs:subPropertyOf biolink:coexists_with ; skos:definition "holds between two entities that are observed to be located in the same place." ; skos:exactMatch RO:0002325 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "coexists with" . biolink:concept_count_object a owl:ObjectProperty ; rdfs:label "concept count object" ; rdfs:domain biolink:Association ; rdfs:range linkml:Integer ; rdfs:subPropertyOf biolink:association_slot ; - skos:definition "The number of instances in a dataset/cohort whose records contain the concept in the object slot of an association." . + skos:definition "The number of instances in a dataset/cohort whose records contain the concept in the object slot of an association." ; + linkml:is_a "association slot" . biolink:concept_count_subject a owl:ObjectProperty ; rdfs:label "concept count subject" ; @@ -2365,7 +2729,7 @@ biolink:concept_count_subject a owl:ObjectProperty ; rdfs:range linkml:Integer ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "The number of instances in a dataset/cohort whose records contain the concept in the subject slot of an association." ; - linkml:examples "Example(value='489', description=None)" . + linkml:is_a "association slot" . biolink:concept_pair_count a owl:ObjectProperty ; rdfs:label "concept pair count" ; @@ -2373,14 +2737,15 @@ biolink:concept_pair_count a owl:ObjectProperty ; rdfs:range linkml:Integer ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "The number of instances in a dataset/cohort whose records contain both the subject and object concept of an association." ; - linkml:examples "Example(value='1731', description=None)" . + linkml:is_a "association slot" . biolink:created_with a owl:ObjectProperty ; rdfs:label "created with" ; rdfs:domain biolink:Dataset ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:node_property ; - skos:exactMatch pav:createdWith . + skos:exactMatch pav:createdWith ; + linkml:is_a "node property" . biolink:end_coordinate a owl:ObjectProperty ; rdfs:label "end coordinate" ; @@ -2390,14 +2755,16 @@ biolink:end_coordinate a owl:ObjectProperty ; skos:altLabel "end" ; skos:closeMatch ; skos:definition "The position at which the subject genomic entity ends on the chromosome or other entity to which it is located on." ; - skos:exactMatch gff3:end . + skos:exactMatch gff3:end ; + linkml:is_a "base coordinate" . biolink:evidence_count a owl:ObjectProperty ; rdfs:label "evidence count" ; rdfs:domain biolink:Association ; rdfs:range linkml:Integer ; rdfs:subPropertyOf biolink:association_slot ; - skos:definition "The number of evidence instances that are connected to an association." . + skos:definition "The number of evidence instances that are connected to an association." ; + linkml:is_a "association slot" . biolink:exact_matches a owl:ObjectProperty ; rdfs:label "exact matches" ; @@ -2409,14 +2776,16 @@ biolink:exact_synonym a owl:ObjectProperty ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:LabelType ; rdfs:subPropertyOf biolink:synonym ; - skos:exactMatch OIO:hasExactSynonym . + skos:exactMatch OIO:hasExactSynonym ; + linkml:is_a "synonym" . biolink:expected_count a owl:ObjectProperty ; rdfs:label "expected count" ; rdfs:domain biolink:Association ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:association_slot ; - skos:definition "The expected (calculated) number of instances in a dataset/cohort whose records contain both the subject and object concept of an association if the subject and object concepts are independent." . + skos:definition "The expected (calculated) number of instances in a dataset/cohort whose records contain both the subject and object concept of an association if the subject and object concepts are independent." ; + linkml:is_a "association slot" . biolink:extraction_confidence_score a owl:ObjectProperty ; rdfs:label "extraction confidence score" ; @@ -2424,14 +2793,15 @@ biolink:extraction_confidence_score a owl:ObjectProperty ; rdfs:range linkml:Integer ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - linkml:examples "Example(value='15', description=None)" . + linkml:is_a "association slot" . biolink:full_name a owl:ObjectProperty ; rdfs:label "full name" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:LabelType ; rdfs:subPropertyOf biolink:node_property ; - skos:definition "a long-form human readable name for a thing" . + skos:definition "a long-form human readable name for a thing" ; + linkml:is_a "node property" . biolink:gene_fusion_with a owl:ObjectProperty, owl:SymmetricProperty ; @@ -2440,14 +2810,16 @@ biolink:gene_fusion_with a owl:ObjectProperty, rdfs:range biolink:Gene ; rdfs:subPropertyOf biolink:genetically_interacts_with ; skos:definition "holds between two independent genes that have fused through translocation, interstitial deletion, or chromosomal inversion to form a new, hybrid gene. Fusion genes are often implicated in various neoplasms and cancers." ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "genetically interacts with" . biolink:genetic_association a owl:ObjectProperty, owl:SymmetricProperty ; rdfs:label "genetic association" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:NamedThing ; - rdfs:subPropertyOf biolink:associated_with . + rdfs:subPropertyOf biolink:associated_with ; + linkml:is_a "associated with" . biolink:genetic_neighborhood_of a owl:ObjectProperty, owl:SymmetricProperty ; @@ -2456,7 +2828,8 @@ biolink:genetic_neighborhood_of a owl:ObjectProperty, rdfs:range biolink:Gene ; rdfs:subPropertyOf biolink:genetically_interacts_with ; skos:definition "holds between two genes located nearby one another on a chromosome. " ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "genetically interacts with" . biolink:has_chemical_formula a owl:ObjectProperty ; rdfs:label "has chemical formula" ; @@ -2464,21 +2837,24 @@ biolink:has_chemical_formula a owl:ObjectProperty ; rdfs:range biolink:ChemicalFormulaValue ; rdfs:subPropertyOf biolink:node_property ; skos:definition "description of chemical compound based on element symbols" ; - skos:exactMatch WIKIDATA_PROPERTY:P274 . + skos:exactMatch WIKIDATA_PROPERTY:P274 ; + linkml:is_a "node property" . biolink:has_confidence_level a owl:ObjectProperty ; rdfs:label "has confidence level" ; rdfs:domain biolink:Association ; rdfs:range biolink:ConfidenceLevel ; rdfs:subPropertyOf biolink:association_slot ; - skos:definition "connects an association to a qualitative term denoting the level of confidence" . + skos:definition "connects an association to a qualitative term denoting the level of confidence" ; + linkml:is_a "association slot" . biolink:has_constituent a owl:ObjectProperty ; rdfs:label "has constituent" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:MolecularEntity ; rdfs:subPropertyOf biolink:node_property ; - skos:definition "one or more molecular entities within a chemical mixture" . + skos:definition "one or more molecular entities within a chemical mixture" ; + linkml:is_a "node property" . biolink:has_receptor a owl:ObjectProperty ; rdfs:label "has receptor" ; @@ -2486,7 +2862,8 @@ biolink:has_receptor a owl:ObjectProperty ; rdfs:range biolink:OrganismalEntity ; rdfs:subPropertyOf biolink:node_property ; skos:definition "the organism or organism part being exposed" ; - skos:exactMatch ExO:0000001 . + skos:exactMatch ExO:0000001 ; + linkml:is_a "node property" . biolink:has_route a owl:ObjectProperty ; rdfs:label "has route" ; @@ -2497,7 +2874,8 @@ biolink:has_route a owl:ObjectProperty ; skos:exactMatch ExO:0000055 ; skos:narrowMatch LOINC:has_pharmaceutical_route, , - . + ; + linkml:is_a "node property" . biolink:has_stressor a owl:ObjectProperty ; rdfs:label "has stressor" ; @@ -2506,14 +2884,16 @@ biolink:has_stressor a owl:ObjectProperty ; rdfs:subPropertyOf biolink:node_property ; skos:altLabel "has stimulus" ; skos:definition "the process or entity that the receptor is being exposed to" ; - skos:exactMatch ExO:0000000 . + skos:exactMatch ExO:0000000 ; + linkml:is_a "node property" . biolink:has_supporting_study_result a owl:ObjectProperty ; rdfs:label "has supporting study result" ; rdfs:domain biolink:Association ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:association_slot ; - skos:definition "connects an association to an instance of supporting study result" . + skos:definition "connects an association to an instance of supporting study result" ; + linkml:is_a "association slot" . biolink:has_topic a owl:ObjectProperty ; rdfs:label "has topic" ; @@ -2523,7 +2903,8 @@ biolink:has_topic a owl:ObjectProperty ; skos:altLabel "descriptors", "topic" ; skos:definition "Connects a node to a vocabulary term or ontology class that describes some aspect of the entity. In general specific characterization is preferred. See https://github.com/biolink/biolink-model/issues/238" ; - skos:exactMatch foaf:topic . + skos:exactMatch foaf:topic ; + linkml:is_a "node property" . biolink:in_cell_population_with a owl:ObjectProperty, owl:SymmetricProperty ; @@ -2532,7 +2913,8 @@ biolink:in_cell_population_with a owl:ObjectProperty, rdfs:range biolink:GeneOrGeneProduct ; rdfs:subPropertyOf biolink:coexists_with ; skos:definition "holds between two genes or gene products that are expressed in the same cell type or population" ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "coexists with" . biolink:in_complex_with a owl:ObjectProperty, owl:SymmetricProperty ; @@ -2543,7 +2925,8 @@ biolink:in_complex_with a owl:ObjectProperty, skos:broadMatch SIO:010285 ; skos:definition "holds between two genes or gene products that are part of (or code for products that are part of) in the same macromolecular complex" ; skos:relatedMatch SIO:010497 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "coexists with" . biolink:in_linkage_disequilibrium_with a owl:ObjectProperty, owl:SymmetricProperty ; @@ -2553,7 +2936,8 @@ biolink:in_linkage_disequilibrium_with a owl:ObjectProperty, rdfs:subPropertyOf biolink:related_to_at_instance_level ; skos:definition "holds between two sequence variants, the presence of which are correlated in a population" ; skos:exactMatch ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:in_pathway_with a owl:ObjectProperty, owl:SymmetricProperty ; @@ -2563,7 +2947,8 @@ biolink:in_pathway_with a owl:ObjectProperty, rdfs:subPropertyOf biolink:coexists_with ; skos:definition "holds between two genes or gene products that are part of in the same biological pathway" ; skos:relatedMatch SIO:010532 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "coexists with" . biolink:indirectly_physically_interacts_with a owl:ObjectProperty, owl:SymmetricProperty ; @@ -2571,7 +2956,8 @@ biolink:indirectly_physically_interacts_with a owl:ObjectProperty, rdfs:domain biolink:NamedThing ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:physically_interacts_with ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "physically interacts with" . biolink:ln_ratio a owl:ObjectProperty ; rdfs:label "ln ratio" ; @@ -2579,7 +2965,7 @@ biolink:ln_ratio a owl:ObjectProperty ; rdfs:range linkml:Float ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "the natural log of the ratio of co-occurrence to expected" ; - linkml:examples "Example(value='2.922827136', description=None)" . + linkml:is_a "association slot" . biolink:ln_ratio_confidence_interval a owl:ObjectProperty ; rdfs:label "ln ratio confidence interval" ; @@ -2587,14 +2973,31 @@ biolink:ln_ratio_confidence_interval a owl:ObjectProperty ; rdfs:range linkml:Float ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "The 99% confidence interval for the ln_ratio calculation (i.e. the range of values within which the true value has a 99% chance of falling)" ; - linkml:examples "Example(value='2.922827136', description=None)" . + linkml:is_a "association slot" . + +biolink:log_odds_ratio a owl:ObjectProperty ; + rdfs:label "log odds ratio" ; + rdfs:domain biolink:Association ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf biolink:association_slot ; + skos:definition "The logarithm of the odds ratio, or the ratio of the odds of event Y occurring in an exposed group versus the odds of event Y occurring in a non-exposed group." ; + linkml:is_a "association slot" . + +biolink:log_odds_ration_95_ci a owl:ObjectProperty ; + rdfs:label "log odds ration 95 ci" ; + rdfs:domain biolink:Association ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf biolink:association_slot ; + skos:definition "The ninety-five percent confidence range in which the true log odds ratio for the sample population falls." ; + linkml:is_a "association slot" . biolink:logical_interpretation a owl:ObjectProperty ; rdfs:label "logical interpretation" ; rdfs:domain biolink:Association ; rdfs:range biolink:LogicalInterpretationEnum ; rdfs:subPropertyOf biolink:association_slot ; - skos:exactMatch os:LogicalInterpretation . + skos:exactMatch os:LogicalInterpretation ; + linkml:is_a "association slot" . biolink:mechanism_of_action a owl:ObjectProperty ; rdfs:label "mechanism of action" ; @@ -2604,7 +3007,8 @@ biolink:mechanism_of_action a owl:ObjectProperty ; skos:definition "a boolean flag to indicate if the edge is part of a path or subgraph of a knowledge graph that constitutes the mechanism of action for a result." ; skos:exactMatch LOINC:MTHU019741, MI:2044, - . + ; + linkml:is_a "association slot" . biolink:narrow_matches a owl:ObjectProperty ; rdfs:label "narrow matches" ; @@ -2616,7 +3020,8 @@ biolink:narrow_synonym a owl:ObjectProperty ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:LabelType ; rdfs:subPropertyOf biolink:synonym ; - skos:exactMatch OIO:hasNarrowSynonym . + skos:exactMatch OIO:hasNarrowSynonym ; + linkml:is_a "synonym" . biolink:negatively_correlated_with a owl:ObjectProperty, owl:SymmetricProperty ; @@ -2627,7 +3032,8 @@ biolink:negatively_correlated_with a owl:ObjectProperty, skos:definition "A relationship that holds between two concepts represented by variables for which a statistical correlation is demonstrated, wherein variable values move in opposite directions (i.e. increased in one or presence of one correlates with a decrease or absence of the other)." ; skos:exactMatch CTD:negative_correlation ; biolink:canonical_predicate "True" ; - biolink:opposite_of "positively correlated with" . + biolink:opposite_of "positively correlated with" ; + linkml:is_a "correlated with" . biolink:object_location_in_text a owl:ObjectProperty ; rdfs:label "object location in text" ; @@ -2635,7 +3041,7 @@ biolink:object_location_in_text a owl:ObjectProperty ; rdfs:range linkml:Integer ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "Character offsets for the text span(s) in the supporting text corresponding to the object concept of the extracted assertion" ; - linkml:examples "Example(value='15', description=None)" . + linkml:is_a "association slot" . biolink:occurs_together_in_literature_with a owl:ObjectProperty, owl:SymmetricProperty ; @@ -2644,19 +3050,19 @@ biolink:occurs_together_in_literature_with a owl:ObjectProperty, rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:correlated_with ; skos:definition "holds between two entities where their co-occurrence is correlated by counts of publications in which both occur, using some threshold of occurrence as defined by the edge provider." ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "correlated with" . biolink:opposite_of a owl:ObjectProperty, owl:SymmetricProperty ; rdfs:label "opposite of" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:NamedThing ; - rdfs:seeAlso "https://doi.org/10.1101/108977", - "https://github.com/biolink/biolink-model/issues/657" ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; skos:definition "x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). (This description is from RO. Needs to be rephrased)." ; skos:exactMatch RO:0002604 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:orthologous_to a owl:ObjectProperty, owl:SymmetricProperty ; @@ -2667,7 +3073,8 @@ biolink:orthologous_to a owl:ObjectProperty, skos:definition "a homology relationship between entities (typically genes) that diverged after a speciation event." ; skos:exactMatch RO:HOM0000017, WIKIDATA_PROPERTY:P684 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "homologous to" . biolink:paralogous_to a owl:ObjectProperty, owl:SymmetricProperty ; @@ -2677,7 +3084,8 @@ biolink:paralogous_to a owl:ObjectProperty, rdfs:subPropertyOf biolink:homologous_to ; skos:definition "a homology relationship that holds between entities (typically genes) that diverged after a duplication event." ; skos:exactMatch RO:HOM0000011 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "homologous to" . biolink:positively_correlated_with a owl:ObjectProperty, owl:SymmetricProperty ; @@ -2688,13 +3096,15 @@ biolink:positively_correlated_with a owl:ObjectProperty, skos:definition "A relationship that holds between two concepts represented by variables for which a statistical correlation is demonstrated, wherein variable values move together in the same direction (i.e. increased in one or presence of one correlates with an increase or presence of the other)." ; skos:exactMatch CTD:positive_correlation ; biolink:canonical_predicate "True" ; - biolink:opposite_of "negatively correlated with" . + biolink:opposite_of "negatively correlated with" ; + linkml:is_a "correlated with" . biolink:reaction_balanced a owl:ObjectProperty ; rdfs:label "reaction balanced" ; rdfs:domain biolink:Association ; rdfs:range linkml:Boolean ; - rdfs:subPropertyOf biolink:association_slot . + rdfs:subPropertyOf biolink:association_slot ; + linkml:is_a "association slot" . biolink:related_condition a owl:ObjectProperty, owl:SymmetricProperty ; @@ -2703,14 +3113,16 @@ biolink:related_condition a owl:ObjectProperty, rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; skos:exactMatch ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:related_synonym a owl:ObjectProperty ; rdfs:label "related synonym" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:LabelType ; rdfs:subPropertyOf biolink:synonym ; - skos:exactMatch OIO:hasRelatedSynonym . + skos:exactMatch OIO:hasRelatedSynonym ; + linkml:is_a "synonym" . biolink:relation a owl:ObjectProperty ; rdfs:label "relation" ; @@ -2721,14 +3133,16 @@ biolink:relative_frequency_object a owl:ObjectProperty ; rdfs:domain biolink:Association ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:association_slot ; - skos:definition "The frequency at which subject and object concepts co-occur in records within a dataset/cohort, relative to the frequency at which the object concept appears in these same records." . + skos:definition "The frequency at which subject and object concepts co-occur in records within a dataset/cohort, relative to the frequency at which the object concept appears in these same records." ; + linkml:is_a "association slot" . biolink:relative_frequency_object_confidence_interval a owl:ObjectProperty ; rdfs:label "relative frequency object confidence interval" ; rdfs:domain biolink:Association ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:association_slot ; - skos:definition "The 99% confidence interval for the relative_frequency_object calculation (i.e. the range of values within which the true value has a 99% chance of falling)" . + skos:definition "The 99% confidence interval for the relative_frequency_object calculation (i.e. the range of values within which the true value has a 99% chance of falling)" ; + linkml:is_a "association slot" . biolink:relative_frequency_subject a owl:ObjectProperty ; rdfs:label "relative frequency subject" ; @@ -2736,21 +3150,23 @@ biolink:relative_frequency_subject a owl:ObjectProperty ; rdfs:range linkml:Float ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "The frequency at which subject and object concepts co-occur in records within a dataset/cohort, relative to the frequency at which the subject concept appears in these same records." ; - linkml:examples "Example(value='0.01840490798', description=None)" . + linkml:is_a "association slot" . biolink:relative_frequency_subject_confidence_interval a owl:ObjectProperty ; rdfs:label "relative frequency subject confidence interval" ; rdfs:domain biolink:Association ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:association_slot ; - skos:definition "The 99% confidence interval for the relative_frequency_subject calculation (i.e. the range of values within which the true value has a 99% chance of falling)" . + skos:definition "The 99% confidence interval for the relative_frequency_subject calculation (i.e. the range of values within which the true value has a 99% chance of falling)" ; + linkml:is_a "association slot" . biolink:retrieved_on a owl:ObjectProperty ; rdfs:label "retrieved on" ; rdfs:domain biolink:Dataset ; rdfs:range linkml:Date ; rdfs:subPropertyOf biolink:node_property ; - skos:exactMatch pav:retrievedOn . + skos:exactMatch pav:retrievedOn ; + linkml:is_a "node property" . biolink:same_as a owl:ObjectProperty, owl:SymmetricProperty ; @@ -2766,14 +3182,16 @@ biolink:same_as a owl:ObjectProperty, CHEMBL.MECHANISM:equivalent_to, WIKIDATA_PROPERTY:P2888 ; skos:narrowMatch ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "exact match" . biolink:sequence_variant_qualifier a owl:ObjectProperty ; rdfs:label "sequence variant qualifier" ; rdfs:domain biolink:Association ; rdfs:range biolink:SequenceVariant ; rdfs:subPropertyOf biolink:association_slot ; - skos:definition "a qualifier used in an association with the variant" . + skos:definition "a qualifier used in an association with the variant" ; + linkml:is_a "association slot" . biolink:start_coordinate a owl:ObjectProperty ; rdfs:label "start coordinate" ; @@ -2783,7 +3201,8 @@ biolink:start_coordinate a owl:ObjectProperty ; skos:altLabel "start" ; skos:closeMatch ; skos:definition "The position at which the subject genomic entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 1)." ; - skos:exactMatch gff3:start . + skos:exactMatch gff3:start ; + linkml:is_a "base coordinate" . biolink:subclass_of a owl:ObjectProperty ; rdfs:label "subclass of" ; @@ -2818,7 +3237,8 @@ biolink:subclass_of a owl:ObjectProperty ; , , rdfs:subPropertyOf ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at concept level" . biolink:subject_location_in_text a owl:ObjectProperty ; rdfs:label "subject location in text" ; @@ -2826,7 +3246,7 @@ biolink:subject_location_in_text a owl:ObjectProperty ; rdfs:range linkml:Integer ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "Character offsets for the text span(s) in the supporting text corresponding to the subject concept of the extracted assertion." ; - linkml:examples "Example(value='15', description=None)" . + linkml:is_a "association slot" . biolink:superclass_of a owl:ObjectProperty ; rdfs:label "superclass of" ; @@ -2845,7 +3265,8 @@ biolink:superclass_of a owl:ObjectProperty ; , , , - . + ; + linkml:is_a "related to at concept level" . biolink:support_graphs a owl:ObjectProperty ; rdfs:label "support graphs" ; @@ -2855,17 +3276,18 @@ biolink:support_graphs a owl:ObjectProperty ; biolink:supporting_data_set a owl:ObjectProperty ; rdfs:label "supporting data set" ; rdfs:domain biolink:Association ; - rdfs:range biolink:InformationResource ; + rdfs:range linkml:String ; rdfs:subPropertyOf biolink:association_slot ; - skos:definition "A set of data used as evidence to generate the knowledge expressed in an Association (e.g. through computation on, reasoning or inference over the retrieved data)." . + skos:definition "A set of data used as evidence to generate the knowledge expressed in an Association (e.g. through computation on, reasoning or inference over the retrieved data)." ; + linkml:is_a "association slot" . biolink:supporting_data_source a owl:ObjectProperty ; rdfs:label "supporting data source" ; rdfs:domain biolink:Association ; - rdfs:range biolink:InformationResource ; + rdfs:range linkml:String ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "An Information Resource from which data was retrieved and subsequently used as evidence to generate the knowledge expressed in an Association (e.g. through computation on, reasoning or inference over the retrieved data)." ; - skos:editorialNote "For example, in this Feature Variable Association Edge generated by the Exposure Agent’s ICEES KP, through statistical analysis of clinical and environmental data supplied by the UNC Clinical Data Warehouse, the Edge is passed to the Ranking Agent’s ARAGORN ARA, and then on to the ARS. The retrieval path for this Edge is as follows: ARS--retrieved_from--> ARAGORN --retrieved_from--> ICEES --supporting_data_from--> UNC Data Warehouse This example illustrates how to represent the source provenance of KP-generated knowledge, including the source of data from which the knowledge was derived. The \"primary knowledge source\" for this edge is \"infores:icees-asthma\". A \"supporting data source\" for this KP- generated knowledge is \"infores:unc-cdw-health.\" The \"aggregator knowledge source\" for this data is \"infores:aragorn-ara\"" . + linkml:is_a "association slot" . biolink:supporting_document_type a owl:ObjectProperty ; rdfs:label "supporting document type" ; @@ -2873,7 +3295,7 @@ biolink:supporting_document_type a owl:ObjectProperty ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "The document type (e.g., Journal Article, Case Study, Preprint) for the supporting document used in a Text Mining Result." ; - linkml:examples "Example(value='Journal Article', description=None)" . + linkml:is_a "association slot" . biolink:supporting_document_year a owl:ObjectProperty ; rdfs:label "supporting document year" ; @@ -2881,7 +3303,7 @@ biolink:supporting_document_year a owl:ObjectProperty ; rdfs:range linkml:Integer ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "The document year (typically the publication year) for the supporting document used in a Text Mining Result." ; - linkml:examples "Example(value='1999', description=None)" . + linkml:is_a "association slot" . biolink:supporting_documents a owl:ObjectProperty ; rdfs:label "supporting documents" ; @@ -2889,49 +3311,55 @@ biolink:supporting_documents a owl:ObjectProperty ; rdfs:range linkml:Uriorcurie ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "One or more referenceable documents that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - linkml:examples "Example(value='PMID:12345678', description=None)" . + linkml:is_a "association slot" . biolink:supporting_study_cohort a owl:ObjectProperty ; rdfs:label "supporting study cohort" ; rdfs:domain biolink:Association ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:supporting_study_metadata ; - skos:definition "A description of a study population/cohort that was interrogated to provide evidence for the association (e.g. the inclusion and exclusion criteria)." . + skos:definition "A description of a study population/cohort that was interrogated to provide evidence for the association (e.g. the inclusion and exclusion criteria)." ; + linkml:is_a "supporting study metadata" . biolink:supporting_study_context a owl:ObjectProperty ; rdfs:label "supporting study context" ; rdfs:domain biolink:Association ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:supporting_study_metadata ; - skos:definition "A term or terms describing the experimental setting/context in which evidence supporting the Association was generated ('context' may be defined by many factors, including taxon, model system (e.g. cell line type), tissue type, disease, etc.)." . + skos:definition "A term or terms describing the experimental setting/context in which evidence supporting the Association was generated ('context' may be defined by many factors, including taxon, model system (e.g. cell line type), tissue type, disease, etc.)." ; + linkml:is_a "supporting study metadata" . biolink:supporting_study_date_range a owl:ObjectProperty ; rdfs:label "supporting study date range" ; rdfs:domain biolink:Association ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:supporting_study_metadata ; - skos:definition "The date range over which data was collected in a study that provided evidence for an Association." . + skos:definition "The date range over which data was collected in a study that provided evidence for an Association." ; + linkml:is_a "supporting study metadata" . biolink:supporting_study_method_description a owl:ObjectProperty ; rdfs:label "supporting study method description" ; rdfs:domain biolink:Association ; rdfs:range linkml:Uriorcurie ; rdfs:subPropertyOf biolink:supporting_study_metadata ; - skos:definition "A uri or curie pointing to information about the methodology used to generate data supporting an Association." . + skos:definition "A uri or curie pointing to information about the methodology used to generate data supporting an Association." ; + linkml:is_a "supporting study metadata" . biolink:supporting_study_method_type a owl:ObjectProperty ; rdfs:label "supporting study method type" ; rdfs:domain biolink:Association ; rdfs:range linkml:Uriorcurie ; rdfs:subPropertyOf biolink:supporting_study_metadata ; - skos:definition "A type of method that was applied in a study used to generate the information used as evidence (e.g. a type of experimental assay, or statistical calculation, or computational analysis)." . + skos:definition "A type of method that was applied in a study used to generate the information used as evidence (e.g. a type of experimental assay, or statistical calculation, or computational analysis)." ; + linkml:is_a "supporting study metadata" . biolink:supporting_study_size a owl:ObjectProperty ; rdfs:label "supporting study size" ; rdfs:domain biolink:Association ; rdfs:range linkml:Integer ; rdfs:subPropertyOf biolink:supporting_study_metadata ; - skos:definition "The sample size used in a study that provided evidence for the association (e.g. 'n' of a cohort for a clinical study)." . + skos:definition "The sample size used in a study that provided evidence for the association (e.g. 'n' of a cohort for a clinical study)." ; + linkml:is_a "supporting study metadata" . biolink:supporting_text a owl:ObjectProperty ; rdfs:label "supporting text" ; @@ -2939,7 +3367,7 @@ biolink:supporting_text a owl:ObjectProperty ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "The segment of text from a document that supports the mined assertion." ; - linkml:examples "Example(value='The administration of 50g/ml bupivacaine promoted maximum breast cancer.', description=None)" . + linkml:is_a "association slot" . biolink:supporting_text_section_type a owl:ObjectProperty ; rdfs:label "supporting text section type" ; @@ -2947,21 +3375,31 @@ biolink:supporting_text_section_type a owl:ObjectProperty ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "The section of the supporting text of a Text Mining Result within the supporting document. This is in the form of the name of the document section (e.g., Abstract, Introduction) that contains the supporting text." ; - linkml:examples "Example(value='Introduction', description=None)" . + linkml:is_a "association slot" . biolink:temporal_interval_qualifier a owl:ObjectProperty ; rdfs:label "temporal interval qualifier" ; rdfs:domain biolink:Association ; rdfs:range biolink:TimeType ; rdfs:subPropertyOf biolink:temporal_context_qualifier ; - skos:definition "a constraint of a time interval placed upon the truth value of an association." . + skos:definition "a constraint of a time interval placed upon the truth value of an association." ; + linkml:is_a "temporal context qualifier" . + +biolink:total_sample_size a owl:ObjectProperty ; + rdfs:label "total sample size" ; + rdfs:domain biolink:Association ; + rdfs:range linkml:Integer ; + rdfs:subPropertyOf biolink:dataset_count ; + skos:definition "The total number of patients or participants within a sample population." ; + linkml:is_a "dataset count" . biolink:update_date a owl:ObjectProperty ; rdfs:label "update date" ; rdfs:domain biolink:NamedThing ; rdfs:range linkml:Date ; rdfs:subPropertyOf biolink:node_property ; - skos:definition "date on which an entity was updated. This can be applied to nodes or edges" . + skos:definition "date on which an entity was updated. This can be applied to nodes or edges" ; + linkml:is_a "node property" . biolink:version a owl:ObjectProperty ; rdfs:label "version" ; @@ -2969,14 +3407,16 @@ biolink:version a owl:ObjectProperty ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:node_property ; skos:broadMatch pav:version, - owl:versionInfo . + owl:versionInfo ; + linkml:is_a "node property" . biolink:version_of a owl:ObjectProperty ; rdfs:label "version of" ; rdfs:domain biolink:DatasetVersion ; rdfs:range biolink:DatasetSummary ; rdfs:subPropertyOf biolink:node_property ; - skos:exactMatch dct:isVersionOf . + skos:exactMatch dct:isVersionOf ; + linkml:is_a "node property" . biolink:xenologous_to a owl:ObjectProperty, owl:SymmetricProperty ; @@ -2986,7 +3426,8 @@ biolink:xenologous_to a owl:ObjectProperty, rdfs:subPropertyOf biolink:homologous_to ; skos:definition "a homology relationship characterized by an interspecies (horizontal) transfer since the common ancestor." ; skos:exactMatch RO:HOM0000018 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "homologous to" . GOP:systematic_synonym a owl:ObjectProperty ; rdfs:label "systematic synonym" ; @@ -2994,7 +3435,8 @@ GOP:systematic_synonym a owl:ObjectProperty ; rdfs:range biolink:LabelType ; rdfs:subPropertyOf biolink:node_property ; skos:definition "more commonly used for gene symbols in yeast" ; - skos:exactMatch GOP:systematic_synonym . + skos:exactMatch GOP:systematic_synonym ; + linkml:is_a "node property" . dcat:downloadURL a owl:ObjectProperty . @@ -3012,11 +3454,16 @@ biolink:Activity a owl:Class ; STY:T062, STY:T064, STY:T065, - STY:T066 . + STY:T066 ; + linkml:attributes "{}" ; + linkml:is_a "named thing" ; + linkml:mixins "activity and behavior" . biolink:AdministrativeEntity a owl:Class ; rdfs:label "administrative entity" ; - rdfs:subClassOf biolink:NamedThing . + rdfs:subClassOf biolink:NamedThing ; + linkml:attributes "{}" ; + linkml:is_a "named thing" . biolink:Article a owl:Class ; rdfs:label "article" ; @@ -3024,6 +3471,10 @@ biolink:Article a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:issue ], + [ a owl:Restriction ; + owl:onClass linkml:Uriorcurie ; + owl:onProperty biolink:published_in ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -3032,14 +3483,12 @@ biolink:Article a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:volume ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty biolink:published_in ; - owl:qualifiedCardinality 1 ], biolink:Publication ; skos:definition "a piece of writing on a particular topic presented as a stand-alone section of a larger publication " ; skos:exactMatch fabio:article, - SIO:000154 . + SIO:000154 ; + linkml:attributes "{}" ; + linkml:is_a "publication" . biolink:Behavior a owl:Class ; rdfs:label "behavior" ; @@ -3050,13 +3499,19 @@ biolink:Behavior a owl:Class ; ; skos:narrowMatch STY:T041, STY:T054, - STY:T055 . + STY:T055 ; + linkml:attributes "{}" ; + linkml:is_a "biological process" ; + linkml:mixins "activity and behavior", + "ontology class" . biolink:BehavioralFeature a owl:Class ; rdfs:label "behavioral feature" ; rdfs:subClassOf biolink:PhenotypicFeature ; skos:definition "A phenotypic feature which is behavioral in nature." ; - skos:exactMatch . + skos:exactMatch ; + linkml:attributes "{}" ; + linkml:is_a "phenotypic feature" . biolink:BookChapter a owl:Class ; rdfs:label "book chapter" ; @@ -3072,7 +3527,9 @@ biolink:BookChapter a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:volume ], - biolink:Publication . + biolink:Publication ; + linkml:attributes "{}" ; + linkml:is_a "publication" . biolink:Case a owl:Class ; rdfs:label "case" ; @@ -3080,7 +3537,10 @@ biolink:Case a owl:Class ; biolink:SubjectOfInvestigation ; skos:altLabel "patient", "proband" ; - skos:definition "An individual (human) organism that has a patient role in some clinical context." . + skos:definition "An individual (human) organism that has a patient role in some clinical context." ; + linkml:attributes "{}" ; + linkml:is_a "individual organism" ; + linkml:mixins "subject of investigation" . biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "cell line to disease or phenotypic feature association" ; @@ -3091,7 +3551,11 @@ biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; biolink:Association, biolink:CellLineToEntityAssociationMixin, biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ; - skos:definition "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." . + skos:definition "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." ; + linkml:attributes "{}" ; + linkml:is_a "association" ; + linkml:mixins "cell line to entity association mixin", + "entity to disease or phenotypic feature association mixin" . biolink:ChemicalExposure a owl:Class ; rdfs:label "chemical exposure" ; @@ -3103,15 +3567,17 @@ biolink:ChemicalExposure a owl:Class ; biolink:ExposureEvent ; skos:definition "A chemical exposure is an intake of a particular chemical entity." ; skos:exactMatch ECTO:9000000, - SIO:001399 . + SIO:001399 ; + linkml:attributes "{}" ; + linkml:is_a "attribute" ; + linkml:mixins "exposure event" . biolink:ChemicalFormulaValue a owl:Class ; rdfs:label "chemical formula value" ; rdfs:subClassOf [ a owl:Restriction ; owl:onDataRange xsd:string ; owl:onProperty linkml:topValue ; - owl:qualifiedCardinality 1 ] ; - skos:editorialNote "Should be implemented as a stronger type" . + owl:qualifiedCardinality 1 ] . biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "chemical or drug or treatment to disease or phenotypic feature association" ; @@ -3126,28 +3592,40 @@ biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a owl:C biolink:Association, biolink:ChemicalToEntityAssociationMixin, biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ; - skos:definition "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect." . + skos:definition "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect." ; + linkml:attributes "{}" ; + linkml:is_a "association" ; + linkml:mixins "chemical to entity association mixin", + "entity to disease or phenotypic feature association mixin" . biolink:ClinicalCourse a owl:Class ; rdfs:label "clinical course" ; rdfs:subClassOf biolink:ClinicalAttribute ; skos:definition "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual" ; - skos:exactMatch . + skos:exactMatch ; + linkml:attributes "{}" ; + linkml:is_a "clinical attribute" . biolink:ClinicalIntervention a owl:Class ; rdfs:label "clinical intervention" ; - rdfs:subClassOf biolink:ClinicalEntity . + rdfs:subClassOf biolink:ClinicalEntity ; + linkml:attributes "{}" ; + linkml:is_a "clinical entity" . biolink:ClinicalModifier a owl:Class ; rdfs:label "clinical modifier" ; rdfs:subClassOf biolink:ClinicalAttribute ; - skos:definition "Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects" . + skos:definition "Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects" ; + linkml:attributes "{}" ; + linkml:is_a "clinical attribute" . biolink:CodingSequence a owl:Class ; rdfs:label "coding sequence" ; rdfs:subClassOf biolink:NucleicAcidEntity ; skos:exactMatch , - SIO:001390 . + SIO:001390 ; + linkml:attributes "{}" ; + linkml:is_a "nucleic acid entity" . biolink:ConfidenceLevel a owl:Class ; rdfs:label "confidence level" ; @@ -3155,7 +3633,9 @@ biolink:ConfidenceLevel a owl:Class ; skos:closeMatch ; skos:definition "Level of confidence in a statement" ; skos:exactMatch , - . + ; + linkml:attributes "{}" ; + linkml:is_a "information content entity" . biolink:DrugExposure a owl:Class ; rdfs:label "drug exposure" ; @@ -3166,7 +3646,10 @@ biolink:DrugExposure a owl:Class ; "medication intake" ; skos:broadMatch SIO:001005 ; skos:definition "A drug exposure is an intake of a particular drug." ; - skos:exactMatch ECTO:0000509 . + skos:exactMatch ECTO:0000509 ; + linkml:attributes "{}" ; + linkml:is_a "chemical exposure" ; + linkml:mixins "exposure event" . biolink:DrugToEntityAssociationMixin a owl:Class ; rdfs:label "drug to entity association mixin" ; @@ -3176,7 +3659,9 @@ biolink:DrugToEntityAssociationMixin a owl:Class ; owl:qualifiedCardinality 1 ], biolink:ChemicalEntityToEntityAssociationMixin, linkml:mixin ; - skos:definition "An interaction between a drug and another entity" . + skos:definition "An interaction between a drug and another entity" ; + linkml:attributes "{}" ; + linkml:is_a "chemical entity to entity association mixin" . biolink:DruggableGeneCategoryEnum a owl:Class ; rdfs:label "DruggableGeneCategoryEnum" ; @@ -3194,7 +3679,10 @@ biolink:EnvironmentalExposure a owl:Class ; owl:onProperty biolink:timepoint ], biolink:Attribute, biolink:ExposureEvent ; - skos:definition "A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants." . + skos:definition "A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants." ; + linkml:attributes "{}" ; + linkml:is_a "attribute" ; + linkml:mixins "exposure event" . biolink:Exon a owl:Class ; rdfs:label "exon" ; @@ -3202,14 +3690,17 @@ biolink:Exon a owl:Class ; skos:definition "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." ; skos:exactMatch , SIO:010445, - WIKIDATA:Q373027 . + WIKIDATA:Q373027 ; + linkml:attributes "{}" ; + linkml:is_a "nucleic acid entity" . biolink:FDA_adverse_event_level a owl:ObjectProperty ; rdfs:label "FDA adverse event level" ; rdfs:domain biolink:Association ; rdfs:range biolink:FDAIDAAdverseEventEnum ; rdfs:subPropertyOf biolink:association_slot ; - skos:definition "" . + skos:definition "" ; + linkml:is_a "association slot" . biolink:GeneFamily a owl:Class ; rdfs:label "gene family" ; @@ -3226,7 +3717,11 @@ biolink:GeneFamily a owl:Class ; WIKIDATA:Q2278983 ; skos:narrowMatch , SIO:001380, - WIKIDATA:Q417841 . + WIKIDATA:Q417841 ; + linkml:attributes "{}" ; + linkml:is_a "biological entity" ; + linkml:mixins "chemical entity or gene or gene product", + "gene grouping mixin" . biolink:GeneOrGeneProductOrChemicalEntityAspectEnum a owl:Class ; rdfs:label "GeneOrGeneProductOrChemicalEntityAspectEnum" ; @@ -3283,33 +3778,36 @@ biolink:GeneOrGeneProductOrChemicalEntityAspectEnum a owl:Class ; biolink:GenotypeToDiseaseAssociation a owl:Class ; rdfs:label "genotype to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:onClass biolink:NamedThing ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, biolink:GenotypeToEntityAssociationMixin ; - skos:note "TODO decide no how to model pathogenicity" . + linkml:attributes "{}" ; + linkml:is_a "association" ; + linkml:mixins "entity to disease association mixin", + "genotype to entity association mixin" . biolink:GeographicLocation a owl:Class ; rdfs:label "geographic location" ; @@ -3324,14 +3822,9 @@ biolink:GeographicLocation a owl:Class ; biolink:PlanetaryEntity ; skos:definition "a location that can be described in lat/long coordinates" ; skos:exactMatch STY:T083, - UMLSSG:GEOG . - -biolink:InformationResourceCollection a owl:Class ; - rdfs:label "InformationResourceCollection" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:InformationResource ; - owl:onProperty biolink:information_resources ] ; - skos:definition "A collection of information resources" . + UMLSSG:GEOG ; + linkml:attributes "{}" ; + linkml:is_a "planetary entity" . biolink:LogicalInterpretationEnum a owl:Class ; rdfs:label "LogicalInterpretationEnum" ; @@ -3348,25 +3841,33 @@ biolink:Mammal a owl:Class ; skos:exactMatch STY:T015, , , - . + ; + linkml:attributes "{}" ; + linkml:is_a "cellular organism" ; + linkml:mixins "subject of investigation" . biolink:MappingCollection a owl:Class ; rdfs:label "mapping collection" ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom biolink:PredicateMapping ; owl:onProperty biolink:predicate_mappings ] ; - skos:definition "A collection of deprecated mappings." . + skos:definition "A collection of deprecated mappings." ; + linkml:attributes "{}" . biolink:MolecularMixture a owl:Class ; rdfs:label "molecular mixture" ; rdfs:subClassOf biolink:ChemicalMixture ; - skos:definition "A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry." . + skos:definition "A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry." ; + linkml:attributes "{}" ; + linkml:is_a "chemical mixture" . biolink:OrganismAttribute a owl:Class ; rdfs:label "organism attribute" ; rdfs:subClassOf biolink:Attribute ; skos:definition "describes a characteristic of an organismal entity." ; - skos:exactMatch STY:T032 . + skos:exactMatch STY:T032 ; + linkml:attributes "{}" ; + linkml:is_a "attribute" . biolink:PairwiseGeneToGeneInteraction a owl:Class ; rdfs:label "pairwise gene to gene interaction" ; @@ -3376,7 +3877,9 @@ biolink:PairwiseGeneToGeneInteraction a owl:Class ; owl:qualifiedCardinality 1 ], biolink:GeneToGeneAssociation ; skos:definition "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)" ; - skos:narrowMatch dcid:ProteinProteinInteraction . + skos:narrowMatch dcid:ProteinProteinInteraction ; + linkml:attributes "{}" ; + linkml:is_a "gene to gene association" . biolink:Polypeptide a owl:Class ; rdfs:label "polypeptide" ; @@ -3387,7 +3890,11 @@ biolink:Polypeptide a owl:Class ; skos:definition "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule." ; skos:narrowMatch STY:T087, STY:T116, - . + ; + linkml:attributes "{}" ; + linkml:is_a "biological entity" ; + linkml:mixins "chemical entity or gene or gene product", + "chemical entity or protein or polypeptide" . biolink:ReactionToParticipantAssociation a owl:Class ; rdfs:label "reaction to participant association" ; @@ -3396,34 +3903,42 @@ biolink:ReactionToParticipantAssociation a owl:Class ; owl:onClass biolink:ReactionSideEnum ; owl:onProperty biolink:reaction_side ], [ a owl:Restriction ; - owl:onClass biolink:MolecularEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:stoichiometry ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:ReactionDirectionEnum ; owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:stoichiometry ], - biolink:ChemicalToChemicalAssociation . + owl:onClass biolink:MolecularEntity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], + biolink:ChemicalToChemicalAssociation ; + linkml:attributes "{}" ; + linkml:is_a "chemical to chemical association" . biolink:SequenceAssociation a owl:Class ; rdfs:label "sequence association" ; rdfs:subClassOf biolink:Association ; - skos:definition "An association between a sequence feature and a nucleic acid entity it is localized to." . + skos:definition "An association between a sequence feature and a nucleic acid entity it is localized to." ; + linkml:attributes "{}" ; + linkml:is_a "association" . biolink:SpecificityQuantifier a owl:Class ; rdfs:label "specificity quantifier" ; rdfs:subClassOf biolink:RelationshipQuantifier, - linkml:mixin . + linkml:mixin ; + linkml:attributes "{}" ; + linkml:is_a "relationship quantifier" . biolink:StudyPopulation a owl:Class ; rdfs:label "study population" ; rdfs:subClassOf biolink:PopulationOfIndividualOrganisms ; skos:closeMatch WIKIDATA:Q7229825 ; - skos:definition "A group of people banded together or treated as a group as participants in a research study." . + skos:definition "A group of people banded together or treated as a group as participants in a research study." ; + linkml:attributes "{}" ; + linkml:is_a "population of individual organisms" . biolink:SymbolType a owl:Class ; rdfs:label "symbol type" ; @@ -3435,15 +3950,15 @@ biolink:Treatment a owl:Class ; owl:allValuesFrom biolink:Drug ; owl:onProperty biolink:has_drug ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Device ; - owl:onProperty biolink:has_device ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:TimeType ; + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:allValuesFrom biolink:Procedure ; owl:onProperty biolink:has_procedure ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:TimeType ; - owl:onProperty biolink:timepoint ], + owl:allValuesFrom biolink:Device ; + owl:onProperty biolink:has_device ], biolink:ChemicalOrDrugOrTreatment, biolink:ExposureEvent, biolink:NamedThing ; @@ -3452,38 +3967,45 @@ biolink:Treatment a owl:Class ; skos:broadMatch MAXO:0000058 ; skos:definition "A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures" ; skos:exactMatch , - SIO:001398 . + SIO:001398 ; + linkml:attributes "{}" ; + linkml:is_a "named thing" ; + linkml:mixins "chemical or drug or treatment", + "exposure event" . biolink:VariantToDiseaseAssociation a owl:Class ; rdfs:label "variant to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:NamedThing ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:onClass biolink:NamedThing ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, biolink:VariantToEntityAssociationMixin ; - skos:note "TODO decide no how to model pathogenicity" . + linkml:attributes "{}" ; + linkml:is_a "association" ; + linkml:mixins "entity to disease association mixin", + "variant to entity association mixin" . biolink:VariantToGeneAssociation a owl:Class ; rdfs:label "variant to gene association" ; @@ -3497,7 +4019,10 @@ biolink:VariantToGeneAssociation a owl:Class ; owl:qualifiedCardinality 1 ], biolink:Association, biolink:VariantToEntityAssociationMixin ; - skos:definition "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)" . + skos:definition "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)" ; + linkml:attributes "{}" ; + linkml:is_a "association" ; + linkml:mixins "variant to entity association mixin" . biolink:active_in a owl:ObjectProperty ; rdfs:label "active in" ; @@ -3506,7 +4031,8 @@ biolink:active_in a owl:ObjectProperty ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; owl:inverseOf biolink:has_active_component ; skos:exactMatch RO:0002432 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:acts_upstream_of_negative_effect a owl:ObjectProperty ; rdfs:label "acts upstream of negative effect" ; @@ -3515,7 +4041,8 @@ biolink:acts_upstream_of_negative_effect a owl:ObjectProperty ; rdfs:subPropertyOf biolink:acts_upstream_of ; owl:inverseOf biolink:has_negative_upstream_actor ; skos:exactMatch RO:0004035 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "acts upstream of" . biolink:acts_upstream_of_or_within_negative_effect a owl:ObjectProperty ; rdfs:label "acts upstream of or within negative effect" ; @@ -3524,7 +4051,8 @@ biolink:acts_upstream_of_or_within_negative_effect a owl:ObjectProperty ; rdfs:subPropertyOf biolink:acts_upstream_of_or_within ; owl:inverseOf biolink:has_negative_upstream_or_within_actor ; skos:exactMatch RO:0004033 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "acts upstream of or within" . biolink:acts_upstream_of_or_within_positive_effect a owl:ObjectProperty ; rdfs:label "acts upstream of or within positive effect" ; @@ -3533,7 +4061,8 @@ biolink:acts_upstream_of_or_within_positive_effect a owl:ObjectProperty ; rdfs:subPropertyOf biolink:acts_upstream_of_or_within ; owl:inverseOf biolink:has_positive_upstream_or_within_actor ; skos:exactMatch RO:0004032 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "acts upstream of or within" . biolink:acts_upstream_of_positive_effect a owl:ObjectProperty ; rdfs:label "acts upstream of positive effect" ; @@ -3542,57 +4071,64 @@ biolink:acts_upstream_of_positive_effect a owl:ObjectProperty ; rdfs:subPropertyOf biolink:acts_upstream_of ; owl:inverseOf biolink:has_positive_upstream_actor ; skos:exactMatch RO:0004034 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "acts upstream of" . biolink:address a owl:ObjectProperty ; rdfs:label "address" ; rdfs:domain biolink:NamedThing ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:node_property ; - skos:definition "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?)." . + skos:definition "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?)." ; + linkml:is_a "node property" . biolink:adjusted_p_value a owl:ObjectProperty ; rdfs:label "adjusted p value" ; rdfs:domain biolink:Association ; rdfs:range linkml:Float ; rdfs:subPropertyOf biolink:p_value ; - skos:definition "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." . + skos:definition "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + linkml:is_a "p value" . biolink:adverse_event_of a owl:ObjectProperty ; rdfs:label "adverse event of" ; rdfs:domain biolink:DiseaseOrPhenotypicFeature ; rdfs:range biolink:ChemicalOrDrugOrTreatment ; rdfs:subPropertyOf biolink:affected_by ; - owl:inverseOf biolink:has_adverse_event . + owl:inverseOf biolink:has_adverse_event ; + linkml:is_a "affected by" . biolink:affiliation a owl:ObjectProperty ; rdfs:label "affiliation" ; rdfs:domain biolink:Agent ; rdfs:range linkml:Uriorcurie ; rdfs:subPropertyOf biolink:node_property ; - skos:definition "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations." . + skos:definition "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations." ; + linkml:is_a "node property" . biolink:aggregator_knowledge_source a owl:ObjectProperty ; rdfs:label "aggregator knowledge source" ; rdfs:domain biolink:Association ; - rdfs:range biolink:InformationResource ; + rdfs:range linkml:String ; rdfs:subPropertyOf biolink:knowledge_source ; skos:definition "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - skos:editorialNote "For example, in this Feature Variable Association Edge generated by the Exposure Agent’s ICEES KP, through statistical analysis of clinical and environmental data supplied by the UNC Clinical Data Warehouse, the Edge is passed to the Ranking Agent’s ARAGORN ARA, and then on to the ARS. The retrieval path for this Edge is as follows: ARS--retrieved_from--> ARAGORN --retrieved_from--> ICEES --supporting_data_from--> UNC Data Warehouse This example illustrates how to represent the source provenance of KP-generated knowledge, including the source of data from which the knowledge was derived. The \"primary knowledge source\" for this edge is \"infores:icees-asthma\". A \"supporting data source\" for this KP- generated knowledge is \"infores:unc-cdw-health.\" The \"aggregator knowledge source\" for this data is \"infores:aragorn-ara\"" . + linkml:is_a "knowledge source" . biolink:amount_or_activity_decreased_by a owl:ObjectProperty ; rdfs:label "amount or activity decreased by" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; - owl:inverseOf biolink:decreases_amount_or_activity_of . + owl:inverseOf biolink:decreases_amount_or_activity_of ; + linkml:is_a "related to at instance level" . biolink:amount_or_activity_increased_by a owl:ObjectProperty ; rdfs:label "amount or activity increased by" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; - owl:inverseOf biolink:increases_amount_or_activity_of . + owl:inverseOf biolink:increases_amount_or_activity_of ; + linkml:is_a "related to at instance level" . biolink:assesses a owl:ObjectProperty ; rdfs:label "assesses" ; @@ -3602,7 +4138,8 @@ biolink:assesses a owl:ObjectProperty ; owl:inverseOf biolink:is_assessed_by ; skos:altLabel "was assayed against" ; skos:definition "The effect of a thing on a target was interrogated in some assay. A relationship between some perturbing agent (usually a chemical compound) and some target entity, where the affect of the perturbing agent on the target entity was interrogated in a particular assay. The target might be a particular protein, tissue, phenotype, whole organism, cell line, or other type of biological entity." ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:associated_environmental_context a owl:ObjectProperty ; rdfs:label "associated environmental context" ; @@ -3610,7 +4147,8 @@ biolink:associated_environmental_context a owl:ObjectProperty ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:association_slot ; skos:definition """An attribute that can be applied to an association where the association holds between two entities located or occurring in a particular environment. For example, two microbial taxa may interact in the context of a human gut; a disease may give rise to a particular phenotype in a particular environmental exposure. - # TODO: add examples of values for this property.""" . + # TODO: add examples of values for this property.""" ; + linkml:is_a "association slot" . biolink:associated_with_decreased_likelihood_of a owl:ObjectProperty ; rdfs:label "associated with decreased likelihood of" ; @@ -3619,7 +4157,8 @@ biolink:associated_with_decreased_likelihood_of a owl:ObjectProperty ; rdfs:subPropertyOf biolink:associated_with_likelihood_of ; owl:inverseOf biolink:decreased_likelihood_associated_with ; skos:definition "Expresses a relationship between two named things where the relationship is typically generated statistically and the state or fact of something is less probable." ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "associated with likelihood of" . biolink:associated_with_increased_likelihood_of a owl:ObjectProperty ; rdfs:label "associated with increased likelihood of" ; @@ -3628,7 +4167,8 @@ biolink:associated_with_increased_likelihood_of a owl:ObjectProperty ; rdfs:subPropertyOf biolink:associated_with_likelihood_of ; owl:inverseOf biolink:increased_likelihood_associated_with ; skos:definition "Expresses a relationship between two named things where the relationship is typically generated statistically and the state or fact of something is more probable." ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "associated with likelihood of" . biolink:associated_with_resistance_to a owl:ObjectProperty ; rdfs:label "associated with resistance to" ; @@ -3637,7 +4177,8 @@ biolink:associated_with_resistance_to a owl:ObjectProperty ; rdfs:subPropertyOf biolink:associated_with ; owl:inverseOf biolink:resistance_associated_with ; skos:definition "A relation that holds between a named thing and a chemical that specifies that the change in the named thing is found to be associated with the degree of resistance to treatment by the chemical." ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "associated with" . biolink:associated_with_sensitivity_to a owl:ObjectProperty ; rdfs:label "associated with sensitivity to" ; @@ -3648,7 +4189,8 @@ biolink:associated_with_sensitivity_to a owl:ObjectProperty ; skos:broadMatch ; skos:definition "A relation that holds between a named thing and a chemical that specifies that the change in the named thing is found to be associated with the degree of sensitivity to treatment by the chemical." ; skos:narrowMatch SNOMEDCT:418038007 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "associated with" . biolink:author a owl:ObjectProperty ; rdfs:label "author" ; @@ -3658,21 +4200,24 @@ biolink:author a owl:ObjectProperty ; owl:inverseOf biolink:has_author ; skos:definition "an instance of one (co-)creator primarily responsible for a written work" ; skos:exactMatch dct:creator, - WIKIDATA_PROPERTY:P50 . + WIKIDATA_PROPERTY:P50 ; + linkml:is_a "contributor" . biolink:authors a owl:ObjectProperty ; rdfs:label "authors" ; rdfs:domain biolink:Publication ; rdfs:range biolink:Agent ; rdfs:subPropertyOf biolink:node_property ; - skos:definition "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." . + skos:definition "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + linkml:is_a "node property" . biolink:available_from a owl:ObjectProperty ; rdfs:label "available from" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:DrugAvailabilityEnum ; rdfs:subPropertyOf biolink:node_property ; - skos:definition "" . + skos:definition "" ; + linkml:is_a "node property" . biolink:biomarker_for a owl:ObjectProperty ; rdfs:label "biomarker for" ; @@ -3687,14 +4232,16 @@ biolink:biomarker_for a owl:ObjectProperty ; , , orphanet:465410 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "correlated with" . biolink:can_be_carried_out_by a owl:ObjectProperty ; rdfs:label "can be carried out by" ; rdfs:domain biolink:Occurrent ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:actively_involves ; - owl:inverseOf biolink:capable_of . + owl:inverseOf biolink:capable_of ; + linkml:is_a "actively involves" . biolink:capable_of a owl:ObjectProperty ; rdfs:label "capable of" ; @@ -3706,14 +4253,16 @@ biolink:capable_of a owl:ObjectProperty ; skos:exactMatch RO:0002215 ; skos:narrowMatch , RO:0002500 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "actively involved in" . biolink:catalyst_qualifier a owl:ObjectProperty ; rdfs:label "catalyst qualifier" ; rdfs:domain biolink:Association ; rdfs:range biolink:MacromolecularMachineMixin ; rdfs:subPropertyOf biolink:association_slot ; - skos:definition "a qualifier that connects an association between two causally connected entities (for example, two chemical entities, or a chemical entity in that changes location) and the gene product, gene, or complex that enables or catalyzes the change." . + skos:definition "a qualifier that connects an association between two causally connected entities (for example, two chemical entities, or a chemical entity in that changes location) and the gene product, gene, or complex that enables or catalyzes the change." ; + linkml:is_a "association slot" . biolink:catalyzes a owl:ObjectProperty ; rdfs:label "catalyzes" ; @@ -3722,7 +4271,8 @@ biolink:catalyzes a owl:ObjectProperty ; rdfs:subPropertyOf biolink:participates_in ; owl:inverseOf biolink:has_catalyst ; skos:exactMatch RO:0002327 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "participates in" . biolink:caused_by a owl:ObjectProperty ; rdfs:label "caused by" ; @@ -3741,7 +4291,8 @@ biolink:caused_by a owl:ObjectProperty ; RO:0004019, RO:0004020, RO:0004028, - RO:0009501 . + RO:0009501 ; + linkml:is_a "contribution from" . biolink:causes a owl:ObjectProperty ; rdfs:label "causes" ; @@ -3781,7 +4332,8 @@ biolink:causes a owl:ObjectProperty ; orphanet:410295, orphanet:410296 ; biolink:canonical_predicate "True" ; - biolink:opposite_of "prevents" . + biolink:opposite_of "prevents" ; + linkml:is_a "contributes to" . biolink:chapter a owl:ObjectProperty ; rdfs:label "chapter" ; @@ -3789,7 +4341,8 @@ biolink:chapter a owl:ObjectProperty ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:node_property ; skos:definition "chapter of a book" ; - skos:exactMatch WIKIDATA:Q1980247 . + skos:exactMatch WIKIDATA:Q1980247 ; + linkml:is_a "node property" . biolink:close_match a owl:ObjectProperty, owl:SymmetricProperty ; @@ -3806,14 +4359,16 @@ biolink:close_match a owl:ObjectProperty, , , OIO:hasDbXref ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at concept level" . biolink:completed_by a owl:ObjectProperty ; rdfs:label "completed by" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; - owl:inverseOf biolink:has_completed . + owl:inverseOf biolink:has_completed ; + linkml:is_a "related to at instance level" . biolink:composed_primarily_of a owl:ObjectProperty ; rdfs:label "composed primarily of" ; @@ -3823,7 +4378,8 @@ biolink:composed_primarily_of a owl:ObjectProperty ; owl:inverseOf biolink:primarily_composed_of ; skos:definition "x composed_primarily_of_y if:more than half of the mass of x is made from parts of y." ; skos:exactMatch RO:0002473 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to" . biolink:condition_associated_with_gene a owl:ObjectProperty ; rdfs:label "condition associated with gene" ; @@ -3833,14 +4389,16 @@ biolink:condition_associated_with_gene a owl:ObjectProperty ; owl:inverseOf biolink:gene_associated_with_condition ; skos:altLabel "disease associated with gene" ; skos:definition "holds between a gene and a disease or phenotypic feature that may be influenced, contribute to, or be correlated with the gene or its alleles/products" ; - skos:narrowMatch . + skos:narrowMatch ; + linkml:is_a "genetically associated with" . biolink:consumed_by a owl:ObjectProperty ; rdfs:label "consumed by" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:is_input_of ; - owl:inverseOf biolink:consumes . + owl:inverseOf biolink:consumes ; + linkml:is_a "is input of" . biolink:consumes a owl:ObjectProperty ; rdfs:label "consumes" ; @@ -3849,14 +4407,16 @@ biolink:consumes a owl:ObjectProperty ; rdfs:subPropertyOf biolink:has_input ; owl:inverseOf biolink:consumed_by ; skos:narrowMatch RO:0004009 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "has input" . biolink:contains_process a owl:ObjectProperty ; rdfs:label "contains process" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; - owl:inverseOf biolink:occurs_in . + owl:inverseOf biolink:occurs_in ; + linkml:is_a "related to at instance level" . biolink:contraindicated_for a owl:ObjectProperty ; rdfs:label "contraindicated for" ; @@ -3867,7 +4427,8 @@ biolink:contraindicated_for a owl:ObjectProperty ; skos:definition "Holds between a drug and a disease or phenotype, such that a person with that disease should not be treated with the drug." ; skos:exactMatch ; biolink:canonical_predicate "True" ; - biolink:opposite_of "treats" . + biolink:opposite_of "treats" ; + linkml:is_a "related to at instance level" . biolink:creation_date a owl:ObjectProperty ; rdfs:label "creation date" ; @@ -3877,14 +4438,24 @@ biolink:creation_date a owl:ObjectProperty ; skos:altLabel "publication date" ; skos:definition "date on which an entity was created. This can be applied to nodes or edges" ; skos:exactMatch dct:createdOn, - WIKIDATA_PROPERTY:P577 . + WIKIDATA_PROPERTY:P577 ; + linkml:is_a "node property" . + +biolink:dataset_count a owl:ObjectProperty ; + rdfs:label "dataset count" ; + rdfs:domain biolink:Association ; + rdfs:range linkml:Integer ; + rdfs:subPropertyOf biolink:association_slot ; + skos:definition "The total number of instances (e.g., number of patients, number of rows, etc) in a dataset/cohort." ; + linkml:is_a "association slot" . biolink:decreased_amount_in a owl:ObjectProperty ; rdfs:label "decreased amount in" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; - owl:inverseOf biolink:has_decreased_amount . + owl:inverseOf biolink:has_decreased_amount ; + linkml:is_a "related to at instance level" . biolink:decreased_likelihood_associated_with a owl:ObjectProperty ; rdfs:label "decreased likelihood associated with" ; @@ -3892,7 +4463,8 @@ biolink:decreased_likelihood_associated_with a owl:ObjectProperty ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:likelihood_associated_with ; owl:inverseOf biolink:associated_with_decreased_likelihood_of ; - skos:definition "" . + skos:definition "" ; + linkml:is_a "likelihood associated with" . biolink:decreases_amount_or_activity_of a owl:ObjectProperty ; rdfs:label "decreases amount or activity of" ; @@ -3900,7 +4472,8 @@ biolink:decreases_amount_or_activity_of a owl:ObjectProperty ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; owl:inverseOf biolink:amount_or_activity_decreased_by ; - skos:definition "A grouping mixin to help with searching for all the predicates that decrease the amount or activity of the object." . + skos:definition "A grouping mixin to help with searching for all the predicates that decrease the amount or activity of the object." ; + linkml:is_a "related to at instance level" . biolink:decreases_response_to a owl:ObjectProperty ; rdfs:label "decreases response to" ; @@ -3912,7 +4485,8 @@ biolink:decreases_response_to a owl:ObjectProperty ; skos:exactMatch CTD:decreases_response_to ; skos:narrowMatch CTD:decreases_response_to_substance ; biolink:canonical_predicate "True" ; - biolink:opposite_of "increases response to" . + biolink:opposite_of "increases response to" ; + linkml:is_a "affects response to" . biolink:develops_from a owl:ObjectProperty ; rdfs:label "develops from" ; @@ -3929,14 +4503,16 @@ biolink:develops_from a owl:ObjectProperty ; skos:narrowMatch RO:0002207, RO:0002225, RO:0002226 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:develops_into a owl:ObjectProperty ; rdfs:label "develops into" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; - owl:inverseOf biolink:develops_from . + owl:inverseOf biolink:develops_from ; + linkml:is_a "related to at instance level" . biolink:diagnoses a owl:ObjectProperty ; rdfs:label "diagnoses" ; @@ -3949,7 +4525,8 @@ biolink:diagnoses a owl:ObjectProperty ; skos:definition "a relationship that identifies the nature of (an illness or other problem) by examination of the symptoms." ; skos:exactMatch DrugCentral:5271, SEMMEDDB:DIAGNOSES ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:directly_physically_interacts_with a owl:ObjectProperty, owl:SymmetricProperty ; @@ -3965,7 +4542,8 @@ biolink:directly_physically_interacts_with a owl:ObjectProperty, , PHAROS:drug_targets, DGIdb:cofactor ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "physically interacts with" . biolink:disease_has_basis_in a owl:ObjectProperty ; rdfs:label "disease has basis in" ; @@ -3976,7 +4554,8 @@ biolink:disease_has_basis_in a owl:ObjectProperty ; skos:definition "A relation that holds between a disease and an entity where the state of the entity has contribution to the disease." ; skos:narrowMatch , ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:disease_has_location a owl:ObjectProperty ; rdfs:label "disease has location" ; @@ -3986,7 +4565,8 @@ biolink:disease_has_location a owl:ObjectProperty ; owl:inverseOf biolink:location_of_disease ; skos:definition "A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity." ; skos:exactMatch , - RO:0004026 . + RO:0004026 ; + linkml:is_a "related to" . biolink:disrupted_by a owl:ObjectProperty ; rdfs:label "disrupted by" ; @@ -3994,7 +4574,8 @@ biolink:disrupted_by a owl:ObjectProperty ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:affected_by ; owl:inverseOf biolink:disrupts ; - skos:definition "describes a relationship where the structure, function, or occurrence of one entity is degraded or interfered with by another." . + skos:definition "describes a relationship where the structure, function, or occurrence of one entity is degraded or interfered with by another." ; + linkml:is_a "affected by" . biolink:disrupts a owl:ObjectProperty ; rdfs:label "disrupts" ; @@ -4009,14 +4590,16 @@ biolink:disrupts a owl:ObjectProperty ; skos:narrowMatch RO:0004024, RO:0004025 ; biolink:canonical_predicate "True" ; - biolink:opposite_of "enables" . + biolink:opposite_of "enables" ; + linkml:is_a "affects" . biolink:distribution_download_url a owl:ObjectProperty ; rdfs:label "distribution download url" ; rdfs:domain biolink:DatasetDistribution ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:node_property ; - skos:exactMatch dcat:downloadURL . + skos:exactMatch dcat:downloadURL ; + linkml:is_a "node property" . biolink:drug_regulatory_status_world_wide a owl:ObjectProperty ; rdfs:label "drug regulatory status world wide" ; @@ -4053,7 +4636,8 @@ biolink:editor a owl:ObjectProperty ; rdfs:subPropertyOf biolink:contributor ; owl:inverseOf biolink:has_editor ; skos:definition "editor of a compiled work such as a book or a periodical (newspaper or an academic journal). Note that in the case of publications which have a containing \"published in\" node property, the editor association may not be attached directly to the embedded child publication, but only made in between the parent's publication node and the editorial agent of the encompassing publication (e.g. only from the Book referenced by the 'published_in' property of a book chapter Publication node)." ; - skos:exactMatch WIKIDATA_PROPERTY:P98 . + skos:exactMatch WIKIDATA_PROPERTY:P98 ; + linkml:is_a "contributor" . biolink:enables a owl:ObjectProperty ; rdfs:label "enables" ; @@ -4064,7 +4648,8 @@ biolink:enables a owl:ObjectProperty ; skos:definition "holds between a physical entity and a process, where the physical entity executes the process" ; skos:exactMatch RO:0002327 ; biolink:canonical_predicate "True" ; - biolink:opposite_of "prevents" . + biolink:opposite_of "prevents" ; + linkml:is_a "participates in" . biolink:end_interbase_coordinate a owl:ObjectProperty ; rdfs:label "end interbase coordinate" ; @@ -4073,7 +4658,8 @@ biolink:end_interbase_coordinate a owl:ObjectProperty ; rdfs:subPropertyOf biolink:interbase_coordinate ; skos:closeMatch ; skos:definition "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on." ; - biolink:opposite_of "start interbase coordinate" . + biolink:opposite_of "start interbase coordinate" ; + linkml:is_a "interbase coordinate" . biolink:exacerbates a owl:ObjectProperty ; rdfs:label "exacerbates" ; @@ -4084,7 +4670,8 @@ biolink:exacerbates a owl:ObjectProperty ; skos:broadMatch SEMMEDDB:COMPLICATES ; skos:definition "A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition." ; skos:exactMatch RO:0003309 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "affects" . biolink:expressed_in a owl:ObjectProperty ; rdfs:label "expressed in" ; @@ -4096,7 +4683,8 @@ biolink:expressed_in a owl:ObjectProperty ; skos:exactMatch RO:0002206 ; skos:narrowMatch , ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "located in" . biolink:expresses a owl:ObjectProperty ; rdfs:label "expresses" ; @@ -4106,7 +4694,8 @@ biolink:expresses a owl:ObjectProperty ; owl:inverseOf biolink:expressed_in ; skos:altLabel "anatomy expresses gene" ; skos:definition "holds between an anatomical entity and gene or gene product that is expressed there" ; - skos:exactMatch RO:0002292 . + skos:exactMatch RO:0002292 ; + linkml:is_a "location of" . biolink:format a owl:ObjectProperty ; rdfs:label "format" ; @@ -4114,7 +4703,8 @@ biolink:format a owl:ObjectProperty ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:node_property ; skos:exactMatch dct:format, - WIKIDATA_PROPERTY:P2701 . + WIKIDATA_PROPERTY:P2701 ; + linkml:is_a "node property" . biolink:gene_associated_with_condition a owl:ObjectProperty ; rdfs:label "gene associated with condition" ; @@ -4128,7 +4718,8 @@ biolink:gene_associated_with_condition a owl:ObjectProperty ; skos:narrowMatch , , ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "genetically associated with" . biolink:gene_product_of a owl:ObjectProperty ; rdfs:label "gene product of" ; @@ -4138,7 +4729,8 @@ biolink:gene_product_of a owl:ObjectProperty ; owl:inverseOf biolink:has_gene_product ; skos:definition "definition x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of thatf process is either y or something that is ribosomally translated from x" ; skos:exactMatch RO:0002204 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:genome_build a owl:ObjectProperty ; rdfs:label "genome build" ; @@ -4146,14 +4738,16 @@ biolink:genome_build a owl:ObjectProperty ; rdfs:range biolink:StrandEnum ; rdfs:subPropertyOf biolink:sequence_localization_attribute ; skos:definition "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens." ; - skos:exactMatch gff3:strand . + skos:exactMatch gff3:strand ; + linkml:is_a "sequence localization attribute" . biolink:has_active_component a owl:ObjectProperty ; rdfs:label "has active component" ; rdfs:domain biolink:CellularComponent ; rdfs:range biolink:GeneOrGeneProduct ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; - owl:inverseOf biolink:active_in . + owl:inverseOf biolink:active_in ; + linkml:is_a "related to at instance level" . biolink:has_active_ingredient a owl:ObjectProperty ; rdfs:label "has active ingredient" ; @@ -4164,7 +4758,8 @@ biolink:has_active_ingredient a owl:ObjectProperty ; skos:definition "holds between a drug and a molecular entity in which the latter is a part of the former, and is a biologically active component" ; skos:exactMatch RO:0002248 ; biolink:canonical_predicate "True" ; - biolink:opposite_of "is excipient of" . + biolink:opposite_of "is excipient of" ; + linkml:is_a "has part" . biolink:has_adverse_event a owl:ObjectProperty ; rdfs:label "has adverse event" ; @@ -4174,14 +4769,16 @@ biolink:has_adverse_event a owl:ObjectProperty ; owl:inverseOf biolink:adverse_event_of ; skos:altLabel "adverse effect" ; skos:definition "An untoward medical occurrence in a patient or clinical investigation subject that happens during treatment with a therapeutic agent. Adverse events may be caused by something other than the drug or therapy being given and may include abnormal laboratory finding, symptoms, or diseases temporally associated with the treatment, whether or not considered related to the treatment. Adverse events are unintended effects that occur when a medication is administered correctly." ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "affects" . biolink:has_author a owl:ObjectProperty ; rdfs:label "has author" ; rdfs:domain biolink:Publication ; rdfs:range biolink:Agent ; rdfs:subPropertyOf biolink:has_contributor ; - owl:inverseOf biolink:author . + owl:inverseOf biolink:author ; + linkml:is_a "has contributor" . biolink:has_biomarker a owl:ObjectProperty ; rdfs:label "has biomarker" ; @@ -4192,21 +4789,24 @@ biolink:has_biomarker a owl:ObjectProperty ; skos:definition """holds between a disease or phenotypic feature and a measurable chemical entity that is used as an indicator of the presence or state of the disease or feature. # metabolite""" ; skos:narrowMatch , - . + ; + linkml:is_a "correlated with" . biolink:has_catalyst a owl:ObjectProperty ; rdfs:label "has catalyst" ; rdfs:domain biolink:BiologicalProcessOrActivity ; rdfs:range biolink:Occurrent ; rdfs:subPropertyOf biolink:has_participant ; - owl:inverseOf biolink:catalyzes . + owl:inverseOf biolink:catalyzes ; + linkml:is_a "has participant" . biolink:has_chemical_role a owl:ObjectProperty ; rdfs:label "has chemical role" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:ChemicalRole ; rdfs:subPropertyOf biolink:related_to_at_concept_level ; - skos:definition "A role is particular behaviour which a chemical entity may exhibit." . + skos:definition "A role is particular behaviour which a chemical entity may exhibit." ; + linkml:is_a "related to at concept level" . biolink:has_completed a owl:ObjectProperty ; rdfs:label "has completed" ; @@ -4217,14 +4817,16 @@ biolink:has_completed a owl:ObjectProperty ; skos:definition "holds between an entity and a process that the entity is capable of and has completed" ; skos:exactMatch ; biolink:canonical_predicate "True" ; - biolink:opposite_of "has not completed" . + biolink:opposite_of "has not completed" ; + linkml:is_a "related to at instance level" . biolink:has_contraindication a owl:ObjectProperty ; rdfs:label "has contraindication" ; rdfs:domain biolink:DiseaseOrPhenotypicFeature ; rdfs:range biolink:Drug ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; - owl:inverseOf biolink:contraindicated_for . + owl:inverseOf biolink:contraindicated_for ; + linkml:is_a "related to at instance level" . biolink:has_decreased_amount a owl:ObjectProperty ; rdfs:label "has decreased amount" ; @@ -4234,28 +4836,32 @@ biolink:has_decreased_amount a owl:ObjectProperty ; owl:inverseOf biolink:decreased_amount_in ; skos:narrowMatch ; biolink:canonical_predicate "True" ; - biolink:opposite_of "has increased amount" . + biolink:opposite_of "has increased amount" ; + linkml:is_a "related to at instance level" . biolink:has_device a owl:ObjectProperty ; rdfs:label "has device" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:Device ; rdfs:subPropertyOf biolink:node_property ; - skos:definition "connects an entity to one or more (medical) devices" . + skos:definition "connects an entity to one or more (medical) devices" ; + linkml:is_a "node property" . biolink:has_drug a owl:ObjectProperty ; rdfs:label "has drug" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:Drug ; rdfs:subPropertyOf biolink:node_property ; - skos:definition "connects an entity to one or more drugs" . + skos:definition "connects an entity to one or more drugs" ; + linkml:is_a "node property" . biolink:has_editor a owl:ObjectProperty ; rdfs:label "has editor" ; rdfs:domain biolink:Publication ; rdfs:range biolink:Agent ; rdfs:subPropertyOf biolink:has_contributor ; - owl:inverseOf biolink:editor . + owl:inverseOf biolink:editor ; + linkml:is_a "has contributor" . biolink:has_excipient a owl:ObjectProperty ; rdfs:label "has excipient" ; @@ -4265,7 +4871,8 @@ biolink:has_excipient a owl:ObjectProperty ; owl:inverseOf biolink:is_excipient_of ; skos:definition "holds between a drug and a molecular entities in which the latter is a part of the former, and is a biologically inactive component" ; skos:exactMatch WIKIDATA:Q902638 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "has part" . biolink:has_frameshift_variant a owl:ObjectProperty ; rdfs:label "has frameshift variant" ; @@ -4275,14 +4882,16 @@ biolink:has_frameshift_variant a owl:ObjectProperty ; owl:inverseOf biolink:is_frameshift_variant_of ; skos:altLabel "splice acceptor variant", "splice donor variant", - "splice region variant" . + "splice region variant" ; + linkml:is_a "has sequence variant" . biolink:has_gene a owl:ObjectProperty ; rdfs:label "has gene" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:Gene ; rdfs:subPropertyOf biolink:has_gene_or_gene_product ; - skos:definition "connects an entity associated with one or more genes" . + skos:definition "connects an entity associated with one or more genes" ; + linkml:is_a "has gene or gene product" . biolink:has_gene_product a owl:ObjectProperty ; rdfs:label "has gene product" ; @@ -4295,7 +4904,8 @@ biolink:has_gene_product a owl:ObjectProperty ; skos:exactMatch , RO:0002205, WIKIDATA_PROPERTY:P688 ; - skos:narrowMatch . + skos:narrowMatch ; + linkml:is_a "related to at instance level" . biolink:has_increased_amount a owl:ObjectProperty ; rdfs:label "has increased amount" ; @@ -4305,7 +4915,8 @@ biolink:has_increased_amount a owl:ObjectProperty ; owl:inverseOf biolink:increased_amount_of ; skos:narrowMatch ; biolink:canonical_predicate "True" ; - biolink:opposite_of "has decreased amount" . + biolink:opposite_of "has decreased amount" ; + linkml:is_a "related to at instance level" . biolink:has_member a owl:ObjectProperty ; rdfs:label "has member" ; @@ -4315,7 +4926,8 @@ biolink:has_member a owl:ObjectProperty ; owl:inverseOf biolink:member_of ; skos:definition "Defines a mereological relation between a collection and an item." ; skos:exactMatch RO:0002351, - skos:member . + skos:member ; + linkml:is_a "related to at concept level" . biolink:has_metabolite a owl:ObjectProperty ; rdfs:label "has metabolite" ; @@ -4325,15 +4937,16 @@ biolink:has_metabolite a owl:ObjectProperty ; owl:inverseOf biolink:is_metabolite_of ; skos:definition "holds between two molecular entities in which the second one is derived from the first one as a product of metabolism" ; skos:exactMatch ; - skos:note "The CHEBI ID represents a role rather than a predicate" ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "derives into" . biolink:has_missense_variant a owl:ObjectProperty ; rdfs:label "has missense variant" ; rdfs:domain biolink:GenomicEntity ; rdfs:range biolink:SequenceVariant ; rdfs:subPropertyOf biolink:has_sequence_variant ; - owl:inverseOf biolink:is_missense_variant_of . + owl:inverseOf biolink:is_missense_variant_of ; + linkml:is_a "has sequence variant" . biolink:has_mode_of_inheritance a owl:ObjectProperty ; rdfs:label "has mode of inheritance" ; @@ -4342,7 +4955,8 @@ biolink:has_mode_of_inheritance a owl:ObjectProperty ; rdfs:subPropertyOf biolink:has_manifestation ; owl:inverseOf biolink:mode_of_inheritance_of ; skos:definition "Relates a disease or phenotypic feature to its observed genetic segregation and assumed associated underlying DNA manifestation (i.e. autosomal, sex or mitochondrial chromosome)." ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "has manifestation" . biolink:has_molecular_consequence a owl:ObjectProperty ; rdfs:label "has molecular consequence" ; @@ -4353,7 +4967,8 @@ biolink:has_molecular_consequence a owl:ObjectProperty ; skos:altLabel "allele has activity" ; skos:definition "connects a sequence variant to a class describing the molecular consequence. E.g. SO:0001583" ; skos:narrowMatch ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:has_nearby_variant a owl:ObjectProperty ; rdfs:label "has nearby variant" ; @@ -4365,35 +4980,40 @@ biolink:has_nearby_variant a owl:ObjectProperty ; "5 prime UTR premature start codon gain variant", "5 prime UTR variant", "intron variant", - "non coding transcript exon variant" . + "non coding transcript exon variant" ; + linkml:is_a "has sequence variant" . biolink:has_negative_upstream_actor a owl:ObjectProperty ; rdfs:label "has negative upstream actor" ; rdfs:domain biolink:BiologicalProcess ; rdfs:range biolink:GeneOrGeneProduct ; rdfs:subPropertyOf biolink:has_upstream_actor ; - owl:inverseOf biolink:acts_upstream_of_negative_effect . + owl:inverseOf biolink:acts_upstream_of_negative_effect ; + linkml:is_a "has upstream actor" . biolink:has_negative_upstream_or_within_actor a owl:ObjectProperty ; rdfs:label "has negative upstream or within actor" ; rdfs:domain biolink:BiologicalProcess ; rdfs:range biolink:GeneOrGeneProduct ; rdfs:subPropertyOf biolink:has_upstream_or_within_actor ; - owl:inverseOf biolink:acts_upstream_of_or_within_negative_effect . + owl:inverseOf biolink:acts_upstream_of_or_within_negative_effect ; + linkml:is_a "has upstream or within actor" . biolink:has_non_coding_variant a owl:ObjectProperty ; rdfs:label "has non coding variant" ; rdfs:domain biolink:GenomicEntity ; rdfs:range biolink:SequenceVariant ; rdfs:subPropertyOf biolink:has_sequence_variant ; - owl:inverseOf biolink:is_non_coding_variant_of . + owl:inverseOf biolink:is_non_coding_variant_of ; + linkml:is_a "has sequence variant" . biolink:has_nonsense_variant a owl:ObjectProperty ; rdfs:label "has nonsense variant" ; rdfs:domain biolink:GenomicEntity ; rdfs:range biolink:SequenceVariant ; rdfs:subPropertyOf biolink:has_sequence_variant ; - owl:inverseOf biolink:is_nonsense_variant_of . + owl:inverseOf biolink:is_nonsense_variant_of ; + linkml:is_a "has sequence variant" . biolink:has_not_completed a owl:ObjectProperty ; rdfs:label "has not completed" ; @@ -4404,7 +5024,8 @@ biolink:has_not_completed a owl:ObjectProperty ; skos:definition "holds between an entity and a process that the entity is capable of, but has not completed" ; skos:exactMatch ; biolink:canonical_predicate "True" ; - biolink:opposite_of "has completed" . + biolink:opposite_of "has completed" ; + linkml:is_a "related to at instance level" . biolink:has_numeric_value a owl:ObjectProperty ; rdfs:label "has numeric value" ; @@ -4421,7 +5042,8 @@ biolink:has_nutrient a owl:ObjectProperty ; owl:inverseOf biolink:nutrient_of ; skos:definition "one or more nutrients which are growth factors for a living organism" ; skos:exactMatch WIKIDATA:Q181394 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "has food component" . biolink:has_phenotype a owl:ObjectProperty ; rdfs:label "has phenotype" ; @@ -4433,12 +5055,12 @@ biolink:has_phenotype a owl:ObjectProperty ; skos:broadMatch , ; skos:definition "holds between a biological entity and a phenotype, where a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). In SNOMEDCT, disorders with keyword 'characterized by' should translate into this predicate." ; - skos:editorialNote "check the range" ; skos:exactMatch RO:0002200 ; skos:narrowMatch , RO:0004022, DOID-PROPERTY:has_symptom ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:has_plasma_membrane_part a owl:ObjectProperty ; rdfs:label "has plasma membrane part" ; @@ -4448,49 +5070,56 @@ biolink:has_plasma_membrane_part a owl:ObjectProperty ; owl:inverseOf biolink:plasma_membrane_part_of ; skos:definition "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." ; skos:exactMatch RO:0002104 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "has part" . biolink:has_positive_upstream_actor a owl:ObjectProperty ; rdfs:label "has positive upstream actor" ; rdfs:domain biolink:BiologicalProcess ; rdfs:range biolink:GeneOrGeneProduct ; rdfs:subPropertyOf biolink:has_upstream_actor ; - owl:inverseOf biolink:acts_upstream_of_positive_effect . + owl:inverseOf biolink:acts_upstream_of_positive_effect ; + linkml:is_a "has upstream actor" . biolink:has_positive_upstream_or_within_actor a owl:ObjectProperty ; rdfs:label "has positive upstream or within actor" ; rdfs:domain biolink:BiologicalProcess ; rdfs:range biolink:GeneOrGeneProduct ; rdfs:subPropertyOf biolink:has_upstream_or_within_actor ; - owl:inverseOf biolink:acts_upstream_of_or_within_positive_effect . + owl:inverseOf biolink:acts_upstream_of_or_within_positive_effect ; + linkml:is_a "has upstream or within actor" . biolink:has_predisposing_factor a owl:ObjectProperty ; rdfs:label "has predisposing factor" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:risk_affected_by ; - owl:inverseOf biolink:predisposes . + owl:inverseOf biolink:predisposes ; + linkml:is_a "risk affected by" . biolink:has_procedure a owl:ObjectProperty ; rdfs:label "has procedure" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:Procedure ; rdfs:subPropertyOf biolink:node_property ; - skos:definition "connects an entity to one or more (medical) procedures" . + skos:definition "connects an entity to one or more (medical) procedures" ; + linkml:is_a "node property" . biolink:has_provider a owl:ObjectProperty ; rdfs:label "has provider" ; rdfs:domain biolink:InformationContentEntity ; rdfs:range biolink:Agent ; rdfs:subPropertyOf biolink:has_contributor ; - owl:inverseOf biolink:provider . + owl:inverseOf biolink:provider ; + linkml:is_a "has contributor" . biolink:has_publisher a owl:ObjectProperty ; rdfs:label "has publisher" ; rdfs:domain biolink:Publication ; rdfs:range biolink:Agent ; rdfs:subPropertyOf biolink:has_contributor ; - owl:inverseOf biolink:publisher . + owl:inverseOf biolink:publisher ; + linkml:is_a "has contributor" . biolink:has_qualitative_value a owl:ObjectProperty ; rdfs:label "has qualitative value" ; @@ -4516,7 +5145,8 @@ biolink:has_sequence_location a owl:ObjectProperty ; owl:inverseOf biolink:sequence_location_of ; skos:definition "holds between two nucleic acid entities when the subject can be localized in sequence coordinates on the object. For example, between an exon and a chromosome/contig." ; skos:exactMatch ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:has_side_effect a owl:ObjectProperty ; rdfs:label "has side effect" ; @@ -4526,9 +5156,9 @@ biolink:has_side_effect a owl:ObjectProperty ; owl:inverseOf biolink:is_side_effect_of ; skos:altLabel "adverse drug reaction" ; skos:definition "An unintended, but predictable, secondary effect shown to be correlated with a therapeutic agent, drug or treatment. Side effects happen at normal, recommended doses or treatments, and are unrelated to the intended purpose of the medication." ; - skos:editorialNote "Side effects are listed on drug labels. There can be positive side effects, while adverse events are always negative. Aeolus, Sider are both resources that provide side effects." ; skos:exactMatch ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "affects" . biolink:has_splice_site_variant a owl:ObjectProperty ; rdfs:label "has splice site variant" ; @@ -4537,7 +5167,8 @@ biolink:has_splice_site_variant a owl:ObjectProperty ; rdfs:subPropertyOf biolink:has_sequence_variant ; owl:inverseOf biolink:is_splice_site_variant_of ; skos:altLabel "downstream gene variant", - "upstream gene variant" . + "upstream gene variant" ; + linkml:is_a "has sequence variant" . biolink:has_substrate a owl:ObjectProperty ; rdfs:label "has substrate" ; @@ -4545,7 +5176,8 @@ biolink:has_substrate a owl:ObjectProperty ; rdfs:range biolink:ChemicalEntityOrGeneOrGeneProduct ; rdfs:subPropertyOf biolink:has_participant ; owl:inverseOf biolink:is_substrate_of ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "has participant" . biolink:has_synonymous_variant a owl:ObjectProperty ; rdfs:label "has synonymous variant" ; @@ -4553,21 +5185,24 @@ biolink:has_synonymous_variant a owl:ObjectProperty ; rdfs:range biolink:SequenceVariant ; rdfs:subPropertyOf biolink:has_sequence_variant ; owl:inverseOf biolink:is_synonymous_variant_of ; - skos:altLabel "stop gained" . + skos:altLabel "stop gained" ; + linkml:is_a "has sequence variant" . biolink:has_target a owl:ObjectProperty ; rdfs:label "has target" ; rdfs:domain biolink:Disease ; rdfs:range biolink:Gene ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; - owl:inverseOf biolink:target_for . + owl:inverseOf biolink:target_for ; + linkml:is_a "related to at instance level" . biolink:has_taxonomic_rank a owl:ObjectProperty ; rdfs:label "has taxonomic rank" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:TaxonomicRank ; rdfs:subPropertyOf biolink:node_property ; - skos:exactMatch WIKIDATA:P105 . + skos:exactMatch WIKIDATA:P105 ; + linkml:is_a "node property" . biolink:has_unit a owl:ObjectProperty ; rdfs:label "has unit" ; @@ -4592,13 +5227,15 @@ biolink:has_variant_part a owl:ObjectProperty ; owl:inverseOf biolink:variant_part_of ; skos:definition "holds between a nucleic acid entity and a nucleic acid entity that is a sub-component of it" ; skos:exactMatch ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "has part" . biolink:has_zygosity a owl:ObjectProperty ; rdfs:label "has zygosity" ; rdfs:domain biolink:NucleicAcidEntity ; rdfs:range biolink:Zygosity ; - rdfs:subPropertyOf biolink:node_property . + rdfs:subPropertyOf biolink:node_property ; + linkml:is_a "node property" . biolink:highest_FDA_approval_status a owl:ObjectProperty ; rdfs:label "highest FDA approval status" ; @@ -4610,7 +5247,8 @@ biolink:increased_amount_of a owl:ObjectProperty ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; - owl:inverseOf biolink:has_increased_amount . + owl:inverseOf biolink:has_increased_amount ; + linkml:is_a "related to at instance level" . biolink:increased_likelihood_associated_with a owl:ObjectProperty ; rdfs:label "increased likelihood associated with" ; @@ -4618,7 +5256,8 @@ biolink:increased_likelihood_associated_with a owl:ObjectProperty ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:likelihood_associated_with ; owl:inverseOf biolink:associated_with_increased_likelihood_of ; - skos:definition "" . + skos:definition "" ; + linkml:is_a "likelihood associated with" . biolink:increases_amount_or_activity_of a owl:ObjectProperty ; rdfs:label "increases amount or activity of" ; @@ -4626,7 +5265,8 @@ biolink:increases_amount_or_activity_of a owl:ObjectProperty ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; owl:inverseOf biolink:amount_or_activity_increased_by ; - skos:definition "A grouping mixin to help with searching for all the predicates that increase the amount or activity of the object." . + skos:definition "A grouping mixin to help with searching for all the predicates that increase the amount or activity of the object." ; + linkml:is_a "related to at instance level" . biolink:increases_response_to a owl:ObjectProperty ; rdfs:label "increases response to" ; @@ -4637,19 +5277,8 @@ biolink:increases_response_to a owl:ObjectProperty ; skos:definition "holds between two chemical entities where the action or effect of one increases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) to the other" ; skos:exactMatch CTD:increases_response_to ; biolink:canonical_predicate "True" ; - biolink:opposite_of "decreases response to" . - -biolink:information_resource_status a owl:ObjectProperty ; - rdfs:label "information resource status" ; - rdfs:domain biolink:NamedThing ; - rdfs:range biolink:InformationResourceStatusEnum ; - rdfs:subPropertyOf biolink:node_property ; - skos:definition "the status of the infores identifier, default is released" . - -biolink:information_resources a owl:ObjectProperty ; - rdfs:label "information resources" ; - rdfs:range biolink:InformationResource ; - skos:definition "a collection of information resources" . + biolink:opposite_of "decreases response to" ; + linkml:is_a "affects response to" . biolink:interacting_molecules_category a owl:ObjectProperty ; rdfs:label "interacting molecules category" ; @@ -4657,7 +5286,7 @@ biolink:interacting_molecules_category a owl:ObjectProperty ; rdfs:range biolink:OntologyClass ; rdfs:subPropertyOf biolink:association_slot ; skos:exactMatch MI:1046 ; - linkml:examples "Example(value='MI:1048', description='smallmolecule-protein')" . + linkml:is_a "association slot" . biolink:iri a owl:ObjectProperty ; rdfs:label "iri" ; @@ -4672,28 +5301,32 @@ biolink:is_active_ingredient_of a owl:ObjectProperty ; rdfs:subPropertyOf biolink:part_of ; owl:inverseOf biolink:has_active_ingredient ; skos:definition "holds between a molecular entity and a drug, in which the former is a part of the latter, and is a biologically active component" ; - skos:exactMatch RO:0002249 . + skos:exactMatch RO:0002249 ; + linkml:is_a "part of" . biolink:is_assessed_by a owl:ObjectProperty ; rdfs:label "is assessed by" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; - owl:inverseOf biolink:assesses . + owl:inverseOf biolink:assesses ; + linkml:is_a "related to at instance level" . biolink:is_diagnosed_by a owl:ObjectProperty ; rdfs:label "is diagnosed by" ; rdfs:domain biolink:DiseaseOrPhenotypicFeature ; rdfs:range biolink:DiagnosticAid ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; - owl:inverseOf biolink:diagnoses . + owl:inverseOf biolink:diagnoses ; + linkml:is_a "related to at instance level" . biolink:is_exacerbated_by a owl:ObjectProperty ; rdfs:label "is exacerbated by" ; rdfs:domain biolink:DiseaseOrPhenotypicFeature ; rdfs:range biolink:BiologicalEntity ; rdfs:subPropertyOf biolink:affected_by ; - owl:inverseOf biolink:exacerbates . + owl:inverseOf biolink:exacerbates ; + linkml:is_a "affected by" . biolink:is_excipient_of a owl:ObjectProperty ; rdfs:label "is excipient of" ; @@ -4702,7 +5335,8 @@ biolink:is_excipient_of a owl:ObjectProperty ; rdfs:subPropertyOf biolink:part_of ; owl:inverseOf biolink:has_excipient ; skos:definition "holds between a molecular entity and a drug in which the former is a part of the latter, and is a biologically inactive component" ; - skos:exactMatch WIKIDATA:Q902638 . + skos:exactMatch WIKIDATA:Q902638 ; + linkml:is_a "part of" . biolink:is_frameshift_variant_of a owl:ObjectProperty ; rdfs:label "is frameshift variant of" ; @@ -4715,7 +5349,8 @@ biolink:is_frameshift_variant_of a owl:ObjectProperty ; "stop lost" ; skos:definition "holds between a sequence variant and a gene, such the sequence variant causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." ; skos:exactMatch ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "is sequence variant of" . biolink:is_metabolite a owl:ObjectProperty ; rdfs:label "is metabolite" ; @@ -4723,7 +5358,8 @@ biolink:is_metabolite a owl:ObjectProperty ; rdfs:range linkml:Boolean ; rdfs:subPropertyOf biolink:node_property ; skos:definition "indicates whether a molecular entity is a metabolite" ; - skos:exactMatch . + skos:exactMatch ; + linkml:is_a "node property" . biolink:is_metabolite_of a owl:ObjectProperty ; rdfs:label "is metabolite of" ; @@ -4733,7 +5369,7 @@ biolink:is_metabolite_of a owl:ObjectProperty ; owl:inverseOf biolink:has_metabolite ; skos:definition "holds between two molecular entities in which the first one is derived from the second one as a product of metabolism" ; skos:exactMatch ; - skos:note "The CHEBI ID represents a role rather than a predicate" . + linkml:is_a "derives from" . biolink:is_missense_variant_of a owl:ObjectProperty ; rdfs:label "is missense variant of" ; @@ -4743,14 +5379,16 @@ biolink:is_missense_variant_of a owl:ObjectProperty ; owl:inverseOf biolink:has_missense_variant ; skos:definition "holds between a gene and a sequence variant, such the sequence variant results in a different amino acid sequence but where the length is preserved." ; skos:exactMatch ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "is sequence variant of" . biolink:is_molecular_consequence_of a owl:ObjectProperty ; rdfs:label "is molecular consequence of" ; rdfs:domain biolink:OntologyClass ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; - owl:inverseOf biolink:has_molecular_consequence . + owl:inverseOf biolink:has_molecular_consequence ; + linkml:is_a "related to at instance level" . biolink:is_nearby_variant_of a owl:ObjectProperty ; rdfs:label "is nearby variant of" ; @@ -4759,7 +5397,8 @@ biolink:is_nearby_variant_of a owl:ObjectProperty ; rdfs:subPropertyOf biolink:is_sequence_variant_of ; owl:inverseOf biolink:has_nearby_variant ; skos:definition "holds between a sequence variant and a gene sequence that the variant is genomically close to." ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "is sequence variant of" . biolink:is_non_coding_variant_of a owl:ObjectProperty ; rdfs:label "is non coding variant of" ; @@ -4768,7 +5407,8 @@ biolink:is_non_coding_variant_of a owl:ObjectProperty ; rdfs:subPropertyOf biolink:is_sequence_variant_of ; owl:inverseOf biolink:has_non_coding_variant ; skos:definition "holds between a sequence variant and a gene, where the variant does not affect the coding sequence" ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "is sequence variant of" . biolink:is_nonsense_variant_of a owl:ObjectProperty ; rdfs:label "is nonsense variant of" ; @@ -4778,7 +5418,8 @@ biolink:is_nonsense_variant_of a owl:ObjectProperty ; owl:inverseOf biolink:has_nonsense_variant ; skos:broadMatch ; skos:definition "holds between a sequence variant and a gene, such the sequence variant results in a premature stop codon" ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "is sequence variant of" . biolink:is_output_of a owl:ObjectProperty ; rdfs:label "is output of" ; @@ -4787,14 +5428,16 @@ biolink:is_output_of a owl:ObjectProperty ; rdfs:subPropertyOf biolink:participates_in ; owl:inverseOf biolink:has_output ; skos:exactMatch RO:0002353 ; - skos:narrowMatch RO:0002354 . + skos:narrowMatch RO:0002354 ; + linkml:is_a "participates in" . biolink:is_side_effect_of a owl:ObjectProperty ; rdfs:label "is side effect of" ; rdfs:domain biolink:DiseaseOrPhenotypicFeature ; rdfs:range biolink:ChemicalOrDrugOrTreatment ; rdfs:subPropertyOf biolink:affected_by ; - owl:inverseOf biolink:has_side_effect . + owl:inverseOf biolink:has_side_effect ; + linkml:is_a "affected by" . biolink:is_splice_site_variant_of a owl:ObjectProperty ; rdfs:label "is splice site variant of" ; @@ -4804,21 +5447,24 @@ biolink:is_splice_site_variant_of a owl:ObjectProperty ; owl:inverseOf biolink:has_splice_site_variant ; skos:definition "holds between a sequence variant and a gene, such the sequence variant is in the canonical splice site of one of the gene's exons." ; skos:exactMatch ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "is sequence variant of" . biolink:is_substrate_of a owl:ObjectProperty ; rdfs:label "is substrate of" ; rdfs:domain biolink:ChemicalEntityOrGeneOrGeneProduct ; rdfs:range biolink:ChemicalEntityOrGeneOrGeneProduct ; rdfs:subPropertyOf biolink:participates_in ; - owl:inverseOf biolink:has_substrate . + owl:inverseOf biolink:has_substrate ; + linkml:is_a "participates in" . biolink:is_supplement a owl:ObjectProperty ; rdfs:label "is supplement" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:ChemicalMixture ; rdfs:subPropertyOf biolink:node_property ; - skos:definition "" . + skos:definition "" ; + linkml:is_a "node property" . biolink:is_synonymous_variant_of a owl:ObjectProperty ; rdfs:label "is synonymous variant of" ; @@ -4828,21 +5474,24 @@ biolink:is_synonymous_variant_of a owl:ObjectProperty ; owl:inverseOf biolink:has_synonymous_variant ; skos:definition "holds between a sequence variant and a gene, such the sequence variant is in the coding sequence of the gene, but results in the same amino acid sequence" ; skos:exactMatch ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "is sequence variant of" . biolink:is_toxic a owl:ObjectProperty ; rdfs:label "is toxic" ; rdfs:domain biolink:NamedThing ; rdfs:range linkml:Boolean ; rdfs:subPropertyOf biolink:node_property ; - skos:definition "" . + skos:definition "" ; + linkml:is_a "node property" . biolink:keywords a owl:ObjectProperty ; rdfs:label "keywords" ; rdfs:domain biolink:Publication ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:node_property ; - skos:definition "keywords tagging a publication" . + skos:definition "keywords tagging a publication" ; + linkml:is_a "node property" . biolink:lacks_part a owl:ObjectProperty ; rdfs:label "lacks part" ; @@ -4854,7 +5503,8 @@ biolink:lacks_part a owl:ObjectProperty ; ; skos:narrowMatch ; biolink:canonical_predicate "True" ; - biolink:opposite_of "has part" . + biolink:opposite_of "has part" ; + linkml:is_a "related to at instance level" . biolink:latitude a owl:ObjectProperty ; rdfs:label "latitude" ; @@ -4862,7 +5512,8 @@ biolink:latitude a owl:ObjectProperty ; rdfs:range linkml:Float ; rdfs:subPropertyOf biolink:node_property ; skos:definition "latitude" ; - skos:exactMatch wgs:lat . + skos:exactMatch wgs:lat ; + linkml:is_a "node property" . biolink:license a owl:ObjectProperty ; rdfs:label "license" ; @@ -4870,14 +5521,16 @@ biolink:license a owl:ObjectProperty ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:node_property ; skos:exactMatch dct:license ; - skos:narrowMatch WIKIDATA_PROPERTY:P275 . + skos:narrowMatch WIKIDATA_PROPERTY:P275 ; + linkml:is_a "node property" . biolink:location_of_disease a owl:ObjectProperty ; rdfs:label "location of disease" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:related_to ; - owl:inverseOf biolink:disease_has_location . + owl:inverseOf biolink:disease_has_location ; + linkml:is_a "related to" . biolink:longitude a owl:ObjectProperty ; rdfs:label "longitude" ; @@ -4885,7 +5538,8 @@ biolink:longitude a owl:ObjectProperty ; rdfs:range linkml:Float ; rdfs:subPropertyOf biolink:node_property ; skos:definition "longitude" ; - skos:exactMatch wgs:long . + skos:exactMatch wgs:long ; + linkml:is_a "node property" . biolink:mapped_predicate a owl:ObjectProperty ; rdfs:label "mapped predicate" ; @@ -4897,7 +5551,8 @@ biolink:max_tolerated_dose a owl:ObjectProperty ; rdfs:domain biolink:NamedThing ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:node_property ; - skos:definition "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." . + skos:definition "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + linkml:is_a "node property" . biolink:member_of a owl:ObjectProperty ; rdfs:label "member of" ; @@ -4907,7 +5562,8 @@ biolink:member_of a owl:ObjectProperty ; owl:inverseOf biolink:has_member ; skos:closeMatch skos:member ; skos:definition "Defines a mereological relation between a item and a collection." ; - skos:exactMatch RO:0002350 . + skos:exactMatch RO:0002350 ; + linkml:is_a "related to at concept level" . biolink:mentioned_by a owl:ObjectProperty ; rdfs:label "mentioned by" ; @@ -4915,7 +5571,8 @@ biolink:mentioned_by a owl:ObjectProperty ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; owl:inverseOf biolink:mentions ; - skos:definition "refers to is a relation between one named thing and the information content entity that it makes reference to." . + skos:definition "refers to is a relation between one named thing and the information content entity that it makes reference to." ; + linkml:is_a "related to at instance level" . biolink:mentions a owl:ObjectProperty ; rdfs:label "mentions" ; @@ -4925,7 +5582,8 @@ biolink:mentions a owl:ObjectProperty ; owl:inverseOf biolink:mentioned_by ; skos:definition "refers to is a relation between one information content entity and the named thing that it makes reference to." ; skos:exactMatch IAO:0000142 ; - skos:narrowMatch SIO:000628 . + skos:narrowMatch SIO:000628 ; + linkml:is_a "related to at instance level" . biolink:mesh_terms a owl:ObjectProperty ; rdfs:label "mesh terms" ; @@ -4933,21 +5591,24 @@ biolink:mesh_terms a owl:ObjectProperty ; rdfs:range linkml:Uriorcurie ; rdfs:subPropertyOf biolink:node_property ; skos:definition "mesh terms tagging a publication" ; - skos:exactMatch dcid:MeSHTerm . + skos:exactMatch dcid:MeSHTerm ; + linkml:is_a "node property" . biolink:missing_from a owl:ObjectProperty ; rdfs:label "missing from" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; - owl:inverseOf biolink:lacks_part . + owl:inverseOf biolink:lacks_part ; + linkml:is_a "related to at instance level" . biolink:mode_of_inheritance_of a owl:ObjectProperty ; rdfs:label "mode of inheritance of" ; rdfs:domain biolink:GeneticInheritance ; rdfs:range biolink:DiseaseOrPhenotypicFeature ; rdfs:subPropertyOf biolink:manifestation_of ; - owl:inverseOf biolink:has_mode_of_inheritance . + owl:inverseOf biolink:has_mode_of_inheritance ; + linkml:is_a "manifestation of" . biolink:model_of a owl:ObjectProperty ; rdfs:label "model of" ; @@ -4958,28 +5619,32 @@ biolink:model_of a owl:ObjectProperty ; skos:definition "holds between a thing and some other thing it approximates for purposes of scientific study, in virtue of its exhibiting similar features of the studied entity." ; skos:exactMatch RO:0003301 ; skos:narrowMatch ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:models a owl:ObjectProperty ; rdfs:label "models" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; - owl:inverseOf biolink:model_of . + owl:inverseOf biolink:model_of ; + linkml:is_a "related to at instance level" . biolink:negated a owl:ObjectProperty ; rdfs:label "negated" ; rdfs:domain biolink:Association ; rdfs:range linkml:Boolean ; rdfs:subPropertyOf biolink:association_slot ; - skos:definition "if set to true, then the association is negated i.e. is not true" . + skos:definition "if set to true, then the association is negated i.e. is not true" ; + linkml:is_a "association slot" . biolink:not_completed_by a owl:ObjectProperty ; rdfs:label "not completed by" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; - owl:inverseOf biolink:has_not_completed . + owl:inverseOf biolink:has_not_completed ; + linkml:is_a "related to at instance level" . biolink:nutrient_of a owl:ObjectProperty ; rdfs:label "nutrient of" ; @@ -4987,7 +5652,8 @@ biolink:nutrient_of a owl:ObjectProperty ; rdfs:range biolink:ChemicalEntity ; rdfs:subPropertyOf biolink:food_component_of ; owl:inverseOf biolink:has_nutrient ; - skos:definition "holds between a one or more chemical entities present in food, irrespective of nutritional value (i.e. could also be a contaminant or additive)" . + skos:definition "holds between a one or more chemical entities present in food, irrespective of nutritional value (i.e. could also be a contaminant or additive)" ; + linkml:is_a "food component of" . biolink:object_category a owl:ObjectProperty ; rdfs:label "object category" ; @@ -4996,7 +5662,7 @@ biolink:object_category a owl:ObjectProperty ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; biolink:denormalized "True" ; - linkml:examples "Example(value='biolink:Disease', description=\"The object category of the association between the gene 'BRCA1' and the disease 'breast cancer' is 'biolink:Disease'.\")" . + linkml:is_a "association slot" . biolink:object_category_closure a owl:ObjectProperty ; rdfs:label "object category closure" ; @@ -5005,7 +5671,7 @@ biolink:object_category_closure a owl:ObjectProperty ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; biolink:denormalized "True" ; - linkml:examples "Example(value='[\\'biolink:Disease\", \"biolink:NamedThing\\']', description='The object category closure of the association between the gene \\'BRCA1\\' and the disease \\'breast cancer\\' is the set of all biolink classes that are ancestors of \\'biolink:Disease\\' in the biolink model. Note: typically the \"subclass of\" and \"part of\" relations are used to construct the closure, but other relations may be used as well.')" . + linkml:is_a "association slot" . biolink:object_closure a owl:ObjectProperty ; rdfs:label "object closure" ; @@ -5014,13 +5680,14 @@ biolink:object_closure a owl:ObjectProperty ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; biolink:denormalized "True" ; - linkml:examples "Example(value=\"['MONDO:0000167', 'MONDO:0005395']\", description='The object closure of the association between the gene \\'BRCA1\\' and the disease \\'breast cancer\\' is the set of all diseases that are ancestors of \\'breast cancer\\' in the MONDO ontology. Note: typically the \"subclass of\" and \"part of\" relations are used to construct the closure, but other relations may be used as well.')" . + linkml:is_a "association slot" . biolink:object_derivative_qualifier a owl:ObjectProperty ; rdfs:label "object derivative qualifier" ; rdfs:domain biolink:Association ; rdfs:range linkml:String ; - rdfs:subPropertyOf biolink:derivative_qualifier . + rdfs:subPropertyOf biolink:derivative_qualifier ; + linkml:is_a "derivative qualifier" . biolink:object_label_closure a owl:ObjectProperty ; rdfs:label "object label closure" ; @@ -5029,7 +5696,7 @@ biolink:object_label_closure a owl:ObjectProperty ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; biolink:denormalized "True" ; - linkml:examples "Example(value=\"['breast cancer', 'cancer']\", description=\"The object label closure of the association between the gene 'BRCA1' and the disease 'breast cancer' is the set of all labels that are ancestors of 'breast cancer' in the biolink model.\")" . + linkml:is_a "association slot" . biolink:object_namespace a owl:ObjectProperty ; rdfs:label "object namespace" ; @@ -5039,7 +5706,7 @@ biolink:object_namespace a owl:ObjectProperty ; skos:altLabel "object prefix" ; skos:definition "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; biolink:denormalized "True" ; - linkml:examples "Example(value='MONDO', description=\"The object namespace of the association between the gene 'BRCA1' and the disease 'breast cancer' is 'MONDO'.\")" . + linkml:is_a "association slot" . biolink:occurs_in a owl:ObjectProperty ; rdfs:label "occurs in" ; @@ -5064,21 +5731,24 @@ biolink:occurs_in a owl:ObjectProperty ; PathWhiz:in_species, SEMMEDDB:OCCURS_IN, SEMMEDDB:PROCESS_OF ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:occurs_in_disease a owl:ObjectProperty ; rdfs:label "occurs in disease" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; - owl:inverseOf biolink:disease_has_basis_in . + owl:inverseOf biolink:disease_has_basis_in ; + linkml:is_a "related to at instance level" . biolink:original_object a owl:ObjectProperty ; rdfs:label "original object" ; rdfs:domain biolink:Association ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:association_slot ; - skos:definition "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." . + skos:definition "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + linkml:is_a "association slot" . biolink:original_predicate a owl:ObjectProperty ; rdfs:label "original predicate" ; @@ -5087,14 +5757,16 @@ biolink:original_predicate a owl:ObjectProperty ; rdfs:subPropertyOf biolink:association_slot ; skos:altLabel "original relation", "relation" ; - skos:definition "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." . + skos:definition "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + linkml:is_a "association slot" . biolink:original_subject a owl:ObjectProperty ; rdfs:label "original subject" ; rdfs:domain biolink:Association ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:association_slot ; - skos:definition "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." . + skos:definition "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + linkml:is_a "association slot" . biolink:p_value a owl:ObjectProperty ; rdfs:label "p value" ; @@ -5105,7 +5777,8 @@ biolink:p_value a owl:ObjectProperty ; skos:definition "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; skos:exactMatch EDAM-DATA:1669, , - . + ; + linkml:is_a "association slot" . biolink:pages a owl:ObjectProperty ; rdfs:label "pages" ; @@ -5113,7 +5786,8 @@ biolink:pages a owl:ObjectProperty ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:node_property ; skos:definition "page number of source referenced for statement or publication" ; - skos:exactMatch WIKIDATA_PROPERTY:P304 . + skos:exactMatch WIKIDATA_PROPERTY:P304 ; + linkml:is_a "node property" . biolink:phase a owl:ObjectProperty ; rdfs:label "phase" ; @@ -5121,28 +5795,32 @@ biolink:phase a owl:ObjectProperty ; rdfs:range biolink:PhaseEnum ; rdfs:subPropertyOf biolink:sequence_localization_attribute ; skos:definition "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2." ; - skos:exactMatch gff3:phase . + skos:exactMatch gff3:phase ; + linkml:is_a "sequence localization attribute" . biolink:phenotype_of a owl:ObjectProperty ; rdfs:label "phenotype of" ; rdfs:domain biolink:PhenotypicFeature ; rdfs:range biolink:BiologicalEntity ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; - owl:inverseOf biolink:has_phenotype . + owl:inverseOf biolink:has_phenotype ; + linkml:is_a "related to at instance level" . biolink:plasma_membrane_part_of a owl:ObjectProperty ; rdfs:label "plasma membrane part of" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:part_of ; - owl:inverseOf biolink:has_plasma_membrane_part . + owl:inverseOf biolink:has_plasma_membrane_part ; + linkml:is_a "part of" . biolink:population_context_qualifier a owl:ObjectProperty ; rdfs:label "population context qualifier" ; rdfs:domain biolink:Association ; rdfs:range biolink:PopulationOfIndividualOrganisms ; rdfs:subPropertyOf biolink:qualifier ; - skos:definition "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." . + skos:definition "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; + linkml:is_a "qualifier" . biolink:preceded_by a owl:ObjectProperty ; rdfs:label "preceded by" ; @@ -5155,7 +5833,8 @@ biolink:preceded_by a owl:ObjectProperty ; skos:exactMatch ; skos:narrowMatch , RO:0002087, - RO:0002285 . + RO:0002285 ; + linkml:is_a "temporally related to" . biolink:precedes a owl:ObjectProperty ; rdfs:label "precedes" ; @@ -5174,7 +5853,8 @@ biolink:precedes a owl:ObjectProperty ; RO:0002090, RO:0002411, RO:0002412 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "temporally related to" . biolink:predicate_mappings a owl:ObjectProperty ; rdfs:label "predicate mappings" ; @@ -5190,7 +5870,8 @@ biolink:predisposes a owl:ObjectProperty ; skos:definition "holds between two entities where exposure to one entity increases the chance of developing the other" ; skos:exactMatch SEMMEDDB:PREDISPOSES ; biolink:canonical_predicate "True" ; - biolink:opposite_of "prevents" . + biolink:opposite_of "prevents" ; + linkml:is_a "affects risk for" . biolink:prevented_by a owl:ObjectProperty ; rdfs:label "prevented by" ; @@ -5199,7 +5880,8 @@ biolink:prevented_by a owl:ObjectProperty ; rdfs:subPropertyOf biolink:risk_affected_by ; owl:inverseOf biolink:prevents ; skos:definition "holds between a potential outcome of which the likelihood was reduced by the application or use of an entity." ; - biolink:opposite_of "enabled by" . + biolink:opposite_of "enabled by" ; + linkml:is_a "risk affected by" . biolink:prevents a owl:ObjectProperty ; rdfs:label "prevents" ; @@ -5211,22 +5893,24 @@ biolink:prevents a owl:ObjectProperty ; skos:exactMatch SEMMEDDB:PREVENTS ; skos:narrowMatch RO:0002599 ; biolink:canonical_predicate "True" ; - biolink:opposite_of "predisposes" . + biolink:opposite_of "predisposes" ; + linkml:is_a "affects risk for" . biolink:primarily_composed_of a owl:ObjectProperty ; rdfs:label "primarily composed of" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:related_to ; - owl:inverseOf biolink:composed_primarily_of . + owl:inverseOf biolink:composed_primarily_of ; + linkml:is_a "related to" . biolink:primary_knowledge_source a owl:ObjectProperty ; rdfs:label "primary knowledge source" ; rdfs:domain biolink:Association ; - rdfs:range biolink:InformationResource ; + rdfs:range linkml:String ; rdfs:subPropertyOf biolink:knowledge_source ; skos:definition "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - skos:editorialNote "For example: a single ChemicalToGene Edge originally curated by ClinicalTrials.org, is aggregated by ChEMBL, then incorporated into the MolePro KP, then sent via TRAPI message to the ARAGORN ARA, and finally sent to the NCATS ARS. The retrieval path for this Edge is as follows: ARS--retrieved_from--> ARAGORN --retrieved_from--> MolePro --retrieved_from--> ChEMBL --retrieved_from--> ClinicalTrials.gov The \"primary knowledge source\" for this edge is \"infores:clinical-trials-gov\". \"infores:chembl\" and \"infores:molecular_data_provider\" are listed in the \"aggregator knowledge source\" property." . + linkml:is_a "knowledge source" . biolink:produced_by a owl:ObjectProperty ; rdfs:label "produced by" ; @@ -5234,7 +5918,8 @@ biolink:produced_by a owl:ObjectProperty ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; owl:inverseOf biolink:produces ; - skos:exactMatch RO:0003001 . + skos:exactMatch RO:0003001 ; + linkml:is_a "related to at instance level" . biolink:produces a owl:ObjectProperty ; rdfs:label "produces" ; @@ -5250,14 +5935,16 @@ biolink:produces a owl:ObjectProperty ; , ; skos:relatedMatch GOREL:0001010 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:provided_by a owl:ObjectProperty ; rdfs:label "provided by" ; rdfs:domain biolink:NamedThing ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:node_property ; - skos:definition "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." . + skos:definition "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + linkml:is_a "node property" . biolink:provider a owl:ObjectProperty ; rdfs:label "provider" ; @@ -5265,7 +5952,8 @@ biolink:provider a owl:ObjectProperty ; rdfs:range biolink:InformationContentEntity ; rdfs:subPropertyOf biolink:contributor ; owl:inverseOf biolink:has_provider ; - skos:definition "person, group, organization or project that provides a piece of information (e.g. a knowledge association)." . + skos:definition "person, group, organization or project that provides a piece of information (e.g. a knowledge association)." ; + linkml:is_a "contributor" . biolink:publications a owl:ObjectProperty ; rdfs:label "publications" ; @@ -5275,7 +5963,7 @@ biolink:publications a owl:ObjectProperty ; skos:altLabel "supporting documents", "supporting publications" ; skos:definition "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - skos:note "The notion of a ‘Publication’ is considered broadly to include any document made available for public consumption. It covers journal issues, individual articles, and books - and also things like article pre-prints, white papers, patents, drug labels, web pages, protocol documents, etc. " . + linkml:is_a "association slot" . biolink:publisher a owl:ObjectProperty ; rdfs:label "publisher" ; @@ -5285,7 +5973,8 @@ biolink:publisher a owl:ObjectProperty ; owl:inverseOf biolink:has_publisher ; skos:definition "organization or person responsible for publishing books, periodicals, podcasts, games or software. Note that in the case of publications which have a containing \"published in\" node property, the publisher association may not be attached directly to the embedded child publication, but only made in between the parent's publication node and the publisher agent of the encompassing publication (e.g. only from the Journal referenced by the 'published_in' property of an journal article Publication node)." ; skos:exactMatch dct:publisher, - WIKIDATA_PROPERTY:P123 . + WIKIDATA_PROPERTY:P123 ; + linkml:is_a "contributor" . biolink:reaction_direction a owl:ObjectProperty ; rdfs:label "reaction direction" ; @@ -5293,21 +5982,24 @@ biolink:reaction_direction a owl:ObjectProperty ; rdfs:range biolink:ReactionDirectionEnum ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; - skos:narrowMatch . + skos:narrowMatch ; + linkml:is_a "association slot" . biolink:reaction_side a owl:ObjectProperty ; rdfs:label "reaction side" ; rdfs:domain biolink:Association ; rdfs:range biolink:ReactionSideEnum ; rdfs:subPropertyOf biolink:association_slot ; - skos:definition "the side of a reaction being modeled (ie: left or right)" . + skos:definition "the side of a reaction being modeled (ie: left or right)" ; + linkml:is_a "association slot" . biolink:regulated_by a owl:ObjectProperty ; rdfs:label "regulated by" ; rdfs:domain biolink:PhysicalEssenceOrOccurrent ; rdfs:range biolink:PhysicalEssenceOrOccurrent ; rdfs:subPropertyOf biolink:affected_by ; - owl:inverseOf biolink:regulates . + owl:inverseOf biolink:regulates ; + linkml:is_a "affected by" . biolink:regulates a owl:ObjectProperty ; rdfs:label "regulates" ; @@ -5322,44 +6014,50 @@ biolink:regulates a owl:ObjectProperty ; CHEMBL.MECHANISM:modulator, WIKIDATA_PROPERTY:P128 ; skos:definition "A more specific form of affects, that implies the effect results from a biologically evolved control mechanism. Gene-affects-gene relationships will (almost) always involve regulation. Exogenous/environmental chemical-affects-gene relationships are not cases of regulation in this definition. Instead these would be captured using the 'affects' predicate, or possibly one of the 'interacts with' predicates depending on the nature of the interaction." ; - skos:editorialNote "The RO definition of 'directly regulates the activity of' is an exact_mapping here because it describes genetic regulation from the point of view of one genetic entity regulating another, as opposed to \"RO:0002211\" which describes process to process regulation." ; skos:exactMatch RO:0002448 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "affects" ; + linkml:mixins "interacts with" . biolink:resistance_associated_with a owl:ObjectProperty ; rdfs:label "resistance associated with" ; rdfs:domain biolink:ChemicalEntity ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:associated_with ; - owl:inverseOf biolink:associated_with_resistance_to . + owl:inverseOf biolink:associated_with_resistance_to ; + linkml:is_a "associated with" . biolink:resource_id a owl:ObjectProperty ; rdfs:label "resource id" ; rdfs:domain biolink:RetrievalSource ; rdfs:range linkml:Uriorcurie ; rdfs:subPropertyOf biolink:node_property ; - skos:definition "The CURIE for an Information Resource that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." . + skos:definition "The CURIE for an Information Resource that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + linkml:is_a "node property" . biolink:resource_role a owl:ObjectProperty ; rdfs:label "resource role" ; rdfs:domain biolink:RetrievalSource ; rdfs:range biolink:ResourceRoleEnum ; rdfs:subPropertyOf biolink:node_property ; - skos:definition "The role played by the InformationResource in serving as a source for an Edge. Note that a given Edge should have one and only one 'primary' source, and may have any number of 'aggregator' or 'supporting data' sources." . + skos:definition "The role played by the InformationResource in serving as a source for an Edge. Note that a given Edge should have one and only one 'primary' source, and may have any number of 'aggregator' or 'supporting data' sources." ; + linkml:is_a "node property" . biolink:response_decreased_by a owl:ObjectProperty ; rdfs:label "response decreased by" ; rdfs:domain biolink:ChemicalEntityOrGeneOrGeneProduct ; rdfs:range biolink:ChemicalEntityOrGeneOrGeneProduct ; rdfs:subPropertyOf biolink:response_affected_by ; - owl:inverseOf biolink:decreases_response_to . + owl:inverseOf biolink:decreases_response_to ; + linkml:is_a "response affected by" . biolink:response_increased_by a owl:ObjectProperty ; rdfs:label "response increased by" ; rdfs:domain biolink:ChemicalEntityOrGeneOrGeneProduct ; rdfs:range biolink:ChemicalEntityOrGeneOrGeneProduct ; rdfs:subPropertyOf biolink:response_affected_by ; - owl:inverseOf biolink:increases_response_to . + owl:inverseOf biolink:increases_response_to ; + linkml:is_a "response affected by" . biolink:retrieval_source_ids a owl:ObjectProperty ; rdfs:label "retrieval source ids" ; @@ -5371,7 +6069,8 @@ biolink:rights a owl:ObjectProperty ; rdfs:domain biolink:InformationContentEntity ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:node_property ; - skos:exactMatch dct:rights . + skos:exactMatch dct:rights ; + linkml:is_a "node property" . biolink:routes_of_delivery a owl:ObjectProperty ; rdfs:label "routes of delivery" ; @@ -5383,21 +6082,24 @@ biolink:sensitivity_associated_with a owl:ObjectProperty ; rdfs:domain biolink:ChemicalEntity ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:associated_with ; - owl:inverseOf biolink:associated_with_sensitivity_to . + owl:inverseOf biolink:associated_with_sensitivity_to ; + linkml:is_a "associated with" . biolink:sequence_location_of a owl:ObjectProperty ; rdfs:label "sequence location of" ; rdfs:domain biolink:NucleicAcidEntity ; rdfs:range biolink:NucleicAcidEntity ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; - owl:inverseOf biolink:has_sequence_location . + owl:inverseOf biolink:has_sequence_location ; + linkml:is_a "related to at instance level" . biolink:source_web_page a owl:ObjectProperty ; rdfs:label "source web page" ; rdfs:domain biolink:DatasetSummary ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:node_property ; - skos:broadMatch dct:source . + skos:broadMatch dct:source ; + linkml:is_a "node property" . biolink:start_interbase_coordinate a owl:ObjectProperty ; rdfs:label "start interbase coordinate" ; @@ -5406,14 +6108,16 @@ biolink:start_interbase_coordinate a owl:ObjectProperty ; rdfs:subPropertyOf biolink:interbase_coordinate ; skos:closeMatch ; skos:definition "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0)." ; - biolink:opposite_of "end interbase coordinate" . + biolink:opposite_of "end interbase coordinate" ; + linkml:is_a "interbase coordinate" . biolink:stoichiometry a owl:ObjectProperty ; rdfs:label "stoichiometry" ; rdfs:domain biolink:Association ; rdfs:range linkml:Integer ; rdfs:subPropertyOf biolink:association_slot ; - skos:definition "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." . + skos:definition "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; + linkml:is_a "association slot" . biolink:strand a owl:ObjectProperty ; rdfs:label "strand" ; @@ -5421,7 +6125,8 @@ biolink:strand a owl:ObjectProperty ; rdfs:range biolink:StrandEnum ; rdfs:subPropertyOf biolink:sequence_localization_attribute ; skos:definition "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand)." ; - skos:exactMatch gff3:strand . + skos:exactMatch gff3:strand ; + linkml:is_a "sequence localization attribute" . biolink:subject_category a owl:ObjectProperty ; rdfs:label "subject category" ; @@ -5430,7 +6135,7 @@ biolink:subject_category a owl:ObjectProperty ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; biolink:denormalized "True" ; - linkml:examples "Example(value='biolink:Gene', description=\"The subject category of the association between the gene 'BRCA1' and the disease 'breast cancer' is 'biolink:Gene'.\")" . + linkml:is_a "association slot" . biolink:subject_category_closure a owl:ObjectProperty ; rdfs:label "subject category closure" ; @@ -5439,7 +6144,7 @@ biolink:subject_category_closure a owl:ObjectProperty ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; biolink:denormalized "True" ; - linkml:examples "Example(value='[\\'biolink:Gene\", \"biolink:NamedThing\\']', description='The subject category closure of the association between the gene \\'BRCA1\\' and the disease \\'breast cancer\\' is the set of all biolink classes that are ancestors of \\'biolink:Gene\\' in the biolink model. Note: typically the \"subclass of\" and \"part of\" relations are used to construct the closure, but other relations may be used as well.')" . + linkml:is_a "association slot" . biolink:subject_closure a owl:ObjectProperty ; rdfs:label "subject closure" ; @@ -5447,7 +6152,8 @@ biolink:subject_closure a owl:ObjectProperty ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - biolink:denormalized "True" . + biolink:denormalized "True" ; + linkml:is_a "association slot" . biolink:subject_label_closure a owl:ObjectProperty ; rdfs:label "subject label closure" ; @@ -5456,7 +6162,7 @@ biolink:subject_label_closure a owl:ObjectProperty ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; biolink:denormalized "True" ; - linkml:examples "Example(value=\"['BRACA1']\", description=\"The subject label closure of the association between the gene 'BRCA1' and the disease 'breast cancer' is the set of all labels that are ancestors of 'BRCA1' in the biolink model.\")" . + linkml:is_a "association slot" . biolink:subject_namespace a owl:ObjectProperty ; rdfs:label "subject namespace" ; @@ -5466,7 +6172,7 @@ biolink:subject_namespace a owl:ObjectProperty ; skos:altLabel "subject prefix" ; skos:definition "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; biolink:denormalized "True" ; - linkml:examples "Example(value='NCBIGene', description=\"The subject namespace of the association between the gene 'BRCA1' and the disease 'breast cancer' is 'NCBIGene'.\")" . + linkml:is_a "association slot" . biolink:summary a owl:ObjectProperty ; rdfs:label "summary" ; @@ -5476,7 +6182,8 @@ biolink:summary a owl:ObjectProperty ; skos:altLabel "abstract" ; skos:definition "executive summary of a publication" ; skos:exactMatch dct:abstract, - WIKIDATA:Q333291 . + WIKIDATA:Q333291 ; + linkml:is_a "node property" . biolink:symbol a owl:ObjectProperty ; rdfs:label "symbol" ; @@ -5485,7 +6192,8 @@ biolink:symbol a owl:ObjectProperty ; rdfs:subPropertyOf biolink:node_property ; skos:definition "Symbol for a particular thing" ; skos:exactMatch gpi:DB_Object_Symbol, - AGRKB:symbol . + AGRKB:symbol ; + linkml:is_a "node property" . biolink:target_for a owl:ObjectProperty ; rdfs:label "target for" ; @@ -5494,21 +6202,24 @@ biolink:target_for a owl:ObjectProperty ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; owl:inverseOf biolink:has_target ; skos:definition "A gene is a target of a disease when its products are druggable and when a drug interaction with the gene product could have a therapeutic effect" ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:taxon_of a owl:ObjectProperty ; rdfs:label "taxon of" ; rdfs:domain biolink:OrganismTaxon ; rdfs:range biolink:ThingWithTaxon ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; - owl:inverseOf biolink:in_taxon . + owl:inverseOf biolink:in_taxon ; + linkml:is_a "related to at instance level" . biolink:trade_name a owl:ObjectProperty ; rdfs:label "trade name" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:ChemicalEntity ; rdfs:subPropertyOf biolink:node_property ; - skos:definition "" . + skos:definition "" ; + linkml:is_a "node property" . biolink:transcribed_from a owl:ObjectProperty ; rdfs:label "transcribed from" ; @@ -5519,7 +6230,8 @@ biolink:transcribed_from a owl:ObjectProperty ; skos:definition "x is transcribed from y if and only if x is synthesized from template y" ; skos:exactMatch RO:0002510, SIO:010081 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:transcribed_to a owl:ObjectProperty ; rdfs:label "transcribed to" ; @@ -5529,7 +6241,8 @@ biolink:transcribed_to a owl:ObjectProperty ; owl:inverseOf biolink:transcribed_from ; skos:definition "inverse of transcribed from" ; skos:exactMatch RO:0002511, - SIO:010080 . + SIO:010080 ; + linkml:is_a "related to at instance level" . biolink:translates_to a owl:ObjectProperty ; rdfs:label "translates to" ; @@ -5540,7 +6253,8 @@ biolink:translates_to a owl:ObjectProperty ; skos:closeMatch RO:0002513, SIO:010082 ; skos:definition "x (amino acid chain/polypeptide) is the ribosomal translation of y (transcript) if and only if a ribosome reads y (transcript) through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces x (amino acid chain/polypeptide)" ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:translation_of a owl:ObjectProperty ; rdfs:label "translation of" ; @@ -5550,7 +6264,8 @@ biolink:translation_of a owl:ObjectProperty ; owl:inverseOf biolink:translates_to ; skos:closeMatch RO:0002512, SIO:010083 ; - skos:definition "inverse of translates to" . + skos:definition "inverse of translates to" ; + linkml:is_a "related to at instance level" . biolink:treated_by a owl:ObjectProperty ; rdfs:label "treated by" ; @@ -5561,7 +6276,8 @@ biolink:treated_by a owl:ObjectProperty ; skos:definition "holds between a disease or phenotypic feature and a therapeutic process or chemical entity that is used to treat the condition" ; skos:exactMatch , WIKIDATA_PROPERTY:P2176 ; - skos:narrowMatch RO:0002302 . + skos:narrowMatch RO:0002302 ; + linkml:is_a "is ameliorated by" . biolink:treats a owl:ObjectProperty ; rdfs:label "treats" ; @@ -5599,21 +6315,24 @@ biolink:treats a owl:ObjectProperty ; ; skos:relatedMatch ; biolink:canonical_predicate "True" ; - biolink:opposite_of "contraindicated for" . + biolink:opposite_of "contraindicated for" ; + linkml:is_a "ameliorates" . biolink:upstream_resource_ids a owl:ObjectProperty ; rdfs:label "upstream resource ids" ; rdfs:domain biolink:RetrievalSource ; rdfs:range linkml:Uriorcurie ; rdfs:subPropertyOf biolink:node_property ; - skos:definition "An upstream InformationResource from which the resource being described directly retrieved a record of the knowledge expressed in the Edge, or data used to generate this knowledge. This is an array because there are cases where a merged Edge holds knowledge that was retrieved from multiple sources. e.g. an Edge provided by the ARAGORN ARA can expressing knowledge it retrieved from both the automat-mychem-info and molepro KPs, which both provided it with records of this single fact." . + skos:definition "An upstream InformationResource from which the resource being described directly retrieved a record of the knowledge expressed in the Edge, or data used to generate this knowledge. This is an array because there are cases where a merged Edge holds knowledge that was retrieved from multiple sources. e.g. an Edge provided by the ARAGORN ARA can expressing knowledge it retrieved from both the automat-mychem-info and molepro KPs, which both provided it with records of this single fact." ; + linkml:is_a "node property" . biolink:variant_part_of a owl:ObjectProperty ; rdfs:label "variant part of" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:part_of ; - owl:inverseOf biolink:has_variant_part . + owl:inverseOf biolink:has_variant_part ; + linkml:is_a "part of" . linkml:topValue a owl:DatatypeProperty ; rdfs:label "value" . @@ -5633,20 +6352,16 @@ dct:distribution a owl:ObjectProperty ; rdfs:domain biolink:DatasetVersion ; rdfs:range biolink:DatasetDistribution ; rdfs:subPropertyOf biolink:node_property ; - skos:exactMatch dct:distribution . - -dct:type a owl:ObjectProperty ; - rdfs:label "publication type" ; - rdfs:range linkml:String ; - skos:definition "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - skos:exactMatch dct:type . + skos:exactMatch dct:distribution ; + linkml:is_a "node property" . schema:logo a owl:ObjectProperty ; rdfs:label "source logo" ; rdfs:domain biolink:DatasetSummary ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:node_property ; - skos:exactMatch schema:logo . + skos:exactMatch schema:logo ; + linkml:is_a "node property" . os:AllSomeInterpretation a owl:Class ; rdfs:label "all_some" . @@ -5654,25 +6369,24 @@ os:AllSomeInterpretation a owl:Class ; os:SomeSomeInterpretation a owl:Class ; rdfs:label "some_some" . -biolink:AnatomicalContextQualifierEnum a owl:Class ; - rdfs:label "AnatomicalContextQualifierEnum" ; - owl:unionOf [ rdf:rest () ] . - biolink:AnatomicalEntityToAnatomicalEntityAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:AnatomicalEntity ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:AnatomicalEntity ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - biolink:Association . + biolink:Association ; + linkml:attributes "{}" ; + linkml:is_a "association" . biolink:Annotation a owl:Class ; rdfs:label "annotation" ; - skos:definition "Biolink Model root class for entity annotations." . + skos:definition "Biolink Model root class for entity annotations." ; + linkml:attributes "{}" . biolink:CaseToEntityAssociationMixin a owl:Class ; rdfs:label "case to entity association mixin" ; @@ -5681,58 +6395,74 @@ biolink:CaseToEntityAssociationMixin a owl:Class ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], linkml:mixin ; - skos:definition "An abstract association for use where the case is the subject" . + skos:definition "An abstract association for use where the case is the subject" ; + linkml:attributes "{}" . a owl:Class ; - rdfs:label "activation" . + rdfs:label "activation" ; + linkml:is_a "binding" . a owl:Class ; - rdfs:label "agonism" . + rdfs:label "agonism" ; + linkml:is_a "activation" . a owl:Class ; - rdfs:label "antagonism" . + rdfs:label "antagonism" ; + linkml:is_a "inhibition" . a owl:Class ; - rdfs:label "antibody_inhibition" . + rdfs:label "antibody_inhibition" ; + linkml:is_a "inhibition" . a owl:Class ; rdfs:label "binding" . a owl:Class ; - rdfs:label "inducer" . + rdfs:label "inducer" ; + linkml:is_a "binding" . a owl:Class ; - rdfs:label "inhibition" . + rdfs:label "inhibition" ; + linkml:is_a "binding" . a owl:Class ; - rdfs:label "inverse_agonism" . + rdfs:label "inverse_agonism" ; + linkml:is_a "inhibition" . a owl:Class ; - rdfs:label "molecular_channel_blockage" . + rdfs:label "molecular_channel_blockage" ; + linkml:is_a "inhibition" . a owl:Class ; - rdfs:label "molecular_channel_opening" . + rdfs:label "molecular_channel_opening" ; + linkml:is_a "activation" . a owl:Class ; - rdfs:label "negative_allosteric_modulation" . + rdfs:label "negative_allosteric_modulation" ; + linkml:is_a "inhibition" . a owl:Class ; - rdfs:label "positive_allosteric_modulation" . + rdfs:label "positive_allosteric_modulation" ; + linkml:is_a "activation" . a owl:Class ; - rdfs:label "potentiation" . + rdfs:label "potentiation" ; + linkml:is_a "binding" . a owl:Class ; - rdfs:label "releasing_activity" . + rdfs:label "releasing_activity" ; + linkml:is_a "activation" . a owl:Class ; rdfs:label "signaling_mediated_control" . a owl:Class ; - rdfs:label "stabilization" . + rdfs:label "stabilization" ; + linkml:is_a "activation" . a owl:Class ; - rdfs:label "stimulation" . + rdfs:label "stimulation" ; + linkml:is_a "activation" . a owl:Class ; rdfs:label "transcriptional_regulation" . @@ -5741,7 +6471,10 @@ biolink:CellLine a owl:Class ; rdfs:label "cell line" ; rdfs:subClassOf biolink:OrganismalEntity, biolink:SubjectOfInvestigation ; - skos:exactMatch . + skos:exactMatch ; + linkml:attributes "{}" ; + linkml:is_a "organismal entity" ; + linkml:mixins "subject of investigation" . biolink:CellLineToEntityAssociationMixin a owl:Class ; rdfs:label "cell line to entity association mixin" ; @@ -5750,7 +6483,8 @@ biolink:CellLineToEntityAssociationMixin a owl:Class ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], linkml:mixin ; - skos:definition "An relationship between a cell line and another entity" . + skos:definition "An relationship between a cell line and another entity" ; + linkml:attributes "{}" . biolink:ChemicalEntityDerivativeEnum a owl:Class ; rdfs:label "ChemicalEntityDerivativeEnum" ; @@ -5761,32 +6495,39 @@ biolink:ChemicalEntityDerivativeEnum a owl:Class ; rdfs:label "metabolite" . a owl:Class ; - rdfs:label "analog_form" . + rdfs:label "analog_form" ; + linkml:is_a "modified_form" . a owl:Class ; - rdfs:label "gain_of_function_variant_form" . + rdfs:label "gain_of_function_variant_form" ; + linkml:is_a "genetic_variant_form" . a owl:Class ; - rdfs:label "genetic_variant_form" . + rdfs:label "genetic_variant_form" ; + linkml:is_a "modified_form" . a owl:Class ; - rdfs:label "loss_of_function_variant_form" . + rdfs:label "loss_of_function_variant_form" ; + linkml:is_a "genetic_variant_form" . a owl:Class ; rdfs:label "modified_form" . a owl:Class ; - rdfs:label "polymorphic_form" . + rdfs:label "polymorphic_form" ; + linkml:is_a "genetic_variant_form" . a owl:Class ; - rdfs:label "snp_form" . + rdfs:label "snp_form" ; + linkml:is_a "polymorphic_form" . biolink:ChemicalRole a owl:Class ; rdfs:label "chemical role" ; rdfs:subClassOf biolink:Attribute ; skos:definition " A role played by the molecular entity or part thereof within a chemical context." ; skos:exactMatch ; - linkml:examples "Example(value='CHEBI:35469', description=None)" . + linkml:attributes "{}" ; + linkml:is_a "attribute" . biolink:ChemicalToChemicalAssociation a owl:Class ; rdfs:label "chemical to chemical association" ; @@ -5796,12 +6537,17 @@ biolink:ChemicalToChemicalAssociation a owl:Class ; owl:qualifiedCardinality 1 ], biolink:Association, biolink:ChemicalToEntityAssociationMixin ; - skos:definition "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another." . + skos:definition "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another." ; + linkml:attributes "{}" ; + linkml:is_a "association" ; + linkml:mixins "chemical to entity association mixin" . biolink:ClinicalEntity a owl:Class ; rdfs:label "clinical entity" ; rdfs:subClassOf biolink:NamedThing ; - skos:definition "Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities" . + skos:definition "Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities" ; + linkml:attributes "{}" ; + linkml:is_a "named thing" . biolink:Device a owl:Class ; rdfs:label "device" ; @@ -5811,26 +6557,32 @@ biolink:Device a owl:Class ; STY:T075, STY:T122, STY:T203, - UMLSSG:DEVI . + UMLSSG:DEVI ; + linkml:attributes "{}" ; + linkml:is_a "named thing" . biolink:DiagnosticAid a owl:Class ; rdfs:label "diagnostic aid" ; rdfs:subClassOf biolink:NamedThing ; skos:definition "A device or substance used to help diagnose disease or injury" ; skos:exactMatch STY:T130, - . + ; + linkml:attributes "{}" ; + linkml:is_a "named thing" . a owl:Class ; rdfs:label "decreased" . a owl:Class ; - rdfs:label "downregulated" . + rdfs:label "downregulated" ; + linkml:is_a "decreased" . a owl:Class ; rdfs:label "increased" . a owl:Class ; - rdfs:label "upregulated" . + rdfs:label "upregulated" ; + linkml:is_a "increased" . biolink:DrugAvailabilityEnum a owl:Class ; rdfs:label "DrugAvailabilityEnum" ; @@ -5883,21 +6635,24 @@ biolink:EntityToExposureEventAssociationMixin a owl:Class ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], linkml:mixin ; - skos:definition "An association between some entity and an exposure event." . + skos:definition "An association between some entity and an exposure event." ; + linkml:attributes "{}" . biolink:EntityToFeatureOrDiseaseQualifiersMixin a owl:Class ; rdfs:label "entity to feature or disease qualifiers mixin" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; owl:onProperty biolink:severity_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], biolink:FrequencyQualifierMixin, linkml:mixin ; - skos:definition "Qualifiers for entity to disease or phenotype associations." . + skos:definition "Qualifiers for entity to disease or phenotype associations." ; + linkml:attributes "{}" ; + linkml:is_a "frequency qualifier mixin" . biolink:EntityToOutcomeAssociationMixin a owl:Class ; rdfs:label "entity to outcome association mixin" ; @@ -5906,7 +6661,8 @@ biolink:EntityToOutcomeAssociationMixin a owl:Class ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], linkml:mixin ; - skos:definition "An association between some entity and an outcome" . + skos:definition "An association between some entity and an outcome" ; + linkml:attributes "{}" . biolink:EpigenomicEntity a owl:Class ; rdfs:label "epigenomic entity" ; @@ -5914,14 +6670,17 @@ biolink:EpigenomicEntity a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSequence ; owl:onProperty biolink:has_biological_sequence ], - linkml:mixin . + linkml:mixin ; + linkml:attributes "{}" . biolink:EvidenceType a owl:Class ; rdfs:label "evidence type" ; rdfs:subClassOf biolink:InformationContentEntity ; skos:altLabel "evidence code" ; skos:definition "Class of evidence that supports an association" ; - skos:exactMatch . + skos:exactMatch ; + linkml:attributes "{}" ; + linkml:is_a "information content entity" . a owl:Class ; rdfs:label "discovery_and_development_phase" . @@ -5993,18 +6752,15 @@ biolink:FDA_approval_status a owl:ObjectProperty ; rdfs:domain biolink:Association ; rdfs:range biolink:FDAApprovalStatusEnum ; rdfs:subPropertyOf biolink:association_slot ; - skos:definition "" . + skos:definition "" ; + linkml:is_a "association slot" . biolink:FrequencyQuantifier a owl:Class ; rdfs:label "frequency quantifier" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; @@ -6012,81 +6768,108 @@ biolink:FrequencyQuantifier a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], + owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_count ], biolink:RelationshipQuantifier, - linkml:mixin . + linkml:mixin ; + linkml:attributes "{}" ; + linkml:is_a "relationship quantifier" . a owl:Class ; - rdfs:label "ADP-ribosylation" . + rdfs:label "ADP-ribosylation" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "abundance" . + rdfs:label "abundance" ; + linkml:is_a "activity_or_abundance" . a owl:Class ; - rdfs:label "acetylation" . + rdfs:label "acetylation" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "activity" . + rdfs:label "activity" ; + linkml:is_a "activity_or_abundance" . a owl:Class ; rdfs:label "activity_or_abundance" . a owl:Class ; - rdfs:label "acylation" . + rdfs:label "acylation" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "alkylation" . + rdfs:label "alkylation" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "amination" . + rdfs:label "amination" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "carbamoylation" . + rdfs:label "carbamoylation" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "carboxylation" . + rdfs:label "carboxylation" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "cleavage" . + rdfs:label "cleavage" ; + linkml:is_a "degradation" . a owl:Class ; rdfs:label "degradation" . a owl:Class ; - rdfs:label "ethylation" . + rdfs:label "ethylation" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "expression" . + rdfs:label "expression" ; + linkml:is_a "abundance" . a owl:Class ; - rdfs:label "farnesylation" . + rdfs:label "farnesylation" ; + linkml:is_a "molecular_modification" . a owl:Class ; rdfs:label "folding" . a owl:Class ; - rdfs:label "geranoylation" . + rdfs:label "geranoylation" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "glucuronidation" . + rdfs:label "glucuronidation" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "glutathionylation" . + rdfs:label "glutathionylation" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "glycation" . + rdfs:label "glycation" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "glycosylation" . + rdfs:label "glycosylation" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "hydrolysis" . + rdfs:label "hydrolysis" ; + linkml:is_a "degradation" . a owl:Class ; - rdfs:label "hydroxylation" . + rdfs:label "hydroxylation" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "lipidation" . + rdfs:label "lipidation" ; + linkml:is_a "molecular_modification" . a owl:Class ; rdfs:label "localization" . @@ -6095,7 +6878,8 @@ biolink:FrequencyQuantifier a owl:Class ; rdfs:label "metabolic_processing" . a owl:Class ; - rdfs:label "methylation" . + rdfs:label "methylation" ; + linkml:is_a "molecular_modification" . a owl:Class ; rdfs:label "molecular_modification" . @@ -6104,61 +6888,78 @@ biolink:FrequencyQuantifier a owl:Class ; rdfs:label "mutation_rate" . a owl:Class ; - rdfs:label "myristoylation" . + rdfs:label "myristoylation" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "n_linked_glycosylation" . + rdfs:label "n_linked_glycosylation" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "nitrosation" . + rdfs:label "nitrosation" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "nucleotidylation" . + rdfs:label "nucleotidylation" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "o_linked_glycosylation" . + rdfs:label "o_linked_glycosylation" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "oxidation" . + rdfs:label "oxidation" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "palmitoylation" . + rdfs:label "palmitoylation" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "phosphorylation" . + rdfs:label "phosphorylation" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "prenylation" . + rdfs:label "prenylation" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "reduction" . + rdfs:label "reduction" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "ribosylation" . + rdfs:label "ribosylation" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "secretion" . + rdfs:label "secretion" ; + linkml:is_a "transport" . a owl:Class ; rdfs:label "stability" . a owl:Class ; - rdfs:label "sulfation" . + rdfs:label "sulfation" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "sumoylation" . + rdfs:label "sumoylation" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "synthesis" . + rdfs:label "synthesis" ; + linkml:is_a "abundance" . a owl:Class ; rdfs:label "transport" . a owl:Class ; - rdfs:label "ubiquitination" . + rdfs:label "ubiquitination" ; + linkml:is_a "molecular_modification" . a owl:Class ; - rdfs:label "uptake" . + rdfs:label "uptake" ; + linkml:is_a "transport" . a owl:Class ; rdfs:label "3_prime_utr" . @@ -6181,21 +6982,70 @@ biolink:FrequencyQuantifier a owl:Class ; a owl:Class ; rdfs:label "promoter" . -biolink:InformationResourceStatusEnum a owl:Class ; - rdfs:label "InformationResourceStatusEnum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - . - - a owl:Class ; - rdfs:label "deprecated" . - - a owl:Class ; - rdfs:label "draft" . - - a owl:Class ; - rdfs:label "released" . +biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; + rdfs:label "gene to disease or phenotypic feature association" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:onClass biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty biolink:has_percentage ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_total ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:GeneOrGeneProduct ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], + biolink:Association, + biolink:EntityToPhenotypicFeatureAssociationMixin, + biolink:GeneToEntityAssociationMixin ; + skos:narrowMatch WBVocab:Gene-Phenotype-Association, + SIO:000983, + dcid:DiseaseGeneAssociation ; + linkml:attributes "{}" ; + linkml:is_a "association" ; + linkml:mixins "entity to phenotypic feature association mixin", + "gene to entity association mixin" . biolink:IriType a owl:Class ; rdfs:label "iri type" ; @@ -6214,7 +7064,10 @@ biolink:MaterialSample a owl:Class ; "sample" ; skos:definition "A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO]" ; skos:exactMatch , - SIO:001050 . + SIO:001050 ; + linkml:attributes "{}" ; + linkml:is_a "physical entity" ; + linkml:mixins "subject of investigation" . biolink:MaterialSampleToEntityAssociationMixin a owl:Class ; rdfs:label "material sample to entity association mixin" ; @@ -6223,7 +7076,8 @@ biolink:MaterialSampleToEntityAssociationMixin a owl:Class ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], linkml:mixin ; - skos:definition "An association between a material sample and something." . + skos:definition "An association between a material sample and something." ; + linkml:attributes "{}" . biolink:NarrativeText a owl:Class ; rdfs:label "narrative text" ; @@ -6233,21 +7087,26 @@ biolink:NoncodingRNAProduct a owl:Class ; rdfs:label "noncoding RNA product" ; rdfs:subClassOf biolink:RNAProduct ; skos:exactMatch , - SIO:001235 . + SIO:001235 ; + linkml:attributes "{}" ; + linkml:is_a "RNA product" . biolink:OrganismTaxonToOrganismTaxonAssociation a owl:Class ; rdfs:label "organism taxon to organism taxon association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:Association, biolink:OrganismTaxonToEntityAssociation ; - skos:definition "A relationship between two organism taxon nodes" . + skos:definition "A relationship between two organism taxon nodes" ; + linkml:attributes "{}" ; + linkml:is_a "association" ; + linkml:mixins "organism taxon to entity association" . biolink:PhaseEnum a owl:Class ; rdfs:label "PhaseEnum" ; @@ -6275,7 +7134,10 @@ biolink:Procedure a owl:Class ; skos:narrowMatch STY:T059, STY:T060, STY:T061, - STY:T063 . + STY:T063 ; + linkml:attributes "{}" ; + linkml:is_a "named thing" ; + linkml:mixins "activity and behavior" . biolink:RNAProduct a owl:Class ; rdfs:label "RNA product" ; @@ -6285,7 +7147,10 @@ biolink:RNAProduct a owl:Class ; biolink:GeneProductMixin, biolink:Transcript ; skos:exactMatch , - WIKIDATA:Q11053 . + WIKIDATA:Q11053 ; + linkml:attributes "{}" ; + linkml:is_a "transcript" ; + linkml:mixins "gene product mixin" . biolink:ReactionDirectionEnum a owl:Class ; rdfs:label "ReactionDirectionEnum" ; @@ -6334,7 +7199,13 @@ biolink:RegulatoryRegion a owl:Class ; skos:definition "A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene" ; skos:exactMatch , SIO:001225, - WIKIDATA:Q3238407 . + WIKIDATA:Q3238407 ; + linkml:attributes "{}" ; + linkml:is_a "biological entity" ; + linkml:mixins "chemical entity or gene or gene product", + "genomic entity", + "ontology class", + "physical essence" . biolink:ResourceRoleEnum a owl:Class ; rdfs:label "ResourceRoleEnum" ; @@ -6361,7 +7232,9 @@ biolink:ResourceRoleEnum a owl:Class ; biolink:SocioeconomicAttribute a owl:Class ; rdfs:label "socioeconomic attribute" ; rdfs:subClassOf biolink:Attribute ; - skos:definition "Attributes relating to a socioeconomic manifestation" . + skos:definition "Attributes relating to a socioeconomic manifestation" ; + linkml:attributes "{}" ; + linkml:is_a "attribute" . a owl:Class ; rdfs:label "+" . @@ -6379,7 +7252,9 @@ biolink:TaxonomicRank a owl:Class ; rdfs:label "taxonomic rank" ; rdfs:subClassOf biolink:OntologyClass ; skos:definition "A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom)" ; - skos:exactMatch WIKIDATA:Q427626 . + skos:exactMatch WIKIDATA:Q427626 ; + linkml:attributes "{}" ; + linkml:is_a "ontology class" . biolink:Unit a owl:Class ; rdfs:label "unit" ; @@ -6388,7 +7263,9 @@ biolink:Unit a owl:Class ; biolink:Zygosity a owl:Class ; rdfs:label "zygosity" ; rdfs:subClassOf biolink:Attribute ; - skos:exactMatch . + skos:exactMatch ; + linkml:attributes "{}" ; + linkml:is_a "attribute" . biolink:actively_involved_in a owl:ObjectProperty ; rdfs:label "actively involved in" ; @@ -6404,14 +7281,16 @@ biolink:actively_involved_in a owl:ObjectProperty ; orphanet:317348, orphanet:317349, orphanet:327767 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "participates in" . biolink:actively_involves a owl:ObjectProperty ; rdfs:label "actively involves" ; rdfs:domain biolink:BiologicalProcessOrActivity ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:has_participant ; - owl:inverseOf biolink:actively_involved_in . + owl:inverseOf biolink:actively_involved_in ; + linkml:is_a "has participant" . biolink:ameliorates a owl:ObjectProperty ; rdfs:label "ameliorates" ; @@ -6422,7 +7301,8 @@ biolink:ameliorates a owl:ObjectProperty ; skos:definition "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure, clinical intervention) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition." ; skos:exactMatch RO:0003307 ; biolink:canonical_predicate "True" ; - biolink:opposite_of "exacerbates" . + biolink:opposite_of "exacerbates" ; + linkml:is_a "affects" . biolink:aspect_qualifier a owl:ObjectProperty ; rdfs:label "aspect qualifier" ; @@ -6430,11 +7310,7 @@ biolink:aspect_qualifier a owl:ObjectProperty ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:qualifier ; skos:definition "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association." ; - skos:editorialNote "for good examples of aspects in the gene-> chemical space, please see the GeneOrGeneProductOrChemicalEntityAspectEnum (below) which lists many aspects that can be used to qualify the gene making the full subject a different ontological type. the qualifier ‘expression’ combines with a core concept of ‘Gene X’ to express the composed concept ‘expression of Gene X’ (Gene → Biological Process) the qualifier ‘exposure’ combines with a core concept of ‘Chemical X’ to express the composed concept ‘exposure to Chemical X’ (Chemical → Exposure Process) the qualifier ‘activity’ combines with a core concept of ‘PPARG’ to express the concept ‘activity of PPARG’ (Gene → function/activity) the qualifier ‘emergency Department Visit’ combines with a core concept of ‘Disease X’ to express the concept ‘Emergency Department visits for Disease X’ (Disease → Clinical Event) the qualifier ‘infection’ combines with a core concept of ‘Giardia’ to express the concept ‘Infection with Giardia’ (Taxon → Biological / Pathological Process) the qualifier ‘severity’ combines with a core concept of ‘DILI’ to express the concept ‘the severity level of DILI’ (Disease → (intrinsic) Characteristic/Quality) the qualifier ‘abundance’ combines with a core concept of ‘BRCA2’ to express the concept ‘abundance of BRCA2’ (Gene → (extrinsic) characteristic/quality)" ; - linkml:examples "Example(value='abundance', description=None)", - "Example(value='exposure', description=None)", - "Example(value='expression', description=None)", - "Example(value='stability', description=None)" . + linkml:is_a "qualifier" . biolink:base_coordinate a owl:ObjectProperty ; rdfs:label "base coordinate" ; @@ -6443,7 +7319,8 @@ biolink:base_coordinate a owl:ObjectProperty ; rdfs:subPropertyOf biolink:sequence_localization_attribute ; skos:altLabel "fully-closed", "one-based" ; - skos:definition "A position in the base coordinate system. Base coordinates start at position 1 instead of position 0." . + skos:definition "A position in the base coordinate system. Base coordinates start at position 1 instead of position 0." ; + linkml:is_a "sequence localization attribute" . biolink:broad_match a owl:ObjectProperty ; rdfs:label "broad match" ; @@ -6455,14 +7332,16 @@ biolink:broad_match a owl:ObjectProperty ; skos:exactMatch skos:broadMatch, WIKIDATA:Q39894595 ; biolink:canonical_predicate "True" ; - biolink:opposite_of "narrow match" . + biolink:opposite_of "narrow match" ; + linkml:is_a "related to at concept level" . biolink:causal_mechanism_qualifier a owl:ObjectProperty ; rdfs:label "causal mechanism qualifier" ; rdfs:domain biolink:Association ; rdfs:range biolink:CausalMechanismQualifierEnum ; rdfs:subPropertyOf biolink:statement_qualifier ; - skos:definition "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" . + skos:definition "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; + linkml:is_a "statement qualifier" . biolink:context_qualifier a owl:ObjectProperty ; rdfs:label "context qualifier" ; @@ -6470,8 +7349,7 @@ biolink:context_qualifier a owl:ObjectProperty ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:qualifier ; skos:definition "Restricts the setting/context/location where the core concept (or qualified core concept) resides or occurs." ; - linkml:examples "Example(value='cohort x (e.g. a specific population, referenced by an identifier)', description=None)", - "Example(value='gut microbiome', description=None)" . + linkml:is_a "qualifier" . biolink:contributes_to a owl:ObjectProperty ; rdfs:label "contributes to" ; @@ -6486,14 +7364,16 @@ biolink:contributes_to a owl:ObjectProperty ; , RO:0002255, RO:0003304 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:contribution_from a owl:ObjectProperty ; rdfs:label "contribution from" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; - owl:inverseOf biolink:contributes_to . + owl:inverseOf biolink:contributes_to ; + linkml:is_a "related to at instance level" . biolink:derivative_qualifier a owl:ObjectProperty ; rdfs:label "derivative qualifier" ; @@ -6501,7 +7381,7 @@ biolink:derivative_qualifier a owl:ObjectProperty ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:qualifier ; skos:definition "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’." ; - linkml:examples "Example(value='metabolite', description=None)" . + linkml:is_a "qualifier" . biolink:derives_from a owl:ObjectProperty ; rdfs:label "derives from" ; @@ -6515,7 +7395,8 @@ biolink:derives_from a owl:ObjectProperty ; DOID-PROPERTY:derives_from ; skos:narrowMatch , ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:derives_into a owl:ObjectProperty ; rdfs:label "derives into" ; @@ -6528,7 +7409,8 @@ biolink:derives_into a owl:ObjectProperty ; skos:definition "holds between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" ; skos:exactMatch , RO:0001001, - SEMMEDDB:CONVERTS_TO . + SEMMEDDB:CONVERTS_TO ; + linkml:is_a "related to at instance level" . biolink:direction_qualifier a owl:ObjectProperty ; rdfs:label "direction qualifier" ; @@ -6536,7 +7418,7 @@ biolink:direction_qualifier a owl:ObjectProperty ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:qualifier ; skos:definition "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree." ; - skos:editorialNote "the qualifier ‘increased’ combines with a core concept of ‘Gene X’ and an aspect of ‘expression’ to express the composed concept ‘increased expression of Gene X’ the qualifier ‘decreased’ combines with a core concept of ‘Protein X’ and an aspect of ‘abundance’ to express the composed concept ‘decreased abundance of Protein X’" . + linkml:is_a "qualifier" . biolink:exact_match a owl:ObjectProperty, owl:SymmetricProperty ; @@ -6548,7 +7430,8 @@ biolink:exact_match a owl:ObjectProperty, skos:exactMatch skos:exactMatch, WIKIDATA:P2888, WIKIDATA:Q39893449 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "close match" . biolink:food_component_of a owl:ObjectProperty ; rdfs:label "food component of" ; @@ -6556,7 +7439,8 @@ biolink:food_component_of a owl:ObjectProperty ; rdfs:range biolink:ChemicalEntity ; rdfs:subPropertyOf biolink:part_of ; owl:inverseOf biolink:has_food_component ; - skos:definition "holds between a one or more chemical entities present in food, irrespective of nutritional value (i.e. could also be a contaminant or additive)" . + skos:definition "holds between a one or more chemical entities present in food, irrespective of nutritional value (i.e. could also be a contaminant or additive)" ; + linkml:is_a "part of" . biolink:form_or_variant_qualifier a owl:ObjectProperty ; rdfs:label "form or variant qualifier" ; @@ -6564,12 +7448,7 @@ biolink:form_or_variant_qualifier a owl:ObjectProperty ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:qualifier ; skos:definition "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’." ; - skos:editorialNote "please see the ChemicalOrGeneOrGeneProductFormOrVariantEnum (below) for examples of 'form or variant qualifier' terms in the gene->chemical association space. the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘Mutated forms of Gene X’. the qualifier ‘late stage’ combines with a core concept of ‘Disease X’ to express the more specific concept ‘Late Stage forms of Disease X’ the qualifier ‘recombinant’ combines with a core concept of ‘FLT1 Gene’ to express the composed concept ‘Recombinant forms of the FLT1 gene’ the qualifier ‘chemical analog’ combines with a core concept of ‘Ditiocarb’ to express the composed concept ‘analog forms of Ditiocarb’" ; - linkml:examples "Example(value='chemical analog', description=None)", - "Example(value='late stage', description=None)", - "Example(value='mutation', description=None)", - "Example(value='severe', description=None)", - "Example(value='transplant', description=None)" . + linkml:is_a "qualifier" . biolink:genetically_associated_with a owl:ObjectProperty, owl:SymmetricProperty ; @@ -6580,7 +7459,8 @@ biolink:genetically_associated_with a owl:ObjectProperty, skos:definition "" ; skos:exactMatch WIKIDATA_PROPERTY:P2293 ; biolink:canonical_predicate "True" ; - biolink:description "Co-occurrence of a certain allele of a genetic marker and the phenotype of interest in the same individuals at above-chance level" . + biolink:description "Co-occurrence of a certain allele of a genetic marker and the phenotype of interest in the same individuals at above-chance level" ; + linkml:is_a "associated with" . biolink:genetically_interacts_with a owl:ObjectProperty, owl:SymmetricProperty ; @@ -6590,7 +7470,8 @@ biolink:genetically_interacts_with a owl:ObjectProperty, rdfs:subPropertyOf biolink:interacts_with ; skos:definition "holds between two genes whose phenotypic effects are dependent on each other in some way - such that their combined phenotypic effects are the result of some interaction between the activity of their gene products. Examples include epistasis and synthetic lethality." ; skos:exactMatch RO:0002435 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "interacts with" . biolink:has_attribute_type a owl:ObjectProperty ; rdfs:label "has attribute type" ; @@ -6606,7 +7487,8 @@ biolink:has_evidence a owl:ObjectProperty ; rdfs:range biolink:EvidenceType ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "connects an association to an instance of supporting evidence" ; - skos:exactMatch RO:0002558 . + skos:exactMatch RO:0002558 ; + linkml:is_a "association slot" . biolink:has_food_component a owl:ObjectProperty ; rdfs:label "has food component" ; @@ -6615,14 +7497,16 @@ biolink:has_food_component a owl:ObjectProperty ; rdfs:subPropertyOf biolink:has_part ; owl:inverseOf biolink:food_component_of ; skos:definition "holds between food and one or more chemical entities composing it, irrespective of nutritional value (i.e. could also be a contaminant or additive)" ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "has part" . biolink:has_manifestation a owl:ObjectProperty ; rdfs:label "has manifestation" ; rdfs:domain biolink:Disease ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; - owl:inverseOf biolink:manifestation_of . + owl:inverseOf biolink:manifestation_of ; + linkml:is_a "related to at instance level" . biolink:interbase_coordinate a owl:ObjectProperty ; rdfs:label "interbase coordinate" ; @@ -6632,14 +7516,16 @@ biolink:interbase_coordinate a owl:ObjectProperty ; skos:altLabel "half-open", "space-based", "zero-based" ; - skos:definition "A position in interbase coordinates. Interbase coordinates start at position 0 instead of position 1. This is applied to a sequence localization edge." . + skos:definition "A position in interbase coordinates. Interbase coordinates start at position 0 instead of position 1. This is applied to a sequence localization edge." ; + linkml:is_a "sequence localization attribute" . biolink:is_ameliorated_by a owl:ObjectProperty ; rdfs:label "is ameliorated by" ; rdfs:domain biolink:DiseaseOrPhenotypicFeature ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:affected_by ; - owl:inverseOf biolink:ameliorates . + owl:inverseOf biolink:ameliorates ; + linkml:is_a "affected by" . biolink:is_input_of a owl:ObjectProperty ; rdfs:label "is input of" ; @@ -6647,7 +7533,8 @@ biolink:is_input_of a owl:ObjectProperty ; rdfs:range biolink:BiologicalProcessOrActivity ; rdfs:subPropertyOf biolink:participates_in ; owl:inverseOf biolink:has_input ; - skos:exactMatch RO:0002352 . + skos:exactMatch RO:0002352 ; + linkml:is_a "participates in" . biolink:iso_abbreviation a owl:ObjectProperty ; rdfs:label "iso abbreviation" ; @@ -6655,7 +7542,8 @@ biolink:iso_abbreviation a owl:ObjectProperty ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:node_property ; skos:definition "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself." ; - skos:exactMatch WIKIDATA_PROPERTY:P1160 . + skos:exactMatch WIKIDATA_PROPERTY:P1160 ; + linkml:is_a "node property" . biolink:issue a owl:ObjectProperty ; rdfs:label "issue" ; @@ -6663,7 +7551,8 @@ biolink:issue a owl:ObjectProperty ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:node_property ; skos:definition "issue of a newspaper, a scientific journal or magazine for reference purpose" ; - skos:exactMatch WIKIDATA_PROPERTY:P433 . + skos:exactMatch WIKIDATA_PROPERTY:P433 ; + linkml:is_a "node property" . biolink:located_in a owl:ObjectProperty ; rdfs:label "located in" ; @@ -6715,7 +7604,8 @@ biolink:located_in a owl:ObjectProperty ; UBERON_CORE:in_innermost_side_of, UBERON_CORE:in_outermost_side_of, EFO:0000784 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:location_of a owl:ObjectProperty ; rdfs:label "location of" ; @@ -6730,7 +7620,8 @@ biolink:location_of a owl:ObjectProperty ; SEMMEDDB:LOCATION_OF, WIKIDATA_PROPERTY:P276 ; skos:narrowMatch , - . + ; + linkml:is_a "related to at instance level" . biolink:manifestation_of a owl:ObjectProperty ; rdfs:label "manifestation of" ; @@ -6743,7 +7634,8 @@ biolink:manifestation_of a owl:ObjectProperty ; skos:exactMatch , SEMMEDDB:MANIFESTATION_OF ; skos:narrowMatch ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:narrow_match a owl:ObjectProperty ; rdfs:label "narrow match" ; @@ -6754,7 +7646,8 @@ biolink:narrow_match a owl:ObjectProperty ; skos:definition "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree." ; skos:exactMatch skos:narrowMatch, WIKIDATA:Q39893967 ; - biolink:opposite_of "broad match" . + biolink:opposite_of "broad match" ; + linkml:is_a "related to at concept level" . biolink:overlaps a owl:ObjectProperty, owl:SymmetricProperty ; @@ -6769,7 +7662,8 @@ biolink:overlaps a owl:ObjectProperty, RO:0002102, RO:0002433, CHEMBL.MECHANISM:overlaps_with ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:part_qualifier a owl:ObjectProperty ; rdfs:label "part qualifier" ; @@ -6777,8 +7671,7 @@ biolink:part_qualifier a owl:ObjectProperty ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:qualifier ; skos:definition "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail)." ; - linkml:examples "Example(value='polyA tail', description=None)", - "Example(value='upstream control region', description=None)" . + linkml:is_a "qualifier" . biolink:physically_interacts_with a owl:ObjectProperty, owl:SymmetricProperty ; @@ -6799,7 +7692,9 @@ biolink:physically_interacts_with a owl:ObjectProperty, , , ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "interacts with" ; + linkml:mixins "interacts with" . biolink:published_in a owl:ObjectProperty ; rdfs:label "published in" ; @@ -6807,7 +7702,8 @@ biolink:published_in a owl:ObjectProperty ; rdfs:range linkml:Uriorcurie ; rdfs:subPropertyOf biolink:node_property ; skos:definition "CURIE identifier of a broader publication context within which the publication may be placed, e.g. a specified book or journal." ; - skos:exactMatch WIKIDATA_PROPERTY:P1433 . + skos:exactMatch WIKIDATA_PROPERTY:P1433 ; + linkml:is_a "node property" . biolink:qualified_predicate a owl:ObjectProperty ; rdfs:label "qualified predicate" ; @@ -6815,14 +7711,15 @@ biolink:qualified_predicate a owl:ObjectProperty ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:qualifier ; skos:definition "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - skos:editorialNote "to express the statement that “Chemical X causes increased expression of Gene Y”, the core triple is read using the fields subject:ChemX, predicate:affects, object:GeneY . . . and the full statement is read using the fields subject:ChemX, qualified_predicate:causes, object:GeneY, object_aspect: expression, object_direction:increased. The predicate ‘affects’ is needed for the core triple reading, but does not make sense in the full statement reading (because “Chemical X affects increased expression of Gene Y'' is not what we mean to say here: it causes increased expression of Gene Y)" . + linkml:is_a "qualifier" . biolink:qualifiers a owl:ObjectProperty ; rdfs:label "qualifiers" ; rdfs:domain biolink:Association ; rdfs:range biolink:OntologyClass ; rdfs:subPropertyOf biolink:association_slot ; - skos:definition "connects an association to qualifiers that modify or qualify the meaning of that association" . + skos:definition "connects an association to qualifiers that modify or qualify the meaning of that association" ; + linkml:is_a "association slot" . biolink:similar_to a owl:ObjectProperty, owl:SymmetricProperty ; @@ -6833,7 +7730,8 @@ biolink:similar_to a owl:ObjectProperty, skos:definition "holds between an entity and some other entity with similar features." ; skos:exactMatch RO:HOM0000000, ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:species_context_qualifier a owl:ObjectProperty ; rdfs:label "species context qualifier" ; @@ -6841,22 +7739,22 @@ biolink:species_context_qualifier a owl:ObjectProperty ; rdfs:range biolink:OrganismTaxon ; rdfs:subPropertyOf biolink:statement_qualifier ; skos:definition "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; - skos:editorialNote "Ontology CURIEs are expected as values here, the examples below are intended to help clarify the content of the CURIEs." ; - linkml:examples "Example(value='human', description=None)", - "Example(value='zebrafish', description=None)" . + linkml:is_a "statement qualifier" . biolink:subject_direction_qualifier a owl:ObjectProperty ; rdfs:label "subject direction qualifier" ; rdfs:domain biolink:Association ; rdfs:range biolink:DirectionQualifierEnum ; - rdfs:subPropertyOf biolink:direction_qualifier . + rdfs:subPropertyOf biolink:direction_qualifier ; + linkml:is_a "direction qualifier" . biolink:temporal_context_qualifier a owl:ObjectProperty ; rdfs:label "temporal context qualifier" ; rdfs:domain biolink:Association ; rdfs:range biolink:TimeType ; rdfs:subPropertyOf biolink:qualifier ; - skos:definition "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier." . + skos:definition "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier." ; + linkml:is_a "qualifier" . biolink:temporally_related_to a owl:ObjectProperty, owl:SymmetricProperty ; @@ -6880,7 +7778,8 @@ biolink:temporally_related_to a owl:ObjectProperty, RO:0002493, RO:0002496, RO:0002497 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:xref a owl:ObjectProperty ; rdfs:label "xref" ; @@ -6900,21 +7799,31 @@ dct:source a owl:ObjectProperty ; rdfs:domain biolink:DatasetVersion ; rdfs:range biolink:Dataset ; rdfs:subPropertyOf biolink:node_property ; - skos:exactMatch dct:source . + skos:exactMatch dct:source ; + linkml:is_a "node property" . + +dct:type a owl:ObjectProperty ; + rdfs:label "publication type" ; + rdfs:range linkml:String ; + skos:definition "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + skos:exactMatch dct:type . pav:version a owl:ObjectProperty ; rdfs:label "ingest date" ; rdfs:domain biolink:DatasetVersion ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:node_property ; - skos:exactMatch pav:version . + skos:exactMatch pav:version ; + linkml:is_a "node property" . biolink:ActivityAndBehavior a owl:Class ; rdfs:label "activity and behavior" ; rdfs:subClassOf biolink:Occurrent, linkml:mixin ; skos:definition "Activity or behavior of any independent integral living, organization or mechanical actor in the world" ; - skos:exactMatch UMLSSG:ACTI . + skos:exactMatch UMLSSG:ACTI ; + linkml:attributes "{}" ; + linkml:is_a "occurrent" . biolink:CausalMechanismQualifierEnum a owl:Class ; rdfs:label "CausalMechanismQualifierEnum" ; @@ -6948,12 +7857,15 @@ biolink:CellularComponent a owl:Class ; skos:exactMatch STY:T026, , SIO:001400, - WIKIDATA:Q5058355 . + WIKIDATA:Q5058355 ; + linkml:attributes "{}" ; + linkml:is_a "anatomical entity" . biolink:ChemicalEntityOrProteinOrPolypeptide a owl:Class ; rdfs:label "chemical entity or protein or polypeptide" ; rdfs:subClassOf linkml:mixin ; - skos:definition "A union of chemical entities and children, and protein and polypeptide. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities." . + skos:definition "A union of chemical entities and children, and protein and polypeptide. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities." ; + linkml:attributes "{}" . biolink:ChemicalEntityToEntityAssociationMixin a owl:Class ; rdfs:label "chemical entity to entity association mixin" ; @@ -6962,7 +7874,8 @@ biolink:ChemicalEntityToEntityAssociationMixin a owl:Class ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], linkml:mixin ; - skos:definition "An interaction between a chemical entity and another entity" . + skos:definition "An interaction between a chemical entity and another entity" ; + linkml:attributes "{}" . biolink:DatasetDistribution a owl:Class ; rdfs:label "dataset distribution" ; @@ -6972,7 +7885,9 @@ biolink:DatasetDistribution a owl:Class ; owl:onProperty biolink:distribution_download_url ], biolink:InformationContentEntity ; skos:definition "an item that holds distribution level information about a dataset." ; - skos:exactMatch dcat:Distribution . + skos:exactMatch dcat:Distribution ; + linkml:attributes "{}" ; + linkml:is_a "information content entity" . biolink:DatasetSummary a owl:Class ; rdfs:label "dataset summary" ; @@ -6985,7 +7900,9 @@ biolink:DatasetSummary a owl:Class ; owl:onClass linkml:String ; owl:onProperty schema:logo ], biolink:InformationContentEntity ; - skos:definition "an item that holds summary level information about a dataset." . + skos:definition "an item that holds summary level information about a dataset." ; + linkml:attributes "{}" ; + linkml:is_a "information content entity" . biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin a owl:Class ; rdfs:label "disease or phenotypic feature to entity association mixin" ; @@ -6993,7 +7910,8 @@ biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin a owl:Class ; owl:onClass biolink:DiseaseOrPhenotypicFeature ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - linkml:mixin . + linkml:mixin ; + linkml:attributes "{}" . biolink:DiseaseToEntityAssociationMixin a owl:Class ; rdfs:label "disease to entity association mixin" ; @@ -7001,7 +7919,8 @@ biolink:DiseaseToEntityAssociationMixin a owl:Class ; owl:onClass biolink:Disease ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - linkml:mixin . + linkml:mixin ; + linkml:attributes "{}" . biolink:FDAApprovalStatusEnum a owl:Class ; rdfs:label "FDAApprovalStatusEnum" ; @@ -7029,46 +7948,46 @@ biolink:FrequencyQualifierMixin a owl:Class ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], linkml:mixin ; - skos:definition "Qualifier for frequency type associations" . + skos:definition "Qualifier for frequency type associations" ; + linkml:attributes "{}" . biolink:GeneExpressionMixin a owl:Class ; rdfs:label "gene expression mixin" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:LifeStage ; owl:onProperty biolink:stage_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:expression_site ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:phenotypic_state ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:expression_site ], + owl:onClass biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ], linkml:mixin ; - skos:definition "Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs." . - -biolink:GeneToDiseaseAssociation a owl:Class ; - rdfs:label "gene to disease association" ; - rdfs:subClassOf biolink:Association . + skos:definition "Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs." ; + linkml:attributes "{}" . biolink:GeneToGeneAssociation a owl:Class ; rdfs:label "gene to gene association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:Association ; skos:altLabel "molecular or genetic interaction" ; - skos:definition "abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction." . + skos:definition "abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction." ; + linkml:attributes "{}" ; + linkml:is_a "association" . biolink:GeneticInheritance a owl:Class ; rdfs:label "genetic inheritance" ; @@ -7078,7 +7997,9 @@ biolink:GeneticInheritance a owl:Class ; skos:definition "The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc." ; skos:exactMatch , , - . + ; + linkml:attributes "{}" ; + linkml:is_a "biological entity" . biolink:GenotypeToEntityAssociationMixin a owl:Class ; rdfs:label "genotype to entity association mixin" ; @@ -7086,7 +8007,8 @@ biolink:GenotypeToEntityAssociationMixin a owl:Class ; owl:onClass biolink:Genotype ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - linkml:mixin . + linkml:mixin ; + linkml:attributes "{}" . biolink:IndividualOrganism a owl:Class ; rdfs:label "individual organism" ; @@ -7097,7 +8019,10 @@ biolink:IndividualOrganism a owl:Class ; skos:exactMatch STY:T001, SIO:010000 ; skos:narrowMatch foaf:Person, - WIKIDATA:Q795052 . + WIKIDATA:Q795052 ; + linkml:attributes "{}" ; + linkml:is_a "organismal entity" ; + linkml:mixins "subject of investigation" . biolink:OrganismTaxonToEntityAssociation a owl:Class ; rdfs:label "organism taxon to entity association" ; @@ -7106,7 +8031,8 @@ biolink:OrganismTaxonToEntityAssociation a owl:Class ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], linkml:mixin ; - skos:definition "An association between an organism taxon and another entity" . + skos:definition "An association between an organism taxon and another entity" ; + linkml:attributes "{}" . biolink:Pathway a owl:Class ; rdfs:label "pathway" ; @@ -7115,31 +8041,43 @@ biolink:Pathway a owl:Class ; skos:exactMatch , WIKIDATA:Q4915012 ; skos:narrowMatch , - SIO:010526 . + SIO:010526 ; + linkml:attributes "{}" ; + linkml:is_a "biological process" ; + linkml:mixins "ontology class" . biolink:PlanetaryEntity a owl:Class ; rdfs:label "planetary entity" ; rdfs:subClassOf biolink:NamedThing ; - skos:definition "Any entity or process that exists at the level of the whole planet" . + skos:definition "Any entity or process that exists at the level of the whole planet" ; + linkml:attributes "{}" ; + linkml:is_a "named thing" . biolink:PredicateMapping a owl:Class ; rdfs:label "predicate mapping" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OrganismTaxon ; owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:narrow_match ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:CausalMechanismQualifierEnum ; @@ -7147,65 +8085,59 @@ biolink:PredicateMapping a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalContextQualifierEnum ; - owl:onProperty biolink:anatomical_context_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:object_context_qualifier ], + owl:onClass biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:broad_match ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:exact_match ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:mapped_predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:narrow_match ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:mapped_predicate ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ] ; - skos:definition "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." . + owl:onClass linkml:String ; + owl:onProperty biolink:subject_aspect_qualifier ] ; + skos:definition "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." ; + linkml:attributes "{}" . biolink:Protein a owl:Class ; rdfs:label "protein" ; @@ -7220,7 +8152,10 @@ biolink:Protein a owl:Class ; SIO:010043, WIKIDATA:Q8054 ; skos:narrowMatch STY:T126, - STY:T192 . + STY:T192 ; + linkml:attributes "{}" ; + linkml:is_a "polypeptide" ; + linkml:mixins "gene product mixin" . biolink:SequenceFeatureRelationship a owl:Class ; rdfs:label "sequence feature relationship" ; @@ -7234,7 +8169,9 @@ biolink:SequenceFeatureRelationship a owl:Class ; owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "For example, a particular exon is part of a particular transcript or gene" ; - skos:exactMatch CHADO:feature_relationship . + skos:exactMatch CHADO:feature_relationship ; + linkml:attributes "{}" ; + linkml:is_a "association" . biolink:acts_upstream_of_or_within a owl:ObjectProperty ; rdfs:label "acts upstream of or within" ; @@ -7243,7 +8180,8 @@ biolink:acts_upstream_of_or_within a owl:ObjectProperty ; rdfs:subPropertyOf biolink:acts_upstream_of ; owl:inverseOf biolink:has_upstream_or_within_actor ; skos:exactMatch RO:0002264 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "acts upstream of" . biolink:affects_response_to a owl:ObjectProperty ; rdfs:label "affects response to" ; @@ -7252,7 +8190,8 @@ biolink:affects_response_to a owl:ObjectProperty ; rdfs:subPropertyOf biolink:affects ; owl:inverseOf biolink:response_affected_by ; skos:exactMatch CTD:affects_response_to ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "affects" . biolink:affects_risk_for a owl:ObjectProperty ; rdfs:label "affects risk for" ; @@ -7261,17 +8200,16 @@ biolink:affects_risk_for a owl:ObjectProperty ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; owl:inverseOf biolink:risk_affected_by ; skos:definition "holds between two entities where exposure to one entity alters the chance of developing the other" ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:anatomical_context_qualifier a owl:ObjectProperty ; rdfs:label "anatomical context qualifier" ; rdfs:domain biolink:Association ; - rdfs:range biolink:AnatomicalContextQualifierEnum ; + rdfs:range linkml:String ; rdfs:subPropertyOf biolink:statement_qualifier ; skos:definition "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; - skos:editorialNote "Anatomical context values can be any term from UBERON. For example, the context qualifier ‘cerebral cortext’ combines with a core concept of ‘neuron’ to express the composed concept ‘neuron in the cerebral cortext’. The species_context_qualifier applies taxonomic context, e.g. species-specific molecular activity. Ontology CURIEs are expected as values here, the examples below are intended to help clarify the content of the CURIEs." ; - linkml:examples "Example(value='blood', description=None)", - "Example(value='cerebral cortext', description=None)" . + linkml:is_a "statement qualifier" . biolink:associated_with_likelihood_of a owl:ObjectProperty ; rdfs:label "associated with likelihood of" ; @@ -7280,7 +8218,8 @@ biolink:associated_with_likelihood_of a owl:ObjectProperty ; rdfs:subPropertyOf biolink:associated_with ; owl:inverseOf biolink:likelihood_associated_with ; skos:definition "A a relationship that holds between two concepts represented by variables for which a statistical dependence is demonstrated, wherein the state or value of one variable predicts the future state or value of the other. E.g. the statement “An Atrial Fibrillation (Afib) diagnosis is associated with likelihood of a Myocardial Infraction (MI) diagnosis” asserts that the state of having Afib is associated with an increased or decreased likelihood that a patient will later exhibit MI." ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "associated with" . biolink:enabled_by a owl:ObjectProperty ; rdfs:label "enabled by" ; @@ -7290,7 +8229,8 @@ biolink:enabled_by a owl:ObjectProperty ; owl:inverseOf biolink:enables ; skos:definition "holds between a process and a physical entity, where the physical entity executes the process" ; skos:exactMatch RO:0002333 ; - biolink:opposite_of "prevented by" . + biolink:opposite_of "prevented by" ; + linkml:is_a "has participant" . biolink:expression_site a owl:ObjectProperty ; rdfs:label "expression site" ; @@ -7298,7 +8238,7 @@ biolink:expression_site a owl:ObjectProperty ; rdfs:range biolink:AnatomicalEntity ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; - linkml:examples "Example(value='UBERON:0002037', description='cerebellum')" . + linkml:is_a "association slot" . biolink:has_output a owl:ObjectProperty ; rdfs:label "has output" ; @@ -7318,14 +8258,16 @@ biolink:has_output a owl:ObjectProperty ; RO:0004008, PathWhiz:has_right_element ; biolink:canonical_predicate "True" ; - biolink:opposite_of "has input" . + biolink:opposite_of "has input" ; + linkml:is_a "has participant" . biolink:has_upstream_or_within_actor a owl:ObjectProperty ; rdfs:label "has upstream or within actor" ; rdfs:domain biolink:BiologicalProcess ; rdfs:range biolink:GeneOrGeneProduct ; rdfs:subPropertyOf biolink:has_upstream_actor ; - owl:inverseOf biolink:acts_upstream_of_or_within . + owl:inverseOf biolink:acts_upstream_of_or_within ; + linkml:is_a "has upstream actor" . biolink:homologous_to a owl:ObjectProperty, owl:SymmetricProperty ; @@ -7338,8 +8280,8 @@ biolink:homologous_to a owl:ObjectProperty, skos:exactMatch RO:HOM0000001, SIO:010302 ; skos:narrowMatch UBERON_CORE:sexually_homologous_to ; - skos:note "typically used to describe homology relationships between genes or gene products" ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "similar to" . biolink:interacts_with a owl:ObjectProperty, owl:SymmetricProperty ; @@ -7348,16 +8290,17 @@ biolink:interacts_with a owl:ObjectProperty, rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; skos:definition "holds between any two entities that directly or indirectly interact with each other" ; - skos:editorialNote "please use a more specific child predicate of interacts with, either physically interacts with or genetically interacts with. " ; - skos:exactMatch SEMMEDDB:INTERACTS_WITH . + skos:exactMatch SEMMEDDB:INTERACTS_WITH ; + linkml:is_a "related to at instance level" . biolink:knowledge_source a owl:ObjectProperty ; rdfs:label "knowledge source" ; rdfs:domain biolink:Association ; - rdfs:range biolink:InformationResource ; + rdfs:range linkml:String ; rdfs:subPropertyOf biolink:association_slot ; skos:closeMatch pav:providedBy ; - skos:definition "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." . + skos:definition "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + linkml:is_a "association slot" . biolink:likelihood_associated_with a owl:ObjectProperty ; rdfs:label "likelihood associated with" ; @@ -7365,32 +8308,37 @@ biolink:likelihood_associated_with a owl:ObjectProperty ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:associated_with ; owl:inverseOf biolink:associated_with_likelihood_of ; - skos:definition "" . + skos:definition "" ; + linkml:is_a "associated with" . biolink:object_aspect_qualifier a owl:ObjectProperty ; rdfs:label "object aspect qualifier" ; rdfs:domain biolink:Association ; rdfs:range linkml:String ; - rdfs:subPropertyOf biolink:aspect_qualifier . + rdfs:subPropertyOf biolink:aspect_qualifier ; + linkml:is_a "aspect qualifier" . biolink:object_form_or_variant_qualifier a owl:ObjectProperty ; rdfs:label "object form or variant qualifier" ; rdfs:domain biolink:Association ; rdfs:range linkml:String ; - rdfs:subPropertyOf biolink:form_or_variant_qualifier . + rdfs:subPropertyOf biolink:form_or_variant_qualifier ; + linkml:is_a "form or variant qualifier" . biolink:object_part_qualifier a owl:ObjectProperty ; rdfs:label "object part qualifier" ; rdfs:domain biolink:Association ; rdfs:range linkml:String ; - rdfs:subPropertyOf biolink:part_qualifier . + rdfs:subPropertyOf biolink:part_qualifier ; + linkml:is_a "part qualifier" . biolink:phenotypic_state a owl:ObjectProperty ; rdfs:label "phenotypic state" ; rdfs:domain biolink:Association ; rdfs:range biolink:DiseaseOrPhenotypicFeature ; rdfs:subPropertyOf biolink:association_slot ; - skos:definition "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." . + skos:definition "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; + linkml:is_a "association slot" . biolink:response_affected_by a owl:ObjectProperty ; rdfs:label "response affected by" ; @@ -7398,33 +8346,38 @@ biolink:response_affected_by a owl:ObjectProperty ; rdfs:range biolink:ChemicalEntityOrGeneOrGeneProduct ; rdfs:subPropertyOf biolink:affected_by ; owl:inverseOf biolink:affects_response_to ; - skos:definition "holds between two chemical entities where the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) of one is affected by the action of the other." . + skos:definition "holds between two chemical entities where the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) of one is affected by the action of the other." ; + linkml:is_a "affected by" . biolink:risk_affected_by a owl:ObjectProperty ; rdfs:label "risk affected by" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; - owl:inverseOf biolink:affects_risk_for . + owl:inverseOf biolink:affects_risk_for ; + linkml:is_a "related to at instance level" . biolink:statement_qualifier a owl:ObjectProperty ; rdfs:label "statement qualifier" ; rdfs:domain biolink:Association ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:qualifier ; - skos:definition "" . + skos:definition "" ; + linkml:is_a "qualifier" . biolink:subject_derivative_qualifier a owl:ObjectProperty ; rdfs:label "subject derivative qualifier" ; rdfs:domain biolink:Association ; rdfs:range linkml:String ; - rdfs:subPropertyOf biolink:derivative_qualifier . + rdfs:subPropertyOf biolink:derivative_qualifier ; + linkml:is_a "derivative qualifier" . biolink:subject_part_qualifier a owl:ObjectProperty ; rdfs:label "subject part qualifier" ; rdfs:domain biolink:Association ; rdfs:range linkml:String ; - rdfs:subPropertyOf biolink:part_qualifier . + rdfs:subPropertyOf biolink:part_qualifier ; + linkml:is_a "part qualifier" . biolink:volume a owl:ObjectProperty ; rdfs:label "volume" ; @@ -7432,7 +8385,8 @@ biolink:volume a owl:ObjectProperty ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:node_property ; skos:definition "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; - skos:exactMatch WIKIDATA_PROPERTY:P478 . + skos:exactMatch WIKIDATA_PROPERTY:P478 ; + linkml:is_a "node property" . biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum a owl:Class ; rdfs:label "ChemicalOrGeneOrGeneProductFormOrVariantEnum" ; @@ -7449,7 +8403,9 @@ biolink:ClinicalAttribute a owl:Class ; rdfs:label "clinical attribute" ; rdfs:subClassOf biolink:Attribute ; skos:definition "Attributes relating to a clinical manifestation" ; - skos:exactMatch STY:T201 . + skos:exactMatch STY:T201 ; + linkml:attributes "{}" ; + linkml:is_a "attribute" . biolink:DatasetVersion a owl:Class ; rdfs:label "dataset version" ; @@ -7466,34 +8422,32 @@ biolink:DatasetVersion a owl:Class ; owl:onClass linkml:String ; owl:onProperty pav:version ], biolink:InformationContentEntity ; - skos:definition "an item that holds version level information about a dataset." . + skos:definition "an item that holds version level information about a dataset." ; + linkml:attributes "{}" ; + linkml:is_a "information content entity" . biolink:FunctionalAssociation a owl:Class ; rdfs:label "functional association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:OntologyClass ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:MacromolecularMachineMixin ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:OntologyClass ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:Association ; - skos:definition "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed." . + skos:definition "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed." ; + linkml:attributes "{}" ; + linkml:is_a "association" . biolink:GeneProductIsoformMixin a owl:Class ; rdfs:label "gene product isoform mixin" ; rdfs:subClassOf biolink:GeneProductMixin, linkml:mixin ; - skos:definition "This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms." . - -biolink:GeneToEntityAssociationMixin a owl:Class ; - rdfs:label "gene to entity association mixin" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - linkml:mixin . + skos:definition "This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms." ; + linkml:attributes "{}" ; + linkml:is_a "gene product mixin" . biolink:MacromolecularMachineToEntityAssociationMixin a owl:Class ; rdfs:label "macromolecular machine to entity association mixin" ; @@ -7502,14 +8456,16 @@ biolink:MacromolecularMachineToEntityAssociationMixin a owl:Class ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], linkml:mixin ; - skos:definition "an association which has a macromolecular machine mixin as a subject" . + skos:definition "an association which has a macromolecular machine mixin as a subject" ; + linkml:attributes "{}" . biolink:PathologicalEntityMixin a owl:Class ; rdfs:label "pathological entity mixin" ; rdfs:subClassOf linkml:mixin ; skos:definition "A pathological (abnormal) structure or process." ; skos:exactMatch ; - skos:narrowMatch . + skos:narrowMatch ; + linkml:attributes "{}" . biolink:PhysicalEntity a owl:Class ; rdfs:label "physical entity" ; @@ -7517,24 +8473,30 @@ biolink:PhysicalEntity a owl:Class ; biolink:PhysicalEssence ; skos:definition "An entity that has material reality (a.k.a. physical essence)." ; skos:exactMatch STY:T072 ; - skos:narrowMatch STY:T073 . + skos:narrowMatch STY:T073 ; + linkml:attributes "{}" ; + linkml:is_a "named thing" ; + linkml:mixins "physical essence" . biolink:QuantityValue a owl:Class ; rdfs:label "quantity value" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_numeric_value ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Unit ; owl:onProperty biolink:has_unit ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty biolink:has_numeric_value ], biolink:Annotation ; - skos:definition "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value" . + skos:definition "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value" ; + linkml:attributes "{}" ; + linkml:is_a "annotation" . biolink:RelationshipQuantifier a owl:Class ; rdfs:label "relationship quantifier" ; - rdfs:subClassOf linkml:mixin . + rdfs:subClassOf linkml:mixin ; + linkml:attributes "{}" . biolink:StrandEnum a owl:Class ; rdfs:label "StrandEnum" ; @@ -7551,13 +8513,15 @@ biolink:acts_upstream_of a owl:ObjectProperty ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; owl:inverseOf biolink:has_upstream_actor ; skos:exactMatch RO:0002263 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:aggregate_statistic a owl:ObjectProperty ; rdfs:label "aggregate statistic" ; rdfs:domain biolink:NamedThing ; rdfs:range linkml:String ; - rdfs:subPropertyOf biolink:node_property . + rdfs:subPropertyOf biolink:node_property ; + linkml:is_a "node property" . biolink:category a owl:ObjectProperty ; rdfs:label "category" ; @@ -7568,7 +8532,8 @@ biolink:category a owl:ObjectProperty ; * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" . +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + linkml:is_a "type" . biolink:coexists_with a owl:ObjectProperty, owl:SymmetricProperty ; @@ -7744,7 +8709,8 @@ biolink:coexists_with a owl:ObjectProperty, UBERON_CORE:transitively_connected_to, UBERON_CORE:transitively_distally_connected_to, UBERON_CORE:transitively_proximally_connected_to ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:has_input a owl:ObjectProperty ; rdfs:label "has input" ; @@ -7769,26 +8735,30 @@ biolink:has_input a owl:ObjectProperty ; , PathWhiz:has_left_element ; biolink:canonical_predicate "True" ; - biolink:opposite_of "has output" . + biolink:opposite_of "has output" ; + linkml:is_a "has participant" . biolink:has_upstream_actor a owl:ObjectProperty ; rdfs:label "has upstream actor" ; rdfs:domain biolink:BiologicalProcess ; rdfs:range biolink:GeneOrGeneProduct ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; - owl:inverseOf biolink:acts_upstream_of . + owl:inverseOf biolink:acts_upstream_of ; + linkml:is_a "related to at instance level" . biolink:object_context_qualifier a owl:ObjectProperty ; rdfs:label "object context qualifier" ; rdfs:domain biolink:Association ; rdfs:range linkml:String ; - rdfs:subPropertyOf biolink:context_qualifier . + rdfs:subPropertyOf biolink:context_qualifier ; + linkml:is_a "context qualifier" . biolink:object_direction_qualifier a owl:ObjectProperty ; rdfs:label "object direction qualifier" ; rdfs:domain biolink:Association ; rdfs:range biolink:DirectionQualifierEnum ; - rdfs:subPropertyOf biolink:direction_qualifier . + rdfs:subPropertyOf biolink:direction_qualifier ; + linkml:is_a "direction qualifier" . biolink:quantifier_qualifier a owl:ObjectProperty ; rdfs:label "quantifier qualifier" ; @@ -7800,7 +8770,8 @@ biolink:quantifier_qualifier a owl:ObjectProperty ; LOINC:analyzes, LOINC:measured_by, LOINC:property_of, - SEMMEDDB:MEASURES . + SEMMEDDB:MEASURES ; + linkml:is_a "association slot" . biolink:stage_qualifier a owl:ObjectProperty ; rdfs:label "stage qualifier" ; @@ -7808,25 +8779,28 @@ biolink:stage_qualifier a owl:ObjectProperty ; rdfs:range biolink:LifeStage ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "stage during which gene or protein expression of takes place." ; - linkml:examples "Example(value='UBERON:0000069', description='larval stage')" . + linkml:is_a "association slot" . biolink:subject_aspect_qualifier a owl:ObjectProperty ; rdfs:label "subject aspect qualifier" ; rdfs:domain biolink:Association ; rdfs:range linkml:String ; - rdfs:subPropertyOf biolink:aspect_qualifier . + rdfs:subPropertyOf biolink:aspect_qualifier ; + linkml:is_a "aspect qualifier" . biolink:subject_context_qualifier a owl:ObjectProperty ; rdfs:label "subject context qualifier" ; rdfs:domain biolink:Association ; rdfs:range linkml:String ; - rdfs:subPropertyOf biolink:context_qualifier . + rdfs:subPropertyOf biolink:context_qualifier ; + linkml:is_a "context qualifier" . biolink:subject_form_or_variant_qualifier a owl:ObjectProperty ; rdfs:label "subject form or variant qualifier" ; rdfs:domain biolink:Association ; rdfs:range linkml:String ; - rdfs:subPropertyOf biolink:form_or_variant_qualifier . + rdfs:subPropertyOf biolink:form_or_variant_qualifier ; + linkml:is_a "form or variant qualifier" . rdfs:label a owl:ObjectProperty . @@ -7839,7 +8813,10 @@ biolink:CellularOrganism a owl:Class ; rdfs:subClassOf biolink:OrganismalEntity, biolink:SubjectOfInvestigation ; skos:definition "" ; - skos:exactMatch . + skos:exactMatch ; + linkml:attributes "{}" ; + linkml:is_a "organismal entity" ; + linkml:mixins "subject of investigation" . biolink:Dataset a owl:Class ; rdfs:label "dataset" ; @@ -7848,26 +8825,50 @@ biolink:Dataset a owl:Class ; skos:exactMatch IAO:0000100, , schema:dataset, - dcid:Dataset . + dcid:Dataset ; + linkml:attributes "{}" ; + linkml:is_a "information content entity" . + +biolink:GeneToDiseaseAssociation a owl:Class ; + rdfs:label "gene to disease association" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:Disease ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:GeneOrGeneProduct ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], + biolink:EntityToDiseaseAssociationMixin, + biolink:GeneToDiseaseOrPhenotypicFeatureAssociation, + biolink:GeneToEntityAssociationMixin ; + skos:closeMatch dcid:DiseaseGeneAssociation ; + skos:exactMatch SIO:000983 ; + linkml:attributes "{}" ; + linkml:is_a "gene to disease or phenotypic feature association" ; + linkml:mixins "entity to disease association mixin", + "gene to entity association mixin" . biolink:LifeStage a owl:Class ; rdfs:label "life stage" ; rdfs:subClassOf biolink:OrganismalEntity ; skos:definition "A stage of development or growth of an organism, including post-natal adult stages" ; skos:exactMatch ; - skos:narrowMatch HsapDv:0000000 . + skos:narrowMatch HsapDv:0000000 ; + linkml:attributes "{}" ; + linkml:is_a "organismal entity" . biolink:MolecularActivity a owl:Class ; rdfs:label "molecular activity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:has_output ], - [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:allValuesFrom biolink:MacromolecularMachineMixin ; owl:onProperty biolink:enabled_by ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MolecularEntity ; + owl:onProperty biolink:has_output ], biolink:BiologicalProcessOrActivity, biolink:Occurrent, biolink:OntologyClass ; @@ -7877,30 +8878,30 @@ biolink:MolecularActivity a owl:Class ; skos:broadMatch STY:T045 ; skos:definition "An execution of a molecular function carried out by a gene product or macromolecular complex." ; skos:exactMatch STY:T044, - . + ; + linkml:attributes "{}" ; + linkml:is_a "biological process or activity" ; + linkml:mixins "occurrent", + "ontology class" . biolink:RetrievalSource a owl:Class ; rdfs:label "retrieval source" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Uriorcurie ; - owl:onProperty biolink:resource_id ; - owl:qualifiedCardinality 1 ], + owl:onProperty biolink:upstream_resource_ids ], [ a owl:Restriction ; owl:onClass biolink:ResourceRoleEnum ; owl:onProperty biolink:resource_role ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Uriorcurie ; - owl:onProperty biolink:upstream_resource_ids ], + owl:onProperty biolink:resource_id ; + owl:qualifiedCardinality 1 ], biolink:InformationContentEntity ; - skos:definition "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." . - -biolink:StudyResult a owl:Class ; - rdfs:label "study result" ; - rdfs:subClassOf biolink:InformationContentEntity ; - skos:definition "A collection of data items from a study that are about a particular study subject or experimental unit (the 'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation of this data as evidence." ; - skos:editorialNote "The data/metadata included in a Study Result object are typically a subset of data from a larger study data set, that are selected by a curator because they may be useful as evidence for deriving knowledge about a specific focus of the study. The notion of a 'study' here is defined broadly to include any research activity at any scale that is aimed at generating knowledge or hypotheses. This may include a single assay or computational analyses, or a larger scale clinical trial or experimental research investigation." . + skos:definition "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." ; + linkml:attributes "{}" ; + linkml:is_a "information content entity" . biolink:VariantToEntityAssociationMixin a owl:Class ; rdfs:label "variant to entity association mixin" ; @@ -7908,7 +8909,8 @@ biolink:VariantToEntityAssociationMixin a owl:Class ; owl:onClass biolink:SequenceVariant ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - linkml:mixin . + linkml:mixin ; + linkml:attributes "{}" . biolink:contributor a owl:ObjectProperty ; rdfs:label "contributor" ; @@ -7917,7 +8919,7 @@ biolink:contributor a owl:ObjectProperty ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; owl:inverseOf biolink:has_contributor ; skos:exactMatch dct:contributor ; - skos:note "This is a grouping for predicates relating entities to their associated contributors realizing them" . + linkml:is_a "related to at instance level" . biolink:has_attribute a owl:ObjectProperty ; rdfs:label "has attribute" ; @@ -8006,7 +9008,8 @@ biolink:has_contributor a owl:ObjectProperty ; rdfs:domain biolink:InformationContentEntity ; rdfs:range biolink:Agent ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; - owl:inverseOf biolink:contributor . + owl:inverseOf biolink:contributor ; + linkml:is_a "related to at instance level" . biolink:in_taxon a owl:ObjectProperty ; rdfs:label "in taxon" ; @@ -8023,14 +9026,16 @@ biolink:in_taxon a owl:ObjectProperty ; skos:exactMatch RO:0002162, WIKIDATA_PROPERTY:P703 ; skos:narrowMatch RO:0002160 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:sequence_localization_attribute a owl:ObjectProperty ; rdfs:label "sequence localization attribute" ; rdfs:domain biolink:GenomicSequenceLocalization ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:association_slot ; - skos:definition "An attribute that can be applied to a genome sequence localization edge. These edges connect a nucleic acid entity such as an exon to an entity such as a chromosome. Edge properties are used to ascribe specific positional information and other metadata to the localization. In pragmatic terms this can be thought of as columns in a GFF3 line." . + skos:definition "An attribute that can be applied to a genome sequence localization edge. These edges connect a nucleic acid entity such as an exon to an entity such as a chromosome. Edge properties are used to ascribe specific positional information and other metadata to the localization. In pragmatic terms this can be thought of as columns in a GFF3 line." ; + linkml:is_a "association slot" . rdf:type a owl:ObjectProperty ; rdfs:label "type" ; @@ -8045,24 +9050,26 @@ biolink:ChemicalMixture a owl:Class ; rdfs:label "chemical mixture" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:drug_regulatory_status_world_wide ], + owl:onClass biolink:ChemicalMixture ; + owl:onProperty biolink:is_supplement ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DrugDeliveryEnum ; + owl:onProperty biolink:routes_of_delivery ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:highest_FDA_approval_status ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DrugDeliveryEnum ; - owl:onProperty biolink:routes_of_delivery ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ChemicalMixture ; - owl:onProperty biolink:is_supplement ], + owl:onClass linkml:String ; + owl:onProperty biolink:drug_regulatory_status_world_wide ], biolink:ChemicalEntity ; skos:closeMatch dcid:ChemicalCompound ; skos:definition "A chemical mixture is a chemical entity composed of two or more molecular entities." ; skos:narrowMatch , - SNOMEDCT:49616005 . + SNOMEDCT:49616005 ; + linkml:attributes "{}" ; + linkml:is_a "chemical entity" . biolink:ChemicalToEntityAssociationMixin a owl:Class ; rdfs:label "chemical to entity association mixin" ; @@ -8072,7 +9079,9 @@ biolink:ChemicalToEntityAssociationMixin a owl:Class ; owl:qualifiedCardinality 1 ], biolink:ChemicalEntityToEntityAssociationMixin, linkml:mixin ; - skos:definition "An interaction between a chemical entity and another entity" . + skos:definition "An interaction between a chemical entity and another entity" ; + linkml:attributes "{}" ; + linkml:is_a "chemical entity to entity association mixin" . biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a owl:Class ; rdfs:label "entity to disease or phenotypic feature association mixin" ; @@ -8080,7 +9089,8 @@ biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a owl:Class ; owl:onClass biolink:DiseaseOrPhenotypicFeature ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - linkml:mixin . + linkml:mixin ; + linkml:attributes "{}" . biolink:GeneGroupingMixin a owl:Class ; rdfs:label "gene grouping mixin" ; @@ -8088,7 +9098,8 @@ biolink:GeneGroupingMixin a owl:Class ; owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:has_gene_or_gene_product ], linkml:mixin ; - skos:definition "any grouping of multiple genes or gene products" . + skos:definition "any grouping of multiple genes or gene products" ; + linkml:attributes "{}" . biolink:GeneOrGeneProductOrChemicalPartQualifierEnum a owl:Class ; rdfs:label "GeneOrGeneProductOrChemicalPartQualifierEnum" ; @@ -8104,17 +9115,19 @@ biolink:GeneOrGeneProductOrChemicalPartQualifierEnum a owl:Class ; biolink:GeneProductMixin a owl:Class ; rdfs:label "gene product mixin" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:LabelType ; - owl:onProperty biolink:synonym ], - [ a owl:Restriction ; owl:allValuesFrom linkml:Uriorcurie ; owl:onProperty biolink:xref ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:LabelType ; + owl:onProperty biolink:synonym ], biolink:GeneOrGeneProduct, linkml:mixin ; skos:definition "The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA molecules." ; skos:exactMatch , , - WIKIDATA:Q424689 . + WIKIDATA:Q424689 ; + linkml:attributes "{}" ; + linkml:is_a "gene or gene product" . biolink:ModelToDiseaseAssociationMixin a owl:Class ; rdfs:label "model to disease association mixin" ; @@ -8127,39 +9140,8 @@ biolink:ModelToDiseaseAssociationMixin a owl:Class ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], linkml:mixin ; - skos:definition "This mixin is used for any association class for which the subject (source node) plays the role of a 'model', in that it recapitulates some features of the disease in a way that is useful for studying the disease outside a patient carrying the disease" . - -biolink:PhenotypicFeature a owl:Class ; - rdfs:label "phenotypic feature" ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeature ; - skos:altLabel "endophenotype", - "phenotype", - "sign", - "symptom", - "trait" ; - skos:broadMatch , - ; - skos:definition "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment." ; - skos:exactMatch MESH:D010641, - , - , - , - SIO:010056, - SNOMEDCT:8116006, - WIKIDATA:Q104053 ; - skos:narrowMatch STY:T184, - , - , - FYPO:0000001, - , - , - , - , - XPO:00000000, - , - WIKIDATA:Q169872, - WIKIDATA:Q25203551 ; - linkml:examples "Example(value='MP:0001262', description='decreased body weight')" . + skos:definition "This mixin is used for any association class for which the subject (source node) plays the role of a 'model', in that it recapitulates some features of the disease in a way that is useful for studying the disease outside a patient carrying the disease" ; + linkml:attributes "{}" . biolink:PopulationOfIndividualOrganisms a owl:Class ; rdfs:label "population of individual organisms" ; @@ -8169,7 +9151,17 @@ biolink:PopulationOfIndividualOrganisms a owl:Class ; skos:exactMatch STY:T098, , , - SIO:001061 . + SIO:001061 ; + linkml:attributes "{}" ; + linkml:is_a "organismal entity" ; + linkml:mixins "subject of investigation" . + +biolink:StudyResult a owl:Class ; + rdfs:label "study result" ; + rdfs:subClassOf biolink:InformationContentEntity ; + skos:definition "A collection of data items from a study that are about a particular study subject or experimental unit (the 'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation of this data as evidence." ; + linkml:attributes "{}" ; + linkml:is_a "information content entity" . biolink:ThingWithTaxon a owl:Class ; rdfs:label "thing with taxon" ; @@ -8177,7 +9169,8 @@ biolink:ThingWithTaxon a owl:Class ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:in_taxon ], linkml:mixin ; - skos:definition "A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; genes, their products and other molecular entities; body parts; biological processes" . + skos:definition "A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; genes, their products and other molecular entities; body parts; biological processes" ; + linkml:attributes "{}" . biolink:correlated_with a owl:ObjectProperty, owl:SymmetricProperty ; @@ -8186,10 +9179,10 @@ biolink:correlated_with a owl:ObjectProperty, rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:associated_with ; skos:definition "A relationship that holds between two concepts represented by variables for which a statistical dependence is demonstrated using a correlation analysis method." ; - skos:editorialNote "These concepts may map exactly to the statistical variables, or represent related entities for which the variables serve as proxies in an Association (e.g. diseases, chemical entities or processes)." ; skos:exactMatch , RO:0002610 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "associated with" . biolink:has_part a owl:ObjectProperty ; rdfs:label "has part" ; @@ -8232,7 +9225,8 @@ biolink:has_part a owl:ObjectProperty ; PathWhiz:has_element_in_bound, PathWhiz:has_protein_in_complex ; biolink:canonical_predicate "True" ; - biolink:opposite_of "lacks part" . + biolink:opposite_of "lacks part" ; + linkml:is_a "overlaps" . biolink:part_of a owl:ObjectProperty ; rdfs:label "part of" ; @@ -8298,7 +9292,8 @@ biolink:part_of a owl:ObjectProperty ; UBERON_CORE:trunk_part_of, CPT:panel_element_of, CPT:panel_element_of_possibly_included, - VANDF:ingredient_of . + VANDF:ingredient_of ; + linkml:is_a "overlaps" . biolink:related_to a owl:ObjectProperty, owl:SymmetricProperty ; @@ -8422,66 +9417,38 @@ biolink:supporting_study_metadata a owl:ObjectProperty ; rdfs:domain biolink:Association ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:association_slot ; - skos:definition "Information about a study used to generate information used as evidence to support the knowledge expressed in an Association. In practice, data creators should use one of the more specific subtypes of this property." . - -biolink:Entity a owl:Class ; - rdfs:label "entity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LabelType ; - owl:onProperty rdfs:label ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:NarrativeText ; - owl:onProperty dct:description ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Attribute ; - owl:onProperty biolink:has_attribute ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:IriType ; - owl:onProperty biolink:iri ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty biolink:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty rdf:type ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:CategoryType ; - owl:onProperty biolink:category ] ; - skos:definition "Root Biolink Model class for all things and informational relationships, real or imagined." . + skos:definition "Information about a study used to generate information used as evidence to support the knowledge expressed in an Association. In practice, data creators should use one of the more specific subtypes of this property." ; + linkml:is_a "association slot" . -biolink:EntityToPhenotypicFeatureAssociationMixin a owl:Class ; - rdfs:label "entity to phenotypic feature association mixin" ; +biolink:Entity a owl:Class ; + rdfs:label "entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], + owl:onClass linkml:String ; + owl:onProperty biolink:id ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], + owl:allValuesFrom biolink:CategoryType ; + owl:onProperty biolink:category ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], + owl:onClass biolink:NarrativeText ; + owl:onProperty dct:description ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:onClass biolink:IriType ; + owl:onProperty biolink:iri ], [ a owl:Restriction ; - owl:onClass biolink:PhenotypicFeature ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], + owl:allValuesFrom linkml:String ; + owl:onProperty rdf:type ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], - biolink:EntityToFeatureOrDiseaseQualifiersMixin, - biolink:FrequencyQuantifier, - linkml:mixin . + owl:onClass biolink:LabelType ; + owl:onProperty rdfs:label ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Attribute ; + owl:onProperty biolink:has_attribute ] ; + skos:definition "Root Biolink Model class for all things and informational relationships, real or imagined." ; + linkml:attributes "{}" . biolink:Genotype a owl:Class ; rdfs:label "genotype" ; @@ -8500,7 +9467,11 @@ biolink:Genotype a owl:Class ; skos:definition "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background" ; skos:exactMatch , SIO:001079 ; - skos:note "Consider renaming as genotypic entity" . + linkml:attributes "{}" ; + linkml:is_a "biological entity" ; + linkml:mixins "genomic entity", + "ontology class", + "physical essence" . biolink:MacromolecularMachineMixin a owl:Class ; rdfs:label "macromolecular machine mixin" ; @@ -8509,12 +9480,47 @@ biolink:MacromolecularMachineMixin a owl:Class ; owl:onClass biolink:SymbolType ; owl:onProperty rdfs:label ], linkml:mixin ; - skos:definition "A union of gene locus, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this." . + skos:definition "A union of gene locus, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this." ; + linkml:attributes "{}" . + +biolink:PhenotypicFeature a owl:Class ; + rdfs:label "phenotypic feature" ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeature ; + skos:altLabel "endophenotype", + "phenotype", + "sign", + "symptom", + "trait" ; + skos:broadMatch , + ; + skos:definition "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment." ; + skos:exactMatch MESH:D010641, + , + , + , + SIO:010056, + SNOMEDCT:8116006, + WIKIDATA:Q104053 ; + skos:narrowMatch STY:T184, + , + , + FYPO:0000001, + , + , + , + , + XPO:00000000, + , + WIKIDATA:Q169872, + WIKIDATA:Q25203551 ; + linkml:attributes "{}" ; + linkml:is_a "disease or phenotypic feature" . biolink:PhysicalEssenceOrOccurrent a owl:Class ; rdfs:label "physical essence or occurrent" ; rdfs:subClassOf linkml:mixin ; - skos:definition "Either a physical or processual entity." . + skos:definition "Either a physical or processual entity." ; + linkml:attributes "{}" . biolink:Transcript a owl:Class ; rdfs:label "transcript" ; @@ -8523,14 +9529,17 @@ biolink:Transcript a owl:Class ; skos:exactMatch , SIO:010450, dcid:RNATranscript, - WIKIDATA:Q7243183 . + WIKIDATA:Q7243183 ; + linkml:attributes "{}" ; + linkml:is_a "nucleic acid entity" . biolink:has_gene_or_gene_product a owl:ObjectProperty ; rdfs:label "has gene or gene product" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:Gene ; rdfs:subPropertyOf biolink:node_property ; - skos:definition "connects an entity with one or more gene or gene products" . + skos:definition "connects an entity with one or more gene or gene products" ; + linkml:is_a "node property" . biolink:has_participant a owl:ObjectProperty ; rdfs:label "has participant" ; @@ -8561,7 +9570,8 @@ biolink:has_participant a owl:ObjectProperty ; PathWhiz:has_nucleic_acid, PathWhiz:has_protein, PathWhiz:has_reaction ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:participates_in a owl:ObjectProperty ; rdfs:label "participates in" ; @@ -8583,7 +9593,8 @@ biolink:participates_in a owl:ObjectProperty ; , RO:0002216, RO:0002505, - . + ; + linkml:is_a "related to at instance level" . biolink:DirectionQualifierEnum a owl:Class ; rdfs:label "DirectionQualifierEnum" ; @@ -8593,38 +9604,47 @@ biolink:DirectionQualifierEnum a owl:Class ; , . -biolink:Disease a owl:Class ; - rdfs:label "disease" ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeature ; - skos:altLabel "condition", - "disorder", - "medical condition" ; - skos:definition "A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." ; - skos:exactMatch STY:T047, - , - , - , - SIO:010299, - dcid:Disease, - UMLSSG:DISO, - WIKIDATA:Q12136 ; - skos:narrowMatch STY:T019, - STY:T020, - STY:T048, - STY:T049, - STY:T190, - STY:T191, - . - -biolink:EntityToDiseaseAssociationMixin a owl:Class ; - rdfs:label "entity to disease association mixin" ; +biolink:EntityToPhenotypicFeatureAssociationMixin a owl:Class ; + rdfs:label "entity to phenotypic feature association mixin" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:Disease ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_total ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty biolink:has_percentage ], + [ a owl:Restriction ; + owl:onClass biolink:PhenotypicFeature ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], biolink:EntityToFeatureOrDiseaseQualifiersMixin, + biolink:FrequencyQuantifier, + linkml:mixin ; + linkml:attributes "{}" ; + linkml:is_a "entity to feature or disease qualifiers mixin" ; + linkml:mixins "frequency quantifier" . + +biolink:GeneToEntityAssociationMixin a owl:Class ; + rdfs:label "gene to entity association mixin" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:GeneOrGeneProduct ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], linkml:mixin ; - skos:definition "mixin class for any association whose object (target node) is a disease" . + linkml:attributes "{}" . biolink:affected_by a owl:ObjectProperty ; rdfs:label "affected by" ; @@ -8632,7 +9652,8 @@ biolink:affected_by a owl:ObjectProperty ; rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; owl:inverseOf biolink:affects ; - skos:definition "describes an entity of which the state or quality is affected by another existing entity." . + skos:definition "describes an entity of which the state or quality is affected by another existing entity." ; + linkml:is_a "related to at instance level" . biolink:affects a owl:ObjectProperty ; rdfs:label "affects" ; @@ -8675,14 +9696,16 @@ biolink:affects a owl:ObjectProperty ; UBERGRAPH:is_increase_of, SEMMEDDB:ADMINISTERED_TO ; skos:relatedMatch ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:has_sequence_variant a owl:ObjectProperty ; rdfs:label "has sequence variant" ; rdfs:domain biolink:GenomicEntity ; rdfs:range biolink:SequenceVariant ; rdfs:subPropertyOf biolink:related_to_at_instance_level ; - owl:inverseOf biolink:is_sequence_variant_of . + owl:inverseOf biolink:is_sequence_variant_of ; + linkml:is_a "related to at instance level" . biolink:is_sequence_variant_of a owl:ObjectProperty ; rdfs:label "is sequence variant of" ; @@ -8695,7 +9718,8 @@ biolink:is_sequence_variant_of a owl:ObjectProperty ; "gene product variant of gene product" ; skos:definition "holds between a sequence variant and a nucleic acid entity" ; skos:narrowMatch WIKIDATA:P3433 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:related_to_at_concept_level a owl:ObjectProperty, owl:SymmetricProperty ; @@ -8704,14 +9728,16 @@ biolink:related_to_at_concept_level a owl:ObjectProperty, rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:related_to ; skos:definition "Represents a relationship held between terminology components that describe the conceptual model of a domain." ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to" . biolink:sex_qualifier a owl:ObjectProperty ; rdfs:label "sex qualifier" ; rdfs:domain biolink:Association ; rdfs:range biolink:BiologicalSex ; rdfs:subPropertyOf biolink:qualifier ; - skos:definition "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." . + skos:definition "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + linkml:is_a "qualifier" . biolink:Drug a owl:Class ; rdfs:label "drug" ; @@ -8725,18 +9751,17 @@ biolink:Drug a owl:Class ; dcid:Drug, WIKIDATA:Q12140 ; skos:narrowMatch STY:T195 ; - skos:note "The CHEBI ID represents a role rather than a substance" . + linkml:attributes "{}" ; + linkml:is_a "molecular mixture" ; + linkml:mixins "chemical or drug or treatment", + "ontology class" . biolink:GenomicSequenceLocalization a owl:Class ; rdfs:label "genomic sequence localization" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:NucleicAcidEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:end_interbase_coordinate ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:PhaseEnum ; @@ -8749,22 +9774,28 @@ biolink:GenomicSequenceLocalization a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:StrandEnum ; owl:onProperty biolink:strand ], - [ a owl:Restriction ; - owl:onClass biolink:NucleicAcidEntity ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:start_interbase_coordinate ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:end_interbase_coordinate ], + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:NucleicAcidEntity ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:NucleicAcidEntity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:SequenceAssociation ; skos:broadMatch dcid:Chromosome ; skos:definition "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; - skos:exactMatch dcid:GenomeAnnotation . + skos:exactMatch dcid:GenomeAnnotation ; + linkml:attributes "{}" ; + linkml:is_a "sequence association" . biolink:associated_with a owl:ObjectProperty, owl:SymmetricProperty ; @@ -8775,7 +9806,8 @@ biolink:associated_with a owl:ObjectProperty, skos:definition "Expresses a relationship between two named things where the relationship is typically generated statistically (though not in all cases), and is weaker than its child, 'correlated with', but stronger than its parent, 'related to'. This relationship holds between two concepts represented by variables for which a statistical dependence is demonstrated. E.g. the statement “Atrial Fibrillation (Afib) is associated with Myocardial Infraction (MI)” asserts that having Afib is not statistically independent from whether a patient will also have MI. Note that in Translator associations, the subject and object concepts may map exactly to the statistical variables, or represent related entities for which the variables serve as proxies in an Association (e.g. diseases, chemical entities or processes)." ; skos:narrowMatch RO:0004029, SNOMEDCT:47429007 ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to at instance level" . biolink:id a owl:ObjectProperty ; rdfs:label "id" ; @@ -8788,20 +9820,8 @@ biolink:id a owl:ObjectProperty ; biolink:ChemicalOrDrugOrTreatment a owl:Class ; rdfs:label "chemical or drug or treatment" ; - rdfs:subClassOf linkml:mixin . - -biolink:InformationResource a owl:Class ; - rdfs:label "information resource" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:LabelType ; - owl:onProperty biolink:synonym ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:InformationResourceStatusEnum ; - owl:onProperty biolink:information_resource_status ], - biolink:InformationContentEntity ; - skos:altLabel "knowledgebase" ; - skos:definition "A database or knowledgebase and its supporting ecosystem of interfaces and services that deliver content to consumers (e.g. web portals, APIs, query endpoints, streaming services, data downloads, etc.). A single Information Resource by this definition may span many different datasets or databases, and include many access endpoints and user interfaces. Information Resources include project-specific resources such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb." . + rdfs:subClassOf linkml:mixin ; + linkml:attributes "{}" . biolink:OrganismalEntity a owl:Class ; rdfs:label "organismal entity" ; @@ -8814,12 +9834,16 @@ biolink:OrganismalEntity a owl:Class ; skos:exactMatch , UMLSSG:LIVB, WIKIDATA:Q7239 ; - skos:narrowMatch STY:T008 . + skos:narrowMatch STY:T008 ; + linkml:attributes "{}" ; + linkml:is_a "biological entity" ; + linkml:mixins "subject of investigation" . biolink:Outcome a owl:Class ; rdfs:label "outcome" ; rdfs:subClassOf linkml:mixin ; - skos:definition "An entity that has the role of being the consequence of an exposure event. This is an abstract mixin grouping of various categories of possible biological or non-biological (e.g. clinical) outcomes." . + skos:definition "An entity that has the role of being the consequence of an exposure event. This is an abstract mixin grouping of various categories of possible biological or non-biological (e.g. clinical) outcomes." ; + linkml:attributes "{}" . biolink:has_count a owl:ObjectProperty ; rdfs:label "has count" ; @@ -8827,32 +9851,31 @@ biolink:has_count a owl:ObjectProperty ; rdfs:range linkml:Integer ; rdfs:subPropertyOf biolink:aggregate_statistic ; skos:definition "number of things with a particular property" ; - skos:exactMatch LOINC:has_count . + skos:exactMatch LOINC:has_count ; + linkml:is_a "aggregate statistic" . biolink:has_percentage a owl:ObjectProperty ; rdfs:label "has percentage" ; rdfs:domain biolink:NamedThing ; rdfs:range linkml:Double ; rdfs:subPropertyOf biolink:aggregate_statistic ; - skos:definition "equivalent to has quotient multiplied by 100" . + skos:definition "equivalent to has quotient multiplied by 100" ; + linkml:is_a "aggregate statistic" . biolink:has_quotient a owl:ObjectProperty ; rdfs:label "has quotient" ; rdfs:domain biolink:NamedThing ; rdfs:range linkml:Double ; - rdfs:subPropertyOf biolink:aggregate_statistic . + rdfs:subPropertyOf biolink:aggregate_statistic ; + linkml:is_a "aggregate statistic" . biolink:has_total a owl:ObjectProperty ; rdfs:label "has total" ; rdfs:domain biolink:NamedThing ; rdfs:range linkml:Integer ; rdfs:subPropertyOf biolink:aggregate_statistic ; - skos:definition "total number of things in a particular reference set" . - -biolink:BiologicalSex a owl:Class ; - rdfs:label "biological sex" ; - rdfs:subClassOf biolink:Attribute ; - skos:exactMatch . + skos:definition "total number of things in a particular reference set" ; + linkml:is_a "aggregate statistic" . biolink:synonym a owl:ObjectProperty ; rdfs:label "synonym" ; @@ -8867,7 +9890,52 @@ biolink:synonym a owl:ObjectProperty ; skos:altLabel, gff3:Alias, gpi:DB_Object_Synonyms, - AGRKB:synonyms . + AGRKB:synonyms ; + linkml:is_a "node property" . + +biolink:BiologicalSex a owl:Class ; + rdfs:label "biological sex" ; + rdfs:subClassOf biolink:Attribute ; + skos:exactMatch ; + linkml:attributes "{}" ; + linkml:is_a "attribute" . + +biolink:Disease a owl:Class ; + rdfs:label "disease" ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeature ; + skos:altLabel "condition", + "disorder", + "medical condition" ; + skos:definition "A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." ; + skos:exactMatch STY:T047, + , + , + , + SIO:010299, + dcid:Disease, + UMLSSG:DISO, + WIKIDATA:Q12136 ; + skos:narrowMatch STY:T019, + STY:T020, + STY:T048, + STY:T049, + STY:T190, + STY:T191, + ; + linkml:attributes "{}" ; + linkml:is_a "disease or phenotypic feature" . + +biolink:EntityToDiseaseAssociationMixin a owl:Class ; + rdfs:label "entity to disease association mixin" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:Disease ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], + biolink:EntityToFeatureOrDiseaseQualifiersMixin, + linkml:mixin ; + skos:definition "mixin class for any association whose object (target node) is a disease" ; + linkml:attributes "{}" ; + linkml:is_a "entity to feature or disease qualifiers mixin" . biolink:NucleicAcidEntity a owl:Class ; rdfs:label "nucleic acid entity" ; @@ -8888,24 +9956,71 @@ biolink:NucleicAcidEntity a owl:Class ; skos:definition "A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included." ; skos:exactMatch ; skos:narrowMatch STY:T086, - STY:T114 . + STY:T114 ; + linkml:attributes "{}" ; + linkml:is_a "molecular entity" ; + linkml:mixins "genomic entity", + "ontology class", + "physical essence", + "thing with taxon" . biolink:SubjectOfInvestigation a owl:Class ; rdfs:label "subject of investigation" ; rdfs:subClassOf linkml:mixin ; - skos:definition "An entity that has the role of being studied in an investigation, study, or experiment" . + skos:definition "An entity that has the role of being studied in an investigation, study, or experiment" ; + linkml:attributes "{}" . biolink:has_biological_sequence a owl:ObjectProperty ; rdfs:label "has biological sequence" ; rdfs:domain biolink:NamedThing ; rdfs:range biolink:BiologicalSequence ; rdfs:subPropertyOf biolink:node_property ; - skos:definition "connects a genomic feature to its sequence" . + skos:definition "connects a genomic feature to its sequence" ; + linkml:is_a "node property" . + +biolink:onset_qualifier a owl:ObjectProperty ; + rdfs:label "onset qualifier" ; + rdfs:domain biolink:Association ; + rdfs:range biolink:Onset ; + rdfs:subPropertyOf biolink:qualifier ; + skos:definition "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + linkml:is_a "qualifier" . + +biolink:severity_qualifier a owl:ObjectProperty ; + rdfs:label "severity qualifier" ; + rdfs:domain biolink:Association ; + rdfs:range biolink:SeverityValue ; + rdfs:subPropertyOf biolink:qualifier ; + skos:definition "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + linkml:is_a "qualifier" . biolink:BiologicalSequence a owl:Class ; rdfs:label "biological sequence" ; rdfs:subClassOf linkml:String . +biolink:Onset a owl:Class ; + rdfs:label "onset" ; + rdfs:subClassOf biolink:ClinicalCourse ; + skos:definition "The age group in which (disease) symptom manifestations appear" ; + skos:exactMatch ; + linkml:attributes "{}" ; + linkml:is_a "clinical course" . + +biolink:SeverityValue a owl:Class ; + rdfs:label "severity value" ; + rdfs:subClassOf biolink:Attribute ; + skos:definition "describes the severity of a phenotypic feature or disease" ; + linkml:attributes "{}" ; + linkml:is_a "attribute" . + +biolink:frequency_qualifier a owl:ObjectProperty ; + rdfs:label "frequency qualifier" ; + rdfs:domain biolink:Association ; + rdfs:range biolink:FrequencyValue ; + rdfs:subPropertyOf biolink:qualifier ; + skos:definition "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + linkml:is_a "qualifier" . + biolink:timepoint a owl:ObjectProperty ; rdfs:label "timepoint" ; rdfs:range biolink:TimeType ; @@ -8917,14 +10032,14 @@ biolink:Agent a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom linkml:Uriorcurie ; owl:onProperty biolink:affiliation ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LabelType ; - owl:onProperty rdfs:label ], [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty biolink:id ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LabelType ; + owl:onProperty rdfs:label ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -8939,7 +10054,9 @@ biolink:Agent a owl:Class ; STY:T094, STY:T095, STY:T096, - UMLSSG:ORGA . + UMLSSG:ORGA ; + linkml:attributes "{}" ; + linkml:is_a "administrative entity" . biolink:BiologicalProcessOrActivity a owl:Class ; rdfs:label "biological process or activity" ; @@ -8955,56 +10072,31 @@ biolink:BiologicalProcessOrActivity a owl:Class ; biolink:BiologicalEntity, biolink:Occurrent, biolink:OntologyClass ; - skos:definition "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system." . + skos:definition "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system." ; + linkml:attributes "{}" ; + linkml:is_a "biological entity" ; + linkml:mixins "occurrent", + "ontology class" . -biolink:PhysicalEssence a owl:Class ; - rdfs:label "physical essence" ; - rdfs:subClassOf biolink:PhysicalEssenceOrOccurrent, - linkml:mixin ; - skos:definition "Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge." . +biolink:FrequencyValue a owl:Class ; + rdfs:label "frequency value" ; + rdfs:subClassOf linkml:String . -biolink:onset_qualifier a owl:ObjectProperty ; - rdfs:label "onset qualifier" ; - rdfs:domain biolink:Association ; - rdfs:range biolink:Onset ; - rdfs:subPropertyOf biolink:qualifier ; - skos:definition "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" . +biolink:PhysicalEssence a owl:Class ; + rdfs:label "physical essence" ; + rdfs:subClassOf biolink:PhysicalEssenceOrOccurrent, + linkml:mixin ; + skos:definition "Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge." ; + linkml:attributes "{}" ; + linkml:is_a "physical essence or occurrent" . biolink:qualifier a owl:ObjectProperty ; rdfs:label "qualifier" ; rdfs:domain biolink:Association ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:association_slot ; - skos:definition "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" . - -biolink:severity_qualifier a owl:ObjectProperty ; - rdfs:label "severity qualifier" ; - rdfs:domain biolink:Association ; - rdfs:range biolink:SeverityValue ; - rdfs:subPropertyOf biolink:qualifier ; - skos:definition "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" . - -biolink:Onset a owl:Class ; - rdfs:label "onset" ; - rdfs:subClassOf biolink:ClinicalCourse ; - skos:definition "The age group in which (disease) symptom manifestations appear" ; - skos:exactMatch . - -biolink:SeverityValue a owl:Class ; - rdfs:label "severity value" ; - rdfs:subClassOf biolink:Attribute ; - skos:definition "describes the severity of a phenotypic feature or disease" . - -biolink:frequency_qualifier a owl:ObjectProperty ; - rdfs:label "frequency qualifier" ; - rdfs:domain biolink:Association ; - rdfs:range biolink:FrequencyValue ; - rdfs:subPropertyOf biolink:qualifier ; - skos:definition "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" . - -biolink:FrequencyValue a owl:Class ; - rdfs:label "frequency value" ; - rdfs:subClassOf linkml:String . + skos:definition "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + linkml:is_a "association slot" . biolink:BiologicalProcess a owl:Class ; rdfs:label "biological process" ; @@ -9015,7 +10107,11 @@ biolink:BiologicalProcess a owl:Class ; skos:definition "One or more causally connected executions of molecular functions" ; skos:exactMatch , SIO:000006, - WIKIDATA:Q2996394 . + WIKIDATA:Q2996394 ; + linkml:attributes "{}" ; + linkml:is_a "biological process or activity" ; + linkml:mixins "occurrent", + "ontology class" . biolink:ExposureEvent a owl:Class ; rdfs:label "exposure event" ; @@ -9028,7 +10124,13 @@ biolink:ExposureEvent a owl:Class ; skos:altLabel "experimental condition", "exposure" ; skos:definition "A (possibly time bounded) incidence of a feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes" ; - skos:exactMatch . + skos:exactMatch ; + linkml:attributes "{}" ; + linkml:is_a "ontology class" . + +biolink:LabelType a owl:Class ; + rdfs:label "label type" ; + rdfs:subClassOf linkml:String . biolink:MolecularEntity a owl:Class ; rdfs:label "molecular entity" ; @@ -9041,56 +10143,41 @@ biolink:MolecularEntity a owl:Class ; skos:narrowMatch STY:T085, STY:T088, , - bioschemas:MolecularEntity . + bioschemas:MolecularEntity ; + linkml:attributes "{}" ; + linkml:is_a "chemical entity" . biolink:TimeType a owl:Class ; rdfs:label "time type" ; rdfs:subClassOf linkml:Time . -biolink:LabelType a owl:Class ; - rdfs:label "label type" ; - rdfs:subClassOf linkml:String . - biolink:Occurrent a owl:Class ; rdfs:label "occurrent" ; rdfs:subClassOf biolink:PhysicalEssenceOrOccurrent, linkml:mixin ; skos:definition "A processual entity." ; - skos:exactMatch . - -biolink:OrganismTaxon a owl:Class ; - rdfs:label "organism taxon" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:TaxonomicRank ; - owl:onProperty biolink:has_taxonomic_rank ], - biolink:NamedThing ; - skos:altLabel "taxon", - "taxonomic classification" ; - skos:definition "A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies." ; - skos:exactMatch STY:T001, - bioschemas:Taxon, - WIKIDATA:Q16521 ; - skos:narrowMatch dcid:BiologicalSpecies . + skos:exactMatch ; + linkml:attributes "{}" ; + linkml:is_a "physical essence or occurrent" . biolink:InformationContentEntity a owl:Class ; rdfs:label "information content entity" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Date ; - owl:onProperty biolink:creation_date ], + owl:onClass linkml:String ; + owl:onProperty biolink:rights ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:license ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:format ], + owl:onClass linkml:Date ; + owl:onProperty biolink:creation_date ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:rights ], + owl:onProperty biolink:format ], biolink:NamedThing ; skos:altLabel "information", "information artefact", @@ -9108,29 +10195,51 @@ biolink:InformationContentEntity a owl:Class ; STY:T169, STY:T171, STY:T185, - UMLSSG:CONC . + UMLSSG:CONC ; + linkml:attributes "{}" ; + linkml:is_a "named thing" . + +biolink:OrganismTaxon a owl:Class ; + rdfs:label "organism taxon" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:TaxonomicRank ; + owl:onProperty biolink:has_taxonomic_rank ], + biolink:NamedThing ; + skos:altLabel "taxon", + "taxonomic classification" ; + skos:definition "A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies." ; + skos:exactMatch STY:T001, + bioschemas:Taxon, + WIKIDATA:Q16521 ; + skos:narrowMatch dcid:BiologicalSpecies ; + linkml:attributes "{}" ; + linkml:is_a "named thing" . biolink:Attribute a owl:Class ; rdfs:label "attribute" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:OntologyClass ; - owl:onProperty biolink:has_attribute_type ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LabelType ; + owl:onProperty rdfs:label ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:NamedThing ; owl:onProperty biolink:has_qualitative_value ], + [ a owl:Restriction ; + owl:onClass biolink:OntologyClass ; + owl:onProperty biolink:has_attribute_type ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:allValuesFrom biolink:QuantityValue ; owl:onProperty biolink:has_quantitative_value ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LabelType ; - owl:onProperty rdfs:label ], biolink:NamedThing, biolink:OntologyClass ; skos:definition "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ; - skos:exactMatch SIO:000614 . + skos:exactMatch SIO:000614 ; + linkml:attributes "{}" ; + linkml:is_a "named thing" ; + linkml:mixins "ontology class" . biolink:BiologicalEntity a owl:Class ; rdfs:label "biological entity" ; @@ -9143,7 +10252,10 @@ biolink:BiologicalEntity a owl:Class ; skos:narrowMatch STY:T050, STY:T129, SIO:010046, - WIKIDATA:Q28845870 . + WIKIDATA:Q28845870 ; + linkml:attributes "{}" ; + linkml:is_a "named thing" ; + linkml:mixins "thing with taxon" . biolink:AnatomicalEntity a owl:Class ; rdfs:label "anatomical entity" ; @@ -9168,18 +10280,21 @@ biolink:AnatomicalEntity a owl:Class ; WBbt:0000100, , ; - skos:relatedMatch SNOMEDCT:123037004 . + skos:relatedMatch SNOMEDCT:123037004 ; + linkml:attributes "{}" ; + linkml:is_a "organismal entity" ; + linkml:mixins "physical essence" . biolink:SequenceVariant a owl:Class ; rdfs:label "sequence variant" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSequence ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty biolink:id ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:BiologicalSequence ; + owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:has_gene ], @@ -9195,50 +10310,65 @@ biolink:SequenceVariant a owl:Class ; VMC:Allele ; skos:definition "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." ; skos:exactMatch WIKIDATA:Q15304597 ; - skos:note "This class is for modeling the specific state at a locus. A single DBSNP rs ID could correspond to more than one sequence variants (e.g CIViC:1252 and CIViC:1253, two distinct BRCA2 alleles for rs28897743)" . + linkml:attributes "{}" ; + linkml:is_a "biological entity" ; + linkml:mixins "genomic entity", + "ontology class", + "physical essence" . biolink:Publication a owl:Class ; rdfs:label "publication" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:summary ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty biolink:keywords ], + owl:onClass biolink:LabelType ; + owl:onProperty rdfs:label ], [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty dct:type ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty biolink:pages ], + owl:onProperty biolink:summary ], [ a owl:Restriction ; owl:allValuesFrom biolink:Agent ; owl:onProperty biolink:authors ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LabelType ; - owl:onProperty rdfs:label ], + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:pages ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty biolink:mesh_terms ], + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:keywords ], [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty biolink:id ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty biolink:mesh_terms ], + [ a owl:Class ; + owl:intersectionOf ( [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty dct:type ] [ a owl:Restriction ; + owl:onProperty dct:type ; + owl:someValuesFrom linkml:String ] ) ], biolink:InformationContentEntity ; skos:definition "Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP). " ; skos:exactMatch IAO:0000311 ; skos:narrowMatch STY:T170, - IAO:0000013 . + IAO:0000013 ; + linkml:attributes "{}" ; + linkml:is_a "information content entity" . biolink:ChemicalEntity a owl:Class ; rdfs:label "chemical entity" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:ChemicalEntity ; + owl:onProperty biolink:trade_name ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:max_tolerated_dose ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalRole ; + owl:onProperty biolink:has_chemical_role ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Boolean ; @@ -9246,13 +10376,6 @@ biolink:ChemicalEntity a owl:Class ; [ a owl:Restriction ; owl:allValuesFrom biolink:DrugAvailabilityEnum ; owl:onProperty biolink:available_from ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ChemicalEntity ; - owl:onProperty biolink:trade_name ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalRole ; - owl:onProperty biolink:has_chemical_role ], biolink:ChemicalEntityOrGeneOrGeneProduct, biolink:ChemicalEntityOrProteinOrPolypeptide, biolink:ChemicalOrDrugOrTreatment, @@ -9263,7 +10386,13 @@ biolink:ChemicalEntity a owl:Class ; , SIO:010004, WIKIDATA:Q79529 ; - skos:narrowMatch WIKIDATA:Q43460564 . + skos:narrowMatch WIKIDATA:Q43460564 ; + linkml:attributes "{}" ; + linkml:is_a "named thing" ; + linkml:mixins "chemical entity or gene or gene product", + "chemical entity or protein or polypeptide", + "chemical or drug or treatment", + "physical essence" . biolink:Gene a owl:Class ; rdfs:label "gene" ; @@ -9290,7 +10419,14 @@ biolink:Gene a owl:Class ; SIO:010035, dcid:Gene, WIKIDATA:Q7187 ; - skos:narrowMatch bioschemas:gene . + skos:narrowMatch bioschemas:gene ; + linkml:attributes "{}" ; + linkml:is_a "biological entity" ; + linkml:mixins "chemical entity or gene or gene product", + "gene or gene product", + "genomic entity", + "ontology class", + "physical essence" . biolink:GenomicEntity a owl:Class ; rdfs:label "genomic entity" ; @@ -9300,19 +10436,25 @@ biolink:GenomicEntity a owl:Class ; owl:onProperty biolink:has_biological_sequence ], linkml:mixin ; skos:narrowMatch STY:T028, - . + ; + linkml:attributes "{}" . biolink:ChemicalEntityOrGeneOrGeneProduct a owl:Class ; rdfs:label "chemical entity or gene or gene product" ; rdfs:subClassOf linkml:mixin ; - skos:definition "A union of chemical entities and children, and gene or gene product. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities." . + skos:definition "A union of chemical entities and children, and gene or gene product. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities." ; + linkml:attributes "{}" . biolink:DiseaseOrPhenotypicFeature a owl:Class ; rdfs:label "disease or phenotypic feature" ; rdfs:subClassOf biolink:BiologicalEntity ; skos:altLabel "phenome" ; skos:definition "Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature." ; - skos:narrowMatch STY:T033 . + skos:narrowMatch STY:T033 ; + linkml:attributes "{}" ; + linkml:is_a "biological entity" ; + linkml:union_of "disease", + "phenotypic feature" . rdf:predicate a owl:ObjectProperty ; rdfs:label "predicate" ; @@ -9320,24 +10462,25 @@ rdf:predicate a owl:ObjectProperty ; rdfs:range biolink:PredicateType ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - skos:editorialNote "Has a value from the Biolink related_to hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; skos:exactMatch OBAN:association_has_predicate, rdf:predicate, - owl:annotatedProperty . + owl:annotatedProperty ; + linkml:is_a "association slot" . + +biolink:PredicateType a owl:Class ; + rdfs:label "predicate type" ; + rdfs:subClassOf linkml:Uriorcurie . biolink:GeneOrGeneProduct a owl:Class ; rdfs:label "gene or gene product" ; rdfs:subClassOf biolink:MacromolecularMachineMixin, linkml:mixin ; - skos:definition "A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another" . - -biolink:PredicateType a owl:Class ; - rdfs:label "predicate type" ; - rdfs:subClassOf linkml:Uriorcurie . + skos:definition "A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another" ; + linkml:attributes "{}" ; + linkml:is_a "macromolecular machine mixin" . biolink:OntologyClass a owl:Class ; rdfs:label "ontology class" ; - rdfs:seeAlso "https://github.com/biolink/biolink-model/issues/486" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty biolink:id ; @@ -9346,9 +10489,7 @@ biolink:OntologyClass a owl:Class ; skos:definition "a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type." ; skos:exactMatch schema:Class, owl:Class ; - skos:note "Note that formally this is a metaclass. Instances of this class are instances in the graph, but can be the object of 'type' edges. For example, if we had a node in the graph representing a specific brain of a specific patient (e.g brain001), this could have a category of bl:Sample, and by typed more specifically with an ontology class UBERON:nnn, which has as category bl:AnatomicalEntity", - "This is modeled as a mixin. 'ontology class' should not be the primary type of a node in the KG. Instead you should use an informative bioloink category, such as AnatomicalEntity (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL), etc" ; - linkml:examples "Example(value='UBERON:0000955', description=\"the class 'brain' from the Uberon anatomy ontology\")" . + linkml:attributes "{}" . biolink:node_property a owl:ObjectProperty ; rdfs:label "node property" ; @@ -9364,7 +10505,8 @@ rdf:object a owl:ObjectProperty ; skos:definition "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; skos:exactMatch OBAN:association_has_object, rdf:object, - owl:annotatedTarget . + owl:annotatedTarget ; + linkml:is_a "association slot" . biolink:association_slot a owl:ObjectProperty ; rdfs:label "association slot" ; @@ -9385,7 +10527,8 @@ rdf:subject a owl:ObjectProperty ; skos:definition "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; skos:exactMatch OBAN:association_has_subject, rdf:subject, - owl:annotatedSource . + owl:annotatedSource ; + linkml:is_a "association slot" . biolink:related_to_at_instance_level a owl:ObjectProperty, owl:SymmetricProperty ; @@ -9394,123 +10537,125 @@ biolink:related_to_at_instance_level a owl:ObjectProperty, rdfs:range biolink:NamedThing ; rdfs:subPropertyOf biolink:related_to ; skos:definition "Represents a relationship held between two instances of a data classes. Much like an assertion component, in an ABox, these represent facts associated with the conceptual model." ; - biolink:canonical_predicate "True" . + biolink:canonical_predicate "True" ; + linkml:is_a "related to" . biolink:Association a owl:Class ; rdfs:label "association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OntologyClass ; - owl:onProperty biolink:subject_category ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:original_object ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty biolink:subject_label_closure ], - [ a owl:Restriction ; owl:allValuesFrom biolink:CategoryType ; owl:onProperty biolink:category ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty biolink:object_closure ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:subject_namespace ], [ a owl:Restriction ; owl:allValuesFrom biolink:RetrievalSource ; owl:onProperty biolink:retrieval_source_ids ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Publication ; + owl:onProperty biolink:publications ], + [ a owl:Restriction ; + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:qualifiers ], + owl:onProperty biolink:object_category_closure ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:subject_namespace ], + owl:onProperty biolink:original_subject ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:object_namespace ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty biolink:object_label_closure ], + owl:onProperty biolink:knowledge_source ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:InformationResource ; + owl:onClass linkml:String ; owl:onProperty biolink:primary_knowledge_source ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty biolink:original_predicate ], + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:object_closure ], + [ a owl:Restriction ; + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:object_label_closure ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:object_category ], [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:subject_label_closure ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:subject_category_closure ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:TimeType ; - owl:onProperty biolink:timepoint ], + owl:onClass linkml:String ; + owl:onProperty biolink:original_object ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty rdf:type ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:OntologyClass ; + owl:onProperty biolink:subject_category ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:allValuesFrom biolink:InformationResource ; - owl:onProperty biolink:aggregator_knowledge_source ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty rdf:type ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Uriorcurie ; + owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:EvidenceType ; owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Boolean ; - owl:onProperty biolink:negated ], + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:subject_closure ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Publication ; - owl:onProperty biolink:publications ], + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:aggregator_knowledge_source ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:original_subject ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:InformationResource ; - owl:onProperty biolink:knowledge_source ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty biolink:subject_closure ], + owl:onClass linkml:Boolean ; + owl:onProperty biolink:negated ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:object_category_closure ], + owl:onProperty biolink:subject_category_closure ], [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:TimeType ; + owl:onProperty biolink:timepoint ], biolink:Entity ; skos:definition "A typed association between two entities, supported by evidence" ; skos:exactMatch OBAN:association, rdf:Statement, owl:Axiom ; - skos:note "This is roughly the model used by biolink and ontobio at the moment" . + linkml:attributes "{}" ; + linkml:is_a "entity" . biolink:NamedThing a owl:Class ; rdfs:label "named thing" ; - rdfs:subClassOf [ a owl:Class ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:provided_by ], + [ a owl:Class ; owl:intersectionOf ( [ a owl:Restriction ; owl:allValuesFrom biolink:CategoryType ; owl:onProperty biolink:category ] [ a owl:Restriction ; owl:onProperty biolink:category ; owl:someValuesFrom biolink:CategoryType ] ) ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty biolink:provided_by ], [ a owl:Restriction ; owl:allValuesFrom linkml:Uriorcurie ; owl:onProperty biolink:xref ], @@ -9520,5 +10665,7 @@ biolink:NamedThing a owl:Class ; , dcid:Thing, UMLSSG:OBJC, - WIKIDATA:Q35120 . + WIKIDATA:Q35120 ; + linkml:attributes "{}" ; + linkml:is_a "entity" . diff --git a/biolink-model.proto b/biolink-model.proto index cef75baf28..2c6a469aac 100644 --- a/biolink-model.proto +++ b/biolink-model.proto @@ -1,7 +1,7 @@ syntax="proto3"; package // metamodel_version: 1.7.0 -// version: 3.3.2 +// version: 3.4.0 // A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose message AccessibleDnaRegion { @@ -71,9 +71,9 @@ message AnatomicalEntityToAnatomicalEntityOntogenicAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -107,9 +107,9 @@ message AnatomicalEntityToAnatomicalEntityPartOfAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -152,7 +152,7 @@ message Article repeated uriorcurie xref = 0 string id = 0 labelType name = 0 - string publicationType = 0 + repeated string publicationType = 0 uriorcurie publishedIn = 0 string isoAbbreviation = 0 string volume = 0 @@ -173,9 +173,9 @@ message Association repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -253,9 +253,9 @@ message BehaviorToBehavioralFeatureAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -400,7 +400,7 @@ message Book repeated uriorcurie meshTerms = 0 repeated uriorcurie xref = 0 labelType name = 0 - string publicationType = 0 + repeated string publicationType = 0 string id = 0 repeated string type = 0 } @@ -424,7 +424,7 @@ message BookChapter repeated uriorcurie xref = 0 string id = 0 labelType name = 0 - string publicationType = 0 + repeated string publicationType = 0 uriorcurie publishedIn = 0 string volume = 0 string chapter = 0 @@ -458,9 +458,9 @@ message CaseToPhenotypicFeatureAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -487,6 +487,51 @@ message CaseToPhenotypicFeatureAssociation double hasQuotient = 0 double hasPercentage = 0 } +message CausalGeneToDiseaseAssociation + { + string id = 0 + iriType iri = 0 + labelType name = 0 + narrativeText description = 0 + repeated attribute hasAttribute = 0 + boolean negated = 0 + repeated ontologyClass qualifiers = 0 + repeated publication publications = 0 + repeated evidenceType hasEvidence = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 + timeType timepoint = 0 + string originalSubject = 0 + uriorcurie originalPredicate = 0 + string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 + repeated string type = 0 + repeated categoryType category = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 + directionQualifierEnum objectDirectionQualifier = 0 + predicateType predicate = 0 + frequencyValue frequencyQualifier = 0 + severityValue severityQualifier = 0 + onset onsetQualifier = 0 + biologicalSex sexQualifier = 0 + integer hasCount = 0 + integer hasTotal = 0 + double hasQuotient = 0 + double hasPercentage = 0 + geneOrGeneProduct subject = 0 + disease object = 0 + } message Cell { string id = 0 @@ -526,9 +571,9 @@ message CellLineAsAModelOfDiseaseAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -565,9 +610,9 @@ message CellLineToDiseaseOrPhenotypicFeatureAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -626,9 +671,9 @@ message ChemicalAffectsGeneAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -694,9 +739,9 @@ message ChemicalEntityAssessesNamedThingAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -730,9 +775,9 @@ message ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -784,9 +829,9 @@ message ChemicalGeneInteractionAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -852,9 +897,9 @@ message ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -889,9 +934,9 @@ message ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -942,9 +987,9 @@ message ChemicalToChemicalAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -983,9 +1028,9 @@ message ChemicalToChemicalDerivationAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -1022,9 +1067,9 @@ message ChemicalToDiseaseOrPhenotypicFeatureAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -1057,9 +1102,9 @@ message ChemicalToPathwayAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -1346,9 +1391,9 @@ message ContributorAssociation boolean negated = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -1371,6 +1416,51 @@ message ContributorAssociation agent object = 0 repeated ontologyClass qualifiers = 0 } +message CorrelatedGeneToDiseaseAssociation + { + string id = 0 + iriType iri = 0 + labelType name = 0 + narrativeText description = 0 + repeated attribute hasAttribute = 0 + boolean negated = 0 + repeated ontologyClass qualifiers = 0 + repeated publication publications = 0 + repeated evidenceType hasEvidence = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 + timeType timepoint = 0 + string originalSubject = 0 + uriorcurie originalPredicate = 0 + string originalObject = 0 + ontologyClass subjectCategory = 0 + ontologyClass objectCategory = 0 + repeated string subjectClosure = 0 + repeated string objectClosure = 0 + repeated ontologyClass subjectCategoryClosure = 0 + repeated ontologyClass objectCategoryClosure = 0 + string subjectNamespace = 0 + string objectNamespace = 0 + repeated string subjectLabelClosure = 0 + repeated string objectLabelClosure = 0 + repeated retrievalSource retrievalSourceIds = 0 + repeated string type = 0 + repeated categoryType category = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 + directionQualifierEnum objectDirectionQualifier = 0 + predicateType predicate = 0 + frequencyValue frequencyQualifier = 0 + severityValue severityQualifier = 0 + onset onsetQualifier = 0 + biologicalSex sexQualifier = 0 + integer hasCount = 0 + integer hasTotal = 0 + double hasQuotient = 0 + double hasPercentage = 0 + geneOrGeneProduct subject = 0 + disease object = 0 + } // an item that refers to a collection of data from a data source. message Dataset { @@ -1529,9 +1619,9 @@ message DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -1566,9 +1656,9 @@ message DiseaseOrPhenotypicFeatureToLocationAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -1603,9 +1693,9 @@ message DiseaseToExposureEventAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -1637,9 +1727,9 @@ message DiseaseToPhenotypicFeatureAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -1728,7 +1818,7 @@ message DrugLabel repeated uriorcurie xref = 0 string id = 0 labelType name = 0 - string publicationType = 0 + repeated string publicationType = 0 } // An interaction between a drug and a gene or gene product. message DrugToGeneAssociation @@ -1744,9 +1834,9 @@ message DrugToGeneAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -1791,13 +1881,12 @@ message DruggableGeneToDiseaseAssociation labelType name = 0 narrativeText description = 0 repeated attribute hasAttribute = 0 - namedThing object = 0 boolean negated = 0 repeated ontologyClass qualifiers = 0 repeated publication publications = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -1815,12 +1904,20 @@ message DruggableGeneToDiseaseAssociation repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 - geneOrGeneProduct subject = 0 - predicateType predicate = 0 - repeated druggableGeneCategoryEnum hasEvidence = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 + directionQualifierEnum objectDirectionQualifier = 0 frequencyValue frequencyQualifier = 0 severityValue severityQualifier = 0 onset onsetQualifier = 0 + biologicalSex sexQualifier = 0 + integer hasCount = 0 + integer hasTotal = 0 + double hasQuotient = 0 + double hasPercentage = 0 + disease object = 0 + geneOrGeneProduct subject = 0 + predicateType predicate = 0 + repeated druggableGeneCategoryEnum hasEvidence = 0 } message EntityToDiseaseAssociation { @@ -1836,9 +1933,9 @@ message EntityToDiseaseAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -1872,9 +1969,9 @@ message EntityToPhenotypicFeatureAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -2016,9 +2113,9 @@ message ExonToTranscriptRelationship repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -2054,9 +2151,9 @@ message ExposureEventToOutcomeAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -2091,9 +2188,9 @@ message ExposureEventToPhenotypicFeatureAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -2173,9 +2270,9 @@ message FunctionalAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -2234,15 +2331,13 @@ message GeneAsAModelOfDiseaseAssociation labelType name = 0 narrativeText description = 0 repeated attribute hasAttribute = 0 - predicateType predicate = 0 - namedThing object = 0 boolean negated = 0 repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -2260,10 +2355,19 @@ message GeneAsAModelOfDiseaseAssociation repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 - geneOrGeneProduct subject = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 + directionQualifierEnum objectDirectionQualifier = 0 + predicateType predicate = 0 frequencyValue frequencyQualifier = 0 severityValue severityQualifier = 0 onset onsetQualifier = 0 + biologicalSex sexQualifier = 0 + integer hasCount = 0 + integer hasTotal = 0 + double hasQuotient = 0 + double hasPercentage = 0 + disease object = 0 + geneOrGeneProduct subject = 0 } // any grouping of multiple genes or gene products related by common descent message GeneFamily @@ -2291,9 +2395,9 @@ message GeneHasVariantThatContributesToDiseaseAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -2311,6 +2415,16 @@ message GeneHasVariantThatContributesToDiseaseAssociation repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 + directionQualifierEnum objectDirectionQualifier = 0 + frequencyValue frequencyQualifier = 0 + severityValue severityQualifier = 0 + onset onsetQualifier = 0 + biologicalSex sexQualifier = 0 + integer hasCount = 0 + integer hasTotal = 0 + double hasQuotient = 0 + double hasPercentage = 0 string subjectFormOrVariantQualifier = 0 geneOrGeneProduct subject = 0 disease object = 0 @@ -2323,16 +2437,13 @@ message GeneToDiseaseAssociation labelType name = 0 narrativeText description = 0 repeated attribute hasAttribute = 0 - namedThing subject = 0 - predicateType predicate = 0 - namedThing object = 0 boolean negated = 0 repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -2350,6 +2461,19 @@ message GeneToDiseaseAssociation repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 + directionQualifierEnum objectDirectionQualifier = 0 + predicateType predicate = 0 + frequencyValue frequencyQualifier = 0 + severityValue severityQualifier = 0 + onset onsetQualifier = 0 + biologicalSex sexQualifier = 0 + integer hasCount = 0 + integer hasTotal = 0 + double hasQuotient = 0 + double hasPercentage = 0 + geneOrGeneProduct subject = 0 + disease object = 0 } message GeneToDiseaseOrPhenotypicFeatureAssociation { @@ -2362,9 +2486,9 @@ message GeneToDiseaseOrPhenotypicFeatureAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -2408,9 +2532,9 @@ message GeneToExpressionSiteAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -2446,9 +2570,9 @@ message GeneToGeneCoexpressionAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -2486,9 +2610,9 @@ message GeneToGeneFamilyAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -2522,9 +2646,9 @@ message GeneToGeneHomologyAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -2558,9 +2682,9 @@ message GeneToGeneProductRelationship repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -2594,9 +2718,9 @@ message GeneToGoTermAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -2630,9 +2754,9 @@ message GeneToPathwayAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -2660,16 +2784,13 @@ message GeneToPhenotypeAssociation labelType name = 0 narrativeText description = 0 repeated attribute hasAttribute = 0 - namedThing subject = 0 - predicateType predicate = 0 - namedThing object = 0 boolean negated = 0 repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -2687,6 +2808,19 @@ message GeneToPhenotypeAssociation repeated retrievalSource retrievalSourceIds = 0 repeated string type = 0 repeated categoryType category = 0 + geneOrGeneProductOrChemicalEntityAspectEnum subjectAspectQualifier = 0 + directionQualifierEnum objectDirectionQualifier = 0 + predicateType predicate = 0 + frequencyValue frequencyQualifier = 0 + severityValue severityQualifier = 0 + onset onsetQualifier = 0 + biologicalSex sexQualifier = 0 + integer hasCount = 0 + integer hasTotal = 0 + double hasQuotient = 0 + double hasPercentage = 0 + geneOrGeneProduct subject = 0 + phenotypicFeature object = 0 } // The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc. message GeneticInheritance @@ -2749,9 +2883,9 @@ message GenomicSequenceLocalization repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -2805,9 +2939,9 @@ message GenotypeAsAModelOfDiseaseAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -2843,9 +2977,9 @@ message GenotypeToDiseaseAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -2882,9 +3016,9 @@ message GenotypeToGeneAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -2918,9 +3052,9 @@ message GenotypeToGenotypePartAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -2955,9 +3089,9 @@ message GenotypeToPhenotypicFeatureAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -2998,9 +3132,9 @@ message GenotypeToVariantAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -3166,9 +3300,9 @@ message InformationContentEntityToNamedThingAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -3190,30 +3324,6 @@ message InformationContentEntityToNamedThingAssociation namedThing object = 0 predicateType predicate = 0 } -// A database or knowledgebase and its supporting ecosystem of interfaces and services that deliver content to consumers (e.g. web portals, APIs, query endpoints, streaming services, data downloads, etc.). A single Information Resource by this definition may span many different datasets or databases, and include many access endpoints and user interfaces. Information Resources include project-specific resources such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb. -message InformationResource - { - iriType iri = 0 - repeated string type = 0 - repeated attribute hasAttribute = 0 - repeated string providedBy = 0 - repeated categoryType category = 0 - string license = 0 - string rights = 0 - string format = 0 - date creationDate = 0 - informationResourceStatusEnum informationResourceStatus = 0 - labelType name = 0 - string id = 0 - repeated uriorcurie xref = 0 - repeated labelType synonym = 0 - narrativeText description = 0 - } -// A collection of information resources -message InformationResourceCollection - { - repeated informationResource informationResources = 0 - } // An animal lacking a vertebral column. This group consists of 98% of all animal species. message Invertebrate { @@ -3249,7 +3359,7 @@ message JournalArticle repeated uriorcurie xref = 0 string id = 0 labelType name = 0 - string publicationType = 0 + repeated string publicationType = 0 uriorcurie publishedIn = 0 string isoAbbreviation = 0 string volume = 0 @@ -3269,6 +3379,23 @@ message LifeStage repeated organismTaxon inTaxon = 0 repeated attribute hasAttribute = 0 } +// A result of a log odds ratio analysis. +message LogOddsAnalysisResult + { + string id = 0 + iriType iri = 0 + repeated string type = 0 + labelType name = 0 + narrativeText description = 0 + repeated attribute hasAttribute = 0 + repeated string providedBy = 0 + repeated uriorcurie xref = 0 + repeated categoryType category = 0 + string license = 0 + string rights = 0 + string format = 0 + date creationDate = 0 + } // A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. message MacromolecularComplex { @@ -3296,9 +3423,9 @@ message MacromolecularMachineToBiologicalProcessAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -3332,9 +3459,9 @@ message MacromolecularMachineToCellularComponentAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -3368,9 +3495,9 @@ message MacromolecularMachineToMolecularActivityAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -3430,9 +3557,9 @@ message MaterialSampleDerivationAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -3469,9 +3596,9 @@ message MaterialSampleToDiseaseOrPhenotypicFeatureAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -3541,9 +3668,9 @@ message MolecularActivityToChemicalEntityAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -3577,9 +3704,9 @@ message MolecularActivityToMolecularActivityAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -3612,9 +3739,9 @@ message MolecularActivityToPathwayAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -3703,9 +3830,9 @@ message NamedThingAssociatedWithLikelihoodOfNamedThingAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -3876,9 +4003,9 @@ message OrganismTaxonToOrganismTaxonInteraction repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -3913,9 +4040,9 @@ message OrganismTaxonToOrganismTaxonSpecialization repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -3949,9 +4076,9 @@ message OrganismToOrganismAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -3985,9 +4112,9 @@ message OrganismalEntityAsAModelOfDiseaseAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -4022,9 +4149,9 @@ message PairwiseGeneToGeneInteraction repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -4057,9 +4184,9 @@ message PairwiseMolecularInteraction repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -4104,7 +4231,7 @@ message Patent repeated uriorcurie xref = 0 string id = 0 labelType name = 0 - string publicationType = 0 + repeated string publicationType = 0 } // An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome. message PathologicalAnatomicalExposure @@ -4341,9 +4468,9 @@ message PopulationToPopulationAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -4399,7 +4526,7 @@ message PredicateMapping string objectDerivativeQualifier = 0 string objectContextQualifier = 0 causalMechanismQualifierEnum causalMechanismQualifier = 0 - anatomicalContextQualifierEnum anatomicalContextQualifier = 0 + string anatomicalContextQualifier = 0 organismTaxon speciesContextQualifier = 0 repeated namedThing exactMatch = 0 repeated namedThing narrowMatch = 0 @@ -4426,7 +4553,7 @@ message PreprintPublication repeated uriorcurie xref = 0 string id = 0 labelType name = 0 - string publicationType = 0 + repeated string publicationType = 0 } // A series of actions conducted in a certain order or manner message Procedure @@ -4543,7 +4670,7 @@ message Publication repeated uriorcurie xref = 0 string id = 0 labelType name = 0 - string publicationType = 0 + repeated string publicationType = 0 } // A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value message QuantityValue @@ -4563,9 +4690,9 @@ message ReactionToCatalystAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -4601,9 +4728,9 @@ message ReactionToParticipantAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -4757,9 +4884,9 @@ message SequenceAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -4791,9 +4918,9 @@ message SequenceFeatureRelationship repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -4849,7 +4976,7 @@ message Serial repeated uriorcurie meshTerms = 0 repeated uriorcurie xref = 0 labelType name = 0 - string publicationType = 0 + repeated string publicationType = 0 string isoAbbreviation = 0 string volume = 0 string issue = 0 @@ -5018,9 +5145,9 @@ message TaxonToTaxonAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -5097,9 +5224,9 @@ message TranscriptToGeneRelationship repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -5163,9 +5290,9 @@ message VariantAsAModelOfDiseaseAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -5201,9 +5328,9 @@ message VariantToDiseaseAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -5241,9 +5368,9 @@ message VariantToGeneAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -5277,9 +5404,9 @@ message VariantToGeneExpressionAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -5317,9 +5444,9 @@ message VariantToPhenotypicFeatureAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -5360,9 +5487,9 @@ message VariantToPopulationAssociation repeated ontologyClass qualifiers = 0 repeated publication publications = 0 repeated evidenceType hasEvidence = 0 - informationResource knowledgeSource = 0 - informationResource primaryKnowledgeSource = 0 - repeated informationResource aggregatorKnowledgeSource = 0 + string knowledgeSource = 0 + string primaryKnowledgeSource = 0 + repeated string aggregatorKnowledgeSource = 0 timeType timepoint = 0 string originalSubject = 0 uriorcurie originalPredicate = 0 @@ -5437,7 +5564,7 @@ message WebPage repeated uriorcurie xref = 0 string id = 0 labelType name = 0 - string publicationType = 0 + repeated string publicationType = 0 } message Zygosity { diff --git a/biolink-model.shacl.ttl b/biolink-model.shacl.ttl index d75f863323..4e090ff7c4 100644 --- a/biolink-model.shacl.ttl +++ b/biolink-model.shacl.ttl @@ -1,5 +1,5 @@ # metamodel_version: 1.7.0 -# version: 3.3.2 +# version: 3.4.0 @prefix biolink: . @prefix dct: . @prefix pav: . @@ -13,11 +13,30 @@ biolink:AccessibleDnaRegion a sh:NodeShape ; sh:closed true ; sh:description "A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path rdfs:label ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -27,59 +46,40 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 6 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], + [ sh:order 7 ; + sh:path rdf:type ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:iri ], - [ sh:order 7 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 3 ; sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ] ; + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:id ] ; sh:targetClass biolink:AccessibleDnaRegion . biolink:Activity a sh:NodeShape ; sh:closed true ; sh:description "An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 6 ; sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:order 5 ; sh:path rdf:type ], [ sh:class biolink:Attribute ; @@ -87,20 +87,18 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:maxCount 1 ; sh:order 7 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ], + sh:path biolink:description ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -121,23 +119,15 @@ biolink:AdministrativeEntity a sh:NodeShape ; sh:maxCount 1 ; sh:order 6 ; sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:order 5 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:iri ], + [ sh:order 5 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -147,148 +137,154 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 8 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:description ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ] ; sh:targetClass biolink:AdministrativeEntity . biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 16 ; sh:path biolink:subject_closure ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "a point in time" ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -296,95 +292,71 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 15 ; sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ] ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityAssociation . biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; sh:closed true ; sh:description "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 17 ; sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:AnatomicalEntity ; + sh:description "the structure at a later time" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "a human-readable description of an entity" ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -392,125 +364,113 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 16 ; sh:path biolink:subject_closure ], [ sh:class biolink:AnatomicalEntity ; - sh:description "the structure at a later time" ; + sh:description "the structure at an earlier time" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], + sh:order 2 ; + sh:path rdf:object ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 28 ; sh:path rdf:type ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + sh:order 15 ; + sh:path biolink:object_category ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the structure at an earlier time" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ] ; + sh:order 18 ; + sh:path biolink:subject_category_closure ] ; sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a sh:NodeShape ; sh:closed true ; sh:description "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], + sh:property [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:order 13 ; + sh:path biolink:original_object ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -518,56 +478,17 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], + sh:order 15 ; + sh:path biolink:object_category ], [ sh:class biolink:AnatomicalEntity ; sh:description "the whole" ; sh:maxCount 1 ; @@ -575,54 +496,109 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the part" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "a point in time" ; + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "the part" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ] ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ] ; sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . biolink:Annotation a sh:NodeShape ; @@ -638,118 +614,148 @@ biolink:Article a sh:NodeShape ; sh:property [ sh:maxCount 1 ; sh:order 11 ; sh:path biolink:rights ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:creation_date ], - [ sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:format ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 8 ; + sh:path biolink:mesh_terms ], [ sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:summary ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:iri ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:order 13 ; + sh:path biolink:creation_date ], [ sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:license ], - [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 5 ; - sh:path biolink:pages ], - [ sh:order 18 ; - sh:path rdf:type ], - [ sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:iso_abbreviation ], - [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:id ], + sh:order 20 ; + sh:path biolink:description ], [ sh:class biolink:Agent ; sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:authors ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:has_attribute ], + [ sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; sh:maxCount 1 ; - sh:order 19 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 9 ; - sh:path biolink:xref ], + sh:order 3 ; + sh:path biolink:issue ], + [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 5 ; + sh:path biolink:pages ], + [ sh:order 18 ; + sh:path rdf:type ], [ sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:volume ], - [ sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 9 ; + sh:path biolink:xref ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:issue ], + sh:order 19 ; + sh:path rdfs:label ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:license ], + [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:id ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 14 ; sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:has_attribute ], [ sh:description "keywords tagging a publication" ; sh:order 7 ; sh:path biolink:keywords ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 8 ; - sh:path biolink:mesh_terms ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:iri ], [ sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; sh:path biolink:published_in ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path dct:description ] ; - sh:targetClass biolink:Article . - -biolink:Association a sh:NodeShape ; - sh:closed true ; - sh:description "A typed association between two entities, supported by evidence" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:format ], + [ sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "a human-readable description of an entity" ; + sh:order 1 ; + sh:path biolink:iso_abbreviation ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:targetClass biolink:Article . + +biolink:Association a sh:NodeShape ; + sh:closed true ; + sh:description "A typed association between two entities, supported by evidence" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:maxCount 1 ; sh:order 30 ; - sh:path dct:description ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink:description ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -757,24 +763,17 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -782,121 +781,89 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 29 ; sh:path rdfs:label ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:object_namespace ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], + sh:order 15 ; + sh:path biolink:object_category ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 16 ; sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ] ; + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ] ; sh:targetClass biolink:Association . biolink:Bacterium a sh:NodeShape ; sh:closed true ; sh:description "A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and are often motile." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], + sh:property [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -906,24 +873,24 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 7 ; @@ -934,74 +901,72 @@ biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:severity_qualifier ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_label_closure ], - [ sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; + sh:property [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; - sh:maxCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:onset_qualifier ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 29 ; - sh:path rdf:type ], - [ sh:class biolink:Behavior ; - sh:description "behavior that is the subject of the association" ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 39 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:has_total ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], + sh:order 6 ; + sh:path biolink:publications ], + [ sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:has_quotient ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_predicate ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_object ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:has_count ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:onset_qualifier ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -1009,162 +974,149 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 28 ; sh:path biolink:category ], - [ sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:has_total ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:iri ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 37 ; + sh:path biolink:severity_qualifier ], + [ sh:class biolink:BehavioralFeature ; + sh:description "behavioral feature that is the object of the association" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 29 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 15 ; + sh:path biolink:subject_category ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_attribute ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "a human-readable description of an entity" ; + sh:order 27 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path dct:description ], + sh:order 21 ; + sh:path biolink:subject_namespace ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:has_count ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:BehavioralFeature ; - sh:description "behavioral feature that is the object of the association" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], + sh:order 22 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 26 ; sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:has_quotient ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Behavior ; + sh:description "behavior that is the subject of the association" ; sh:maxCount 1 ; - sh:order 30 ; - sh:path rdfs:label ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:object_closure ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:subject_namespace ], + sh:order 1 ; + sh:path rdf:subject ], + [ sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:subject_category ] ; + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:has_percentage ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ] ; sh:targetClass biolink:BehaviorToBehavioralFeatureAssociation . biolink:BehavioralExposure a sh:NodeShape ; sh:closed true ; sh:description "A behavioral exposure is a factor relating to behavior impacting an individual." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:QuantityValue ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; sh:order 3 ; sh:path biolink:has_quantitative_value ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 1 ; sh:path rdfs:label ], + [ sh:order 10 ; + sh:path rdf:type ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -1174,20 +1126,27 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 9 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "a point in time" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:order 10 ; - sh:path rdf:type ] ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ] ; sh:targetClass biolink:BehavioralExposure . biolink:BehavioralOutcome a sh:NodeShape ; @@ -1199,19 +1158,17 @@ biolink:BehavioralOutcome a sh:NodeShape ; biolink:BiologicalEntity a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:order 6 ; - sh:path rdf:type ], + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 1 ; sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -1221,68 +1178,75 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 7 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ] ; + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:order 6 ; + sh:path rdf:type ] ; sh:targetClass biolink:BiologicalEntity . biolink:BiologicalProcessOrActivity a sh:NodeShape ; sh:closed true ; sh:description "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_output ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:has_input ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:class biolink:PhysicalEntity ; sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:enabled_by ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; @@ -1292,71 +1256,58 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_output ] ; - sh:targetClass biolink:BiologicalProcessOrActivity . - -biolink:BioticExposure a sh:NodeShape ; - sh:closed true ; - sh:description "An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses)." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 9 ; + sh:order 8 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:targetClass biolink:BiologicalProcessOrActivity . + +biolink:BioticExposure a sh:NodeShape ; + sh:closed true ; + sh:description "An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses)." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; sh:order 3 ; sh:path biolink:has_quantitative_value ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:timepoint ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:iri ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -1364,82 +1315,86 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_attribute_type ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], [ sh:order 10 ; sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ] ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ] ; sh:targetClass biolink:BioticExposure . biolink:Book a sh:NodeShape ; sh:closed true ; sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "Should generally be set to an ontology class defined term for 'book'." ; + sh:property [ sh:description "Should generally be set to an ontology class defined term for 'book'." ; sh:order 14 ; sh:path rdf:type ], - [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:rights ], + [ sh:description "keywords tagging a publication" ; + sh:order 3 ; + sh:path biolink:keywords ], [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:format ], + sh:order 6 ; + sh:path biolink:license ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 10 ; + sh:path biolink:provided_by ], [ sh:description "Books should have industry-standard identifier such as from ISBN." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:id ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:creation_date ], [ sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:license ], + sh:order 16 ; + sh:path biolink:description ], + [ sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:summary ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:rights ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:format ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:iri ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path rdfs:label ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 4 ; + sh:path biolink:mesh_terms ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 10 ; - sh:path biolink:provided_by ], - [ sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:summary ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -1449,21 +1404,39 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "keywords tagging a publication" ; - sh:order 3 ; - sh:path biolink:keywords ] ; + [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 1 ; + sh:path biolink:pages ] ; sh:targetClass biolink:Book . biolink:BookChapter a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "chapter of a book" ; + sh:property [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 4 ; + sh:path biolink:pages ], + [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:id ], + [ sh:description "The enclosing parent book containing the chapter should have industry-standard identifier from ISBN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:published_in ], + [ sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:summary ], + [ sh:description "chapter of a book" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:chapter ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 13 ; - sh:path biolink:provided_by ], + [ sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:volume ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -1473,73 +1446,54 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 16 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 13 ; + sh:path biolink:provided_by ], [ sh:maxCount 1 ; sh:order 9 ; sh:path biolink:license ], - [ sh:description "The enclosing parent book containing the chapter should have industry-standard identifier from ISBN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:published_in ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], [ sh:description "keywords tagging a publication" ; sh:order 6 ; sh:path biolink:keywords ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:authors ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 7 ; + sh:path biolink:mesh_terms ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:summary ], - [ sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:volume ], + [ sh:maxCount 1 ; + sh:order 19 ; + sh:path biolink:description ], [ sh:maxCount 1 ; sh:order 11 ; sh:path biolink:format ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 7 ; - sh:path biolink:mesh_terms ], - [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 4 ; - sh:path biolink:pages ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:creation_date ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:authors ], [ sh:order 17 ; sh:path rdf:type ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:maxCount 1 ; sh:order 10 ; - sh:path biolink:rights ] ; + sh:path biolink:rights ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:creation_date ] ; sh:targetClass biolink:BookChapter . biolink:CaseToEntityAssociationMixin a sh:NodeShape ; @@ -1552,41 +1506,31 @@ biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; - sh:maxCount 1 ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:onset_qualifier ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 30 ; sh:path rdfs:label ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 28 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:onset_qualifier ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:subject_category ], + sh:order 37 ; + sh:path biolink:severity_qualifier ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:timepoint ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], [ sh:class biolink:Case ; sh:description "the case (e.g. patient) that has the property" ; sh:maxCount 1 ; @@ -1594,116 +1538,45 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 1 ; sh:path rdf:subject ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:severity_qualifier ], - [ sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:has_percentage ], - [ sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:has_quotient ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path dct:description ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 29 ; - sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:has_attribute ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:subject_closure ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 15 ; + sh:path biolink:subject_category ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:subject_namespace ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:object_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:object_category ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 36 ; + sh:path biolink:has_percentage ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 28 ; + sh:path biolink:category ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], + sh:order 22 ; + sh:path biolink:object_namespace ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; @@ -1713,946 +1586,1141 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:has_total ], - [ sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:has_count ], + sh:order 20 ; + sh:path biolink:object_category_closure ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 26 ; sh:path biolink:id ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], + sh:order 4 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:subject_namespace ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; - sh:path biolink:original_object ] ; - sh:targetClass biolink:CaseToPhenotypicFeatureAssociation . - -biolink:Cell a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:original_object ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; + sh:order 12 ; + sh:path biolink:original_subject ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 8 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:order 6 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 29 ; sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:has_quotient ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:iri ], + [ sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:has_count ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:order 2 ; - sh:path biolink:xref ] ; - sh:targetClass biolink:Cell . + sh:path rdf:predicate ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:has_total ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:object_category ], + [ sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:description ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ] ; + sh:targetClass biolink:CaseToPhenotypicFeatureAssociation . -biolink:CellLineAsAModelOfDiseaseAssociation a sh:NodeShape ; +biolink:CausalGeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 5 ; + sh:order 8 ; sh:path biolink:publications ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; + sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is shown to cause the disease." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path rdf:subject ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:severity_qualifier ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:has_count ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:onset_qualifier ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 5 ; + sh:path rdf:object ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 4 ; + sh:order 7 ; sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:description ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 34 ; + sh:order 41 ; sh:path biolink:frequency_qualifier ], - [ sh:class biolink:CellLine ; - sh:description "A cell line derived from an organismal entity with a disease state that is used as a model of that disease." ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 30 ; + sh:path biolink:category ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 40 ; + sh:path biolink:onset_qualifier ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; + sh:order 16 ; sh:path biolink:original_object ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:has_quotient ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 31 ; + sh:path rdf:type ], + [ sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:order 36 ; + sh:path biolink:has_total ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 39 ; + sh:path biolink:severity_qualifier ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:iri ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 19 ; + sh:order 22 ; sh:path biolink:object_category_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path rdfs:label ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path rdf:predicate ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 25 ; + sh:order 28 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_attribute ], + [ sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 38 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "The relationship to the disease" ; + sh:order 2 ; + sh:path biolink:sex_qualifier ], + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:minCount 1 ; sh:order 1 ; - sh:path rdf:predicate ], + sh:path biolink:object_direction_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; + sh:order 18 ; sh:path biolink:object_category ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 3 ; + sh:order 6 ; sh:path biolink:negated ] ; - sh:targetClass biolink:CellLineAsAModelOfDiseaseAssociation . + sh:targetClass biolink:CausalGeneToDiseaseAssociation . -biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; +biolink:Cell a sh:NodeShape ; sh:closed true ; - sh:description "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:description "a point in time" ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:order 7 ; + sh:path rdfs:label ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 26 ; + sh:order 4 ; sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; - sh:maxCount 1 ; sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 2 ; - sh:path rdf:object ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:path biolink:has_attribute ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink:description ] ; + sh:targetClass biolink:Cell . + +biolink:CellLineAsAModelOfDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 33 ; + sh:path biolink:onset_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:CellLine ; + sh:description "A cell line derived from an organismal entity with a disease state that is used as a model of that disease." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "The relationship to the disease" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:severity_qualifier ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ] ; - sh:targetClass biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . - -biolink:CellLineToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:description "An relationship between a cell line and another entity" ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:CellLineToEntityAssociationMixin . + sh:path biolink:has_evidence ] ; + sh:targetClass biolink:CellLineAsAModelOfDiseaseAssociation . -biolink:CellularOrganism a sh:NodeShape ; +biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; - sh:description "" ; + sh:description "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 8 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:CellularOrganism . - -biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity, localization, processing, expression, etc.)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:object_part_qualifier ], - [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:subject_context_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:subject_category ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:negated ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:subject_category_closure ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 38 ; + sh:order 25 ; sh:path biolink:id ], - [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:subject_namespace ], - [ sh:in ( "metabolite" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_derivative_qualifier ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 39 ; + sh:order 26 ; sh:path biolink:iri ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:timepoint ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:object_category_closure ], - [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 15 ; - sh:path rdf:object ], - [ sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:causal_mechanism_qualifier ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 25 ; + sh:order 12 ; sh:path biolink:original_predicate ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 36 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_evidence ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 37 ; + sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 28 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:qualifiers ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path dct:description ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 40 ; - sh:path biolink:category ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path rdf:subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 44 ; - sh:path biolink:has_attribute ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path rdf:predicate ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 35 ; - sh:path biolink:subject_label_closure ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:original_subject ], - [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:path rdf:type ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_part_qualifier ], + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; + sh:order 16 ; sh:path biolink:subject_closure ], - [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 41 ; - sh:path rdf:type ], - [ sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:original_object ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path rdfs:label ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 18 ; + sh:order 5 ; sh:path biolink:publications ], - [ sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:object_context_qualifier ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:knowledge_source ] ; - sh:targetClass biolink:ChemicalAffectsGeneAssociation . - -biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:order 31 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], + sh:order 13 ; + sh:path biolink:original_object ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 29 ; sh:path rdfs:label ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:subject_category ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ] ; + sh:targetClass biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . + +biolink:CellLineToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:description "An relationship between a cell line and another entity" ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:CellLineToEntityAssociationMixin . + +biolink:CellularOrganism a sh:NodeShape ; + sh:closed true ; + sh:description "" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:CellularOrganism . + +biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity, localization, processing, expression, etc.)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:object_category_closure ], + [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_part_qualifier ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 30 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:object_category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:iri ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:knowledge_source ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:original_subject ], + [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 40 ; + sh:path biolink:category ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; sh:order 23 ; - sh:path biolink:object_label_closure ], + sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:subject_namespace ], + [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:object_part_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:subject_category ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 15 ; + sh:path rdf:object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 44 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:publications ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 25 ; + sh:path biolink:original_predicate ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 35 ; + sh:path biolink:subject_label_closure ], + [ sh:maxCount 1 ; + sh:order 43 ; + sh:path biolink:description ], + [ sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:object_form_or_variant_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 38 ; + sh:path biolink:id ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:object_namespace ], + [ sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:class biolink:AnatomicalEntity ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:subject_context_qualifier ], + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; + sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:causal_mechanism_qualifier ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 6 ; + sh:order 19 ; sh:path biolink:has_evidence ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 41 ; + sh:path rdf:type ], + [ sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:qualified_predicate ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 36 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:AnatomicalEntity ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:object_context_qualifier ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path rdf:subject ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path rdf:predicate ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path rdfs:label ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 22 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:subject_closure ], + [ sh:in ( "metabolite" ) ; + sh:maxCount 1 ; sh:order 2 ; - sh:path rdf:object ], - [ sh:description "a human-readable description of an entity" ; + sh:path biolink:subject_derivative_qualifier ], + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], + sh:order 5 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:primary_knowledge_source ] ; + sh:targetClass biolink:ChemicalAffectsGeneAssociation . + +biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:object_namespace ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ] ; - sh:targetClass biolink:ChemicalEntityAssessesNamedThingAssociation . - -biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A regulatory relationship between two genes" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:subject_closure ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:order 26 ; - sh:path biolink:id ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:object_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], + sh:path biolink:iri ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; + sh:order 12 ; sh:path biolink:original_predicate ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + [ sh:maxCount 1 ; sh:order 30 ; - sh:path rdfs:label ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 28 ; - sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:path biolink:description ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; sh:path biolink:primary_knowledge_source ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 5 ; + sh:order 4 ; sh:path biolink:qualifiers ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 25 ; + sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_attribute ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; sh:path rdf:type ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ] ; + sh:targetClass biolink:ChemicalEntityAssessesNamedThingAssociation . + +biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A regulatory relationship between two genes" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 32 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 22 ; sh:path biolink:object_namespace ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 29 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:object_category ], + [ sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:description ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:subject_namespace ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category_closure ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -2660,13 +2728,20 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:BlankNode ; sh:order 3 ; sh:path rdf:object ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_label_closure ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "the direction is always from regulator to regulated" ; sh:maxCount 1 ; - sh:order 31 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path rdfs:label ], [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -2674,31 +2749,59 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:BlankNode ; sh:order 1 ; sh:path rdf:subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 28 ; + sh:path biolink:category ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 14 ; + sh:path biolink:original_object ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category_closure ], + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_subject ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_label_closure ], - [ sh:description "the direction is always from regulator to regulated" ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ] ; + sh:order 13 ; + sh:path biolink:original_predicate ], + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:object_direction_qualifier ] ; sh:targetClass biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . biolink:ChemicalEntityOrProteinOrPolypeptide a sh:NodeShape ; @@ -2717,30 +2820,33 @@ biolink:ChemicalExposure a sh:NodeShape ; sh:closed true ; sh:description "A chemical exposure is an intake of a particular chemical entity." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_attribute_type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 1 ; + sh:path biolink:timepoint ], + [ sh:order 10 ; + sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], + sh:order 2 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path biolink:has_quantitative_value ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -2756,182 +2862,163 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], - [ sh:order 10 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "a point in time" ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_attribute_type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:timepoint ] ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ] ; sh:targetClass biolink:ChemicalExposure . biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; sh:closed true ; sh:description "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:property [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 9 ; - sh:path rdf:predicate ], + sh:order 5 ; + sh:path biolink:object_part_qualifier ], [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:object_context_qualifier ], - [ sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:in ( "metabolite" ) ; + [ sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:description ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_derivative_qualifier ], + sh:order 20 ; + sh:path biolink:original_predicate ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 19 ; sh:path biolink:original_subject ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:negated ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical entity or entity that is an interactor" ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path rdf:subject ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 9 ; + sh:path rdf:predicate ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:original_object ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 14 ; + sh:path biolink:has_evidence ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 35 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_attribute ], + [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_part_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], + sh:order 12 ; + sh:path biolink:qualifiers ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:object_namespace ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], [ sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:object_form_or_variant_qualifier ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 31 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:subject_namespace ], + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:in ( "metabolite" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:subject_derivative_qualifier ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 26 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:subject_context_qualifier ], - [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:object_part_qualifier ], - [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_part_qualifier ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 31 ; - sh:path biolink:object_label_closure ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 33 ; - sh:path biolink:id ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:publications ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:subject_context_qualifier ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:object_closure ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 17 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:subject_namespace ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:qualifiers ], - [ sh:description "a point in time" ; + sh:order 7 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:timepoint ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:subject_closure ], + sh:minCount 1 ; + sh:order 33 ; + sh:path biolink:id ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -2940,36 +3027,44 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 10 ; sh:path rdf:object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:object_closure ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 23 ; + sh:path biolink:object_category ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:negated ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:original_object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 22 ; + sh:path biolink:subject_category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:iri ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 8 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path dct:description ] ; + sh:order 27 ; + sh:path biolink:object_category_closure ] ; sh:targetClass biolink:ChemicalGeneInteractionAssociation . biolink:ChemicalOrDrugOrTreatment a sh:NodeShape ; @@ -2981,36 +3076,9 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation sh:closed true ; sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path rdfs:label ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], + sh:property [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 18 ; sh:path biolink:object_closure ], @@ -3018,207 +3086,267 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation sh:maxCount 1 ; sh:order 21 ; sh:path biolink:subject_namespace ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 29 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 15 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_object ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_attribute ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "" ; + sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:FDA_adverse_event_level ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:timepoint ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 29 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path dct:description ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 22 ; sh:path biolink:object_namespace ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 28 ; + sh:path biolink:category ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_subject ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path rdfs:label ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_predicate ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 27 ; sh:path biolink:iri ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:description ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 3 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:subject_category ], - [ sh:description "" ; - sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:FDA_adverse_event_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_label_closure ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:subject_closure ], + sh:order 16 ; + sh:path biolink:object_category ] ; + sh:targetClass biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . + +biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:description ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path rdf:predicate ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:object_category ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 26 ; sh:path biolink:id ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 28 ; - sh:path biolink:category ] ; - sh:targetClass biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . - -biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_attribute ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:subject_namespace ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 29 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], + sh:order 12 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 15 ; + sh:path biolink:subject_category ], + [ sh:description "" ; + sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:FDA_adverse_event_level ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:object_category ], - [ sh:description "a human-readable description of an entity" ; + sh:order 13 ; + sh:path biolink:original_predicate ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 31 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 11 ; + sh:path biolink:timepoint ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:iri ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 14 ; + sh:path biolink:original_object ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:subject_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:subject_namespace ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -3226,119 +3354,66 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 28 ; sh:path biolink:category ], - [ sh:description "" ; - sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:FDA_adverse_event_level ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], + sh:nodeKind sh:BlankNode ; + sh:order 1 ; + sh:path rdf:subject ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 30 ; sh:path rdfs:label ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 22 ; sh:path biolink:object_namespace ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:object_closure ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:subject_category ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 26 ; - sh:path biolink:id ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_label_closure ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 29 ; - sh:path rdf:type ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ] ; + sh:order 32 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . biolink:ChemicalToChemicalAssociation a sh:NodeShape ; sh:closed true ; sh:description "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "a point in time" ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], + sh:order 26 ; + sh:path biolink:iri ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:ChemicalEntity ; sh:description "the chemical element that is the target of the statement" ; sh:maxCount 1 ; @@ -3346,28 +3421,32 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; sh:path biolink:subject_label_closure ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; @@ -3375,84 +3454,79 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:BlankNode ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 16 ; sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; - sh:path biolink:has_evidence ] ; + sh:path biolink:has_evidence ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ] ; sh:targetClass biolink:ChemicalToChemicalAssociation . biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; @@ -3466,44 +3540,44 @@ biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; THEN C1 derives-into C2 <>""" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:property [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:object_namespace ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 29 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:object_category ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 14 ; + sh:path biolink:original_object ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category_closure ], + sh:order 11 ; + sh:path biolink:timepoint ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:description ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -3513,69 +3587,28 @@ biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:has_attribute ], - [ sh:description "a point in time" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 27 ; + sh:path biolink:iri ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 30 ; sh:path rdfs:label ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:knowledge_source ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_predicate ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:object_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 28 ; - sh:path biolink:category ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:subject_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path dct:description ], [ sh:class biolink:ChemicalEntity ; sh:description "the downstream chemical entity" ; sh:maxCount 1 ; @@ -3583,200 +3616,227 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 3 ; sh:path rdf:object ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:object_category ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:subject_namespace ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:MacromolecularMachineMixin ; sh:description "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical." ; sh:nodeKind sh:BlankNode ; sh:order 0 ; sh:path biolink:catalyst_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 24 ; sh:path biolink:object_label_closure ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 29 ; - sh:path rdf:type ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 28 ; + sh:path biolink:category ], [ sh:class biolink:ChemicalEntity ; sh:description "the upstream chemical entity" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path rdf:subject ] ; + sh:path rdf:subject ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:object_namespace ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_subject ] ; sh:targetClass biolink:ChemicalToChemicalDerivationAssociation . biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:property [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 29 ; sh:path rdfs:label ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:object_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "the disease or phenotype that is affected by the chemical" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:order 2 ; + sh:path rdf:object ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:object_namespace ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path rdf:subject ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "the disease or phenotype that is affected by the chemical" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ] ; + sh:path biolink:iri ] ; sh:targetClass biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . biolink:ChemicalToEntityAssociationMixin a sh:NodeShape ; @@ -3789,52 +3849,89 @@ biolink:ChemicalToPathwayAssociation a sh:NodeShape ; sh:closed true ; sh:description "An interaction between a chemical entity and a biological process or pathway." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 26 ; + sh:path biolink:iri ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 28 ; sh:path rdf:type ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 16 ; sh:path biolink:subject_closure ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -3842,58 +3939,15 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical entity that is affecting the pathway" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:Pathway ; sh:description "the pathway that is affected by the chemical" ; sh:maxCount 1 ; @@ -3901,75 +3955,88 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical entity that is affecting the pathway" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], + sh:order 15 ; + sh:path biolink:object_category ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ] ; + sh:order 18 ; + sh:path biolink:subject_category_closure ] ; sh:targetClass biolink:ChemicalToPathwayAssociation . biolink:ChiSquaredAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a chi squared analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + sh:property [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:maxCount 1 ; sh:order 1 ; sh:path biolink:rights ], [ sh:maxCount 1 ; sh:order 0 ; sh:path biolink:license ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -3979,71 +4046,22 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; sh:order 11 ; - sh:path dct:description ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ] ; + sh:path biolink:description ] ; sh:targetClass biolink:ChiSquaredAnalysisResult . -biolink:ClinicalCourse a sh:NodeShape ; - sh:closed true ; - sh:description "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; +biolink:ClinicalCourse a sh:NodeShape ; + sh:closed true ; + sh:description "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:order 9 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:order 11 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -4059,39 +4077,58 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ] ; sh:targetClass biolink:ClinicalCourse . biolink:ClinicalEntity a sh:NodeShape ; sh:closed true ; sh:description "Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path dct:description ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], - [ sh:order 5 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ], + sh:order 6 ; + sh:path rdfs:label ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4101,36 +4138,38 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:order 5 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ] ; + sh:order 3 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:description ] ; sh:targetClass biolink:ClinicalEntity . biolink:ClinicalFinding a sh:NodeShape ; sh:closed true ; sh:description "this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:ClinicalAttribute ; - sh:description "connects any entity to an attribute" ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4140,39 +4179,45 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], + sh:order 7 ; + sh:path rdfs:label ], [ sh:order 6 ; sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:class biolink:ClinicalAttribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ] ; + sh:order 9 ; + sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ] ; sh:targetClass biolink:ClinicalFinding . biolink:ClinicalIntervention a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path dct:description ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:iri ], + [ sh:order 5 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], @@ -4181,11 +4226,9 @@ biolink:ClinicalIntervention a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_attribute ], - [ sh:order 5 ; - sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:description ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 6 ; @@ -4198,19 +4241,35 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 4 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ] ; sh:targetClass biolink:ClinicalIntervention . biolink:ClinicalMeasurement a sh:NodeShape ; sh:closed true ; sh:description "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:description ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; sh:path biolink:xref ], @@ -4226,17 +4285,14 @@ biolink:ClinicalMeasurement a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], [ sh:order 9 ; sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4246,15 +4302,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], @@ -4268,38 +4315,20 @@ biolink:ClinicalModifier a sh:NodeShape ; sh:closed true ; sh:description "Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 9 ; - sh:path rdf:type ], + sh:property [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; sh:path biolink:xref ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], + sh:order 0 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -4307,47 +4336,61 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; sh:order 2 ; sh:path biolink:has_quantitative_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ] ; + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:ClinicalModifier . biolink:ClinicalTrial a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:description ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:iri ], - [ sh:order 5 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4357,50 +4400,26 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path dct:description ], + sh:order 6 ; + sh:path rdfs:label ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:order 5 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 8 ; - sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ] ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:ClinicalTrial . biolink:CodingSequence a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 13 ; - sh:path rdf:type ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -4409,29 +4428,37 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 12 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path dct:description ], + sh:order 14 ; + sh:path rdfs:label ], + [ sh:description "indicates whether a molecular entity is a metabolite" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:is_metabolite ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:order 13 ; + sh:path rdf:type ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:is_toxic ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:iri ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:trade_name ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path rdfs:label ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 10 ; sh:path biolink:xref ], @@ -4440,22 +4467,56 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:description ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:description "indicates whether a molecular entity is a metabolite" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:is_metabolite ] ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:CodingSequence . biolink:Cohort a sh:NodeShape ; sh:closed true ; sh:description "A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -4466,15 +4527,9 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:order 6 ; sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; @@ -4486,39 +4541,44 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:path biolink:iri ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ] ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:Cohort . biolink:CommonDataElement a sh:NodeShape ; sh:closed true ; sh:description "A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. (https://cde.nlm.nih.gov/home)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 7 ; + sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4528,42 +4588,48 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ] ; + sh:targetClass biolink:CommonDataElement . + +biolink:ComplexChemicalExposure a sh:NodeShape ; + sh:closed true ; + sh:description "A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; + sh:order 5 ; sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:path biolink:has_attribute_type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:CommonDataElement . - -biolink:ComplexChemicalExposure a sh:NodeShape ; - sh:closed true ; - sh:description "A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; sh:path biolink:xref ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4575,36 +4641,18 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; sh:order 2 ; sh:path biolink:has_quantitative_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:description ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 0 ; sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; @@ -4612,21 +4660,33 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 3 ; sh:path biolink:has_qualitative_value ], [ sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ] ; + sh:path rdf:type ] ; sh:targetClass biolink:ComplexChemicalExposure . biolink:ComplexMolecularMixture a sh:NodeShape ; sh:closed true ; sh:description "A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:description ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -4635,135 +4695,114 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 14 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 9 ; sh:path biolink:provided_by ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 5 ; sh:path biolink:available_from ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:id ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:trade_name ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], + sh:order 15 ; + sh:path rdfs:label ], [ sh:description "" ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:is_toxic ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:order 14 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], + sh:order 12 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], [ sh:class biolink:ChemicalMixture ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:is_supplement ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:id ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ] ; + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ] ; sh:targetClass biolink:ComplexMolecularMixture . biolink:ConceptCountAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a concept count analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:maxCount 1 ; sh:order 1 ; sh:path biolink:rights ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:creation_date ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:order 9 ; - sh:path rdf:type ] ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ] ; sh:targetClass biolink:ConceptCountAnalysisResult . biolink:ConfidenceLevel a sh:NodeShape ; @@ -4771,14 +4810,32 @@ biolink:ConfidenceLevel a sh:NodeShape ; sh:description "Level of confidence in a statement" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], + sh:order 1 ; + sh:path biolink:rights ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:order 9 ; sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4788,87 +4845,114 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; - sh:path biolink:xref ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ] ; + sh:path biolink:xref ] ; sh:targetClass biolink:ConfidenceLevel . biolink:ContributorAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 26 ; sh:path biolink:iri ], + [ sh:description "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'" ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:class biolink:Agent ; + sh:description "agent helping to realise the given entity (e.g. such as a publication)" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; sh:path biolink:object_label_closure ], @@ -4877,15 +4961,17 @@ biolink:ContributorAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'" ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:class biolink:InformationContentEntity ; sh:description "information content entity which an agent has helped realise" ; sh:maxCount 1 ; @@ -4893,113 +4979,246 @@ biolink:ContributorAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:Agent ; - sh:description "agent helping to realise the given entity (e.g. such as a publication)" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ] ; + sh:targetClass biolink:ContributorAssociation . + +biolink:CorrelatedGeneToDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:iri ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_attribute ], + [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:has_percentage ], + [ sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:onset_qualifier ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; + sh:path biolink:sex_qualifier ], + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; sh:path rdf:object ], + [ sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:has_total ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; - sh:description "this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'" ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 4 ; + sh:order 7 ; sh:path biolink:qualifiers ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 31 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:description ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 28 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path rdf:predicate ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; sh:order 30 ; - sh:path dct:description ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink:category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 39 ; + sh:path biolink:severity_qualifier ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "a point in time" ; + sh:order 8 ; + sh:path biolink:publications ], + [ sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 35 ; + sh:path biolink:has_count ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is shown to correlate with the disease." ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:path rdf:subject ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ] ; - sh:targetClass biolink:ContributorAssociation . + sh:order 32 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:CorrelatedGeneToDiseaseAssociation . biolink:DatasetSummary a sh:NodeShape ; sh:closed true ; sh:description "an item that holds summary level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:license ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:order 5 ; + sh:path biolink:creation_date ], + [ sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:format ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path rdfs:label ], [ sh:maxCount 1 ; sh:order 3 ; sh:path biolink:rights ], @@ -5007,103 +5226,74 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 9 ; sh:path biolink:iri ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:format ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:order 11 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:id ], [ sh:maxCount 1 ; sh:order 0 ; sh:path biolink:source_web_page ], + [ sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], [ sh:maxCount 1 ; - sh:order 1 ; - sh:path schema:logo ], + sh:order 2 ; + sh:path biolink:license ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; sh:path biolink:xref ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:creation_date ] ; + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path schema:logo ], + [ sh:order 11 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:DatasetSummary . biolink:DatasetVersion a sh:NodeShape ; sh:closed true ; sh:description "an item that holds version level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:license ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:id ], - [ sh:order 12 ; - sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:format ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 13 ; sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:rights ], + [ sh:order 12 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:creation_date ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:class biolink:DatasetDistribution ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path dct:distribution ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:rights ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], [ sh:maxCount 1 ; sh:order 1 ; sh:path pav:version ], - [ sh:class biolink:Dataset ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path dct:source ], + [ sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -5112,38 +5302,56 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 11 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; - sh:targetClass biolink:DatasetVersion . - -biolink:DiagnosticAid a sh:NodeShape ; - sh:closed true ; - sh:description "A device or substance used to help diagnose disease or injury" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path dct:description ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:DatasetDistribution ; sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path dct:distribution ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 3 ; + sh:order 10 ; sh:path biolink:iri ], - [ sh:class biolink:Attribute ; + [ sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:license ], + [ sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:format ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:id ], + [ sh:class biolink:Dataset ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path dct:source ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:creation_date ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ] ; + sh:targetClass biolink:DatasetVersion . + +biolink:DiagnosticAid a sh:NodeShape ; + sh:closed true ; + sh:description "A device or substance used to help diagnose disease or injury" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_attribute ], - [ sh:order 5 ; - sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:description ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -5153,35 +5361,50 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:iri ], + [ sh:order 5 ; + sh:path rdf:type ] ; sh:targetClass biolink:DiagnosticAid . biolink:DiseaseOrPhenotypicFeatureExposure a sh:NodeShape ; sh:closed true ; sh:description "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:QuantityValue ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; sh:order 3 ; sh:path biolink:has_quantitative_value ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -5191,31 +5414,28 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 9 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 7 ; sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:order 10 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:order 10 ; - sh:path rdf:type ], + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; @@ -5242,105 +5462,26 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a sh:NodeShape sh:closed true ; sh:description "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; sh:path biolink:object_label_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], [ sh:class biolink:GeneticInheritance ; sh:description "genetic inheritance associated with the specified disease or phenotypic feature." ; sh:maxCount 1 ; @@ -5348,112 +5489,94 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; - sh:path biolink:negated ] ; - sh:targetClass biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . - -biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:path biolink:negated ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 16 ; sh:path biolink:subject_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 15 ; + sh:path biolink:object_category ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category_closure ], - [ sh:description "a point in time" ; + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], [ sh:class biolink:Publication ; @@ -5461,64 +5584,131 @@ biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "anatomical entity in which the disease or feature is found." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ] ; + sh:targetClass biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . + +biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; sh:path biolink:subject_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:subject_category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -5526,28 +5716,44 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 18 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "anatomical entity in which the disease or feature is found." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ] ; + sh:order 7 ; + sh:path biolink:knowledge_source ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . biolink:DiseaseToEntityAssociationMixin a sh:NodeShape ; @@ -5559,32 +5765,86 @@ biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between an exposure event and a disease." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:ExposureEvent ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -5592,49 +5852,51 @@ biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Disease ; + sh:description "disease class" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -5642,164 +5904,84 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 29 ; - sh:path rdfs:label ], - [ sh:class biolink:Disease ; - sh:description "disease class" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ] ; + sh:path rdfs:label ] ; sh:targetClass biolink:DiseaseToExposureEventAssociation . biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:class biolink:OntologyClass ; + sh:property [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:object_category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:subject_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:object_namespace ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:object_closure ], + sh:order 11 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:onset_qualifier ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:severity_qualifier ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path dct:description ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 15 ; + sh:path biolink:subject_category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 28 ; + sh:path biolink:category ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:has_count ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 29 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:description "equivalent to has quotient multiplied by 100" ; + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:has_percentage ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 39 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:iri ], + sh:order 14 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:has_attribute ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + [ sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:has_quotient ], [ sh:class biolink:Disease ; sh:description "disease class" ; sh:maxCount 1 ; @@ -5807,11 +5989,60 @@ biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path rdf:subject ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], + [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:has_percentage ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], + [ sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:description ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:class biolink:PhenotypicFeature ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -5819,96 +6050,86 @@ biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path rdf:object ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:frequency_qualifier ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 28 ; - sh:path biolink:category ], - [ sh:description "a point in time" ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 4 ; + sh:path biolink:negated ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:subject_namespace ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 26 ; - sh:path biolink:id ], - [ sh:description "number of things with a particular property" ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:has_count ], - [ sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:has_quotient ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 12 ; + sh:path biolink:original_subject ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:iri ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:subject_category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 37 ; + sh:path biolink:severity_qualifier ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], - [ sh:description "total number of things in a particular reference set" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:onset_qualifier ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:has_total ], + sh:order 13 ; + sh:path biolink:original_predicate ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category_closure ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 29 ; - sh:path rdf:type ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_label_closure ] ; + sh:order 34 ; + sh:path biolink:has_total ] ; sh:targetClass biolink:DiseaseToPhenotypicFeatureAssociation . biolink:DrugExposure a sh:NodeShape ; sh:closed true ; sh:description "A drug exposure is an intake of a particular drug." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_attribute_type ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; @@ -5916,114 +6137,46 @@ biolink:DrugExposure a sh:NodeShape ; sh:path biolink:has_qualitative_value ], [ sh:order 10 ; sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 2 ; sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:timepoint ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_attribute_type ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; sh:order 1 ; sh:path biolink:has_quantitative_value ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ] ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ] ; sh:targetClass biolink:DrugExposure . biolink:DrugLabel a sh:NodeShape ; sh:closed true ; sh:description "a document accompanying a drug or its container that provides written, printed or graphic information about the drug, including drug contents, specific instructions or warnings for administration, storage and disposal instructions, etc. " ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:format ], - [ sh:description "keywords tagging a publication" ; - sh:order 3 ; - sh:path biolink:keywords ], - [ sh:order 14 ; - sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 10 ; sh:path biolink:provided_by ], [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:order 15 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], [ sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:summary ], - [ sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:rights ], - [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:creation_date ], - [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:license ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -6033,18 +6186,55 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], + [ sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:license ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:order 14 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:rights ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:format ], + [ sh:description "keywords tagging a publication" ; + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:maxCount 1 ; sh:order 16 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:description ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:creation_date ], + [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 4 ; + sh:path biolink:mesh_terms ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:iri ] ; sh:targetClass biolink:DrugLabel . biolink:DrugToEntityAssociationMixin a sh:NodeShape ; @@ -6057,82 +6247,105 @@ biolink:DrugToGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "An interaction between a drug and a gene or gene product." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:property [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Drug ; + sh:description "the drug that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 26 ; sh:path biolink:iri ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:object_category ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "the gene or gene product that is affected by the drug" ; sh:maxCount 1 ; @@ -6140,133 +6353,71 @@ biolink:DrugToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNode ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Drug ; - sh:description "the drug that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:maxCount 1 ; sh:order 30 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:path biolink:description ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ] ; + sh:order 31 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:DrugToGeneAssociation . biolink:DrugToGeneInteractionExposure a sh:NodeShape ; sh:closed true ; sh:description "drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_attribute_type ], - [ sh:order 11 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:iri ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:has_qualitative_value ], + sh:order 4 ; + sh:path biolink:has_attribute_type ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 3 ; sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 9 ; + sh:path biolink:xref ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 8 ; sh:path biolink:provided_by ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:timepoint ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -6276,239 +6427,302 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 10 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 9 ; - sh:path biolink:xref ] ; + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], + [ sh:order 11 ; + sh:path rdf:type ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:timepoint ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 7 ; + sh:path biolink:id ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:description ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ] ; sh:targetClass biolink:DrugToGeneInteractionExposure . biolink:DruggableGeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a point in time" ; + sh:property [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state." ; sh:maxCount 1 ; - sh:order 10 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path rdf:subject ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; sh:path biolink:timepoint ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 12 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 20 ; + sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "connects an association to an instance of supporting evidence" ; + sh:in ( "tclin" "tbio" "tchem" "tdark" ) ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; sh:order 34 ; - sh:path biolink:frequency_qualifier ], + sh:path biolink:has_attribute ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:has_quotient ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 24 ; + sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 28 ; + sh:path biolink:id ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:onset_qualifier ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:path biolink:subject_closure ], + [ sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:description ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "connects an association to an instance of supporting evidence" ; - sh:in ( "tclin" "tbio" "tchem" "tdark" ) ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; - sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:onset_qualifier ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 5 ; + sh:path rdf:object ], + [ sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 35 ; + sh:path biolink:has_count ], + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 8 ; + sh:path biolink:publications ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], + sh:order 39 ; + sh:path biolink:severity_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 4 ; + sh:order 7 ; sh:path biolink:qualifiers ], + [ sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; + sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 4 ; + sh:path rdf:predicate ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 30 ; + sh:path biolink:category ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "a human-readable description of an entity" ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], + sh:order 36 ; + sh:path biolink:has_total ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 31 ; + sh:path rdf:type ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 29 ; + sh:order 32 ; sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], + sh:order 29 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:path biolink:object_category ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:severity_qualifier ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ] ; + sh:order 2 ; + sh:path biolink:sex_qualifier ] ; sh:targetClass biolink:DruggableGeneToDiseaseAssociation . biolink:Entity a sh:NodeShape ; sh:closed false ; sh:description "Root Biolink Model class for all things and informational relationships, real or imagined." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:iri ], - [ sh:order 3 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path rdfs:label ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 2 ; sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path rdfs:label ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:id ], + [ sh:maxCount 1 ; sh:order 5 ; - sh:path dct:description ], + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:iri ], + [ sh:order 3 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 6 ; - sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ] ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Entity . biolink:EntityToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_subject ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 26 ; sh:path biolink:id ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_attribute ], + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path rdfs:label ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_predicate ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -6516,143 +6730,131 @@ biolink:EntityToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path rdf:object ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:FDA_approval_status ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 29 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:object_category ], + [ sh:description "" ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:FDA_approval_status ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:subject_category ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 28 ; + sh:path biolink:category ], + [ sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:description ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:object_category_closure ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 31 ; - sh:path dct:description ], + sh:order 11 ; + sh:path biolink:timepoint ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_attribute ], [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 18 ; sh:path biolink:object_closure ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_label_closure ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:object_namespace ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:subject_namespace ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path rdf:subject ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 29 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path rdfs:label ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:iri ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:path rdf:subject ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 28 ; - sh:path biolink:category ] ; + sh:order 14 ; + sh:path biolink:original_object ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ] ; sh:targetClass biolink:EntityToDiseaseAssociation . biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "mixin class for any association whose object (target node) is a disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:SeverityValue ; + sh:property [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:onset_qualifier ], + [ sh:class biolink:SeverityValue ; sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; @@ -6661,13 +6863,7 @@ biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:order 2 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:onset_qualifier ] ; + sh:path biolink:frequency_qualifier ] ; sh:targetClass biolink:EntityToDiseaseAssociationMixin . biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a sh:NodeShape ; @@ -6691,16 +6887,16 @@ biolink:EntityToFeatureOrDiseaseQualifiersMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:onset_qualifier ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:frequency_qualifier ], [ sh:class biolink:SeverityValue ; sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:severity_qualifier ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:frequency_qualifier ] ; + sh:path biolink:severity_qualifier ] ; sh:targetClass biolink:EntityToFeatureOrDiseaseQualifiersMixin . biolink:EntityToOutcomeAssociationMixin a sh:NodeShape ; @@ -6712,37 +6908,25 @@ biolink:EntityToOutcomeAssociationMixin a sh:NodeShape ; biolink:EntityToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:subject_namespace ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:object_closure ], + sh:order 22 ; + sh:path biolink:object_namespace ], [ sh:description "" ; sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:FDA_approval_status ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 28 ; + sh:path biolink:category ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path dct:description ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -6750,71 +6934,80 @@ biolink:EntityToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path rdf:object ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path rdfs:label ], + sh:order 27 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category_closure ], + sh:order 15 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 29 ; sh:path rdf:type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:negated ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 26 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_object ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:subject_closure ], + [ sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:description ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:subject_namespace ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 11 ; @@ -6824,138 +7017,123 @@ biolink:EntityToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:has_attribute ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 28 ; - sh:path biolink:category ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ], [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 24 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:subject_category ] ; + sh:order 30 ; + sh:path rdfs:label ] ; sh:targetClass biolink:EntityToPhenotypicFeatureAssociation . biolink:EntityToPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "total number of things in a particular reference set" ; + sh:property [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:onset_qualifier ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:has_total ], + [ sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:has_quotient ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:sex_qualifier ], - [ sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:has_count ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:has_quotient ], - [ sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:has_percentage ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:frequency_qualifier ], [ sh:class biolink:SeverityValue ; sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:severity_qualifier ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + [ sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:onset_qualifier ] ; + sh:order 4 ; + sh:path biolink:has_percentage ], + [ sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:has_count ] ; sh:targetClass biolink:EntityToPhenotypicFeatureAssociationMixin . biolink:EnvironmentalExposure a sh:NodeShape ; sh:closed true ; sh:description "A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 10 ; - sh:path rdf:type ], + sh:property [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:timepoint ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], + [ sh:order 10 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -6963,85 +7141,86 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_attribute_type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 9 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 8 ; sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ] ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ] ; sh:targetClass biolink:EnvironmentalExposure . biolink:EnvironmentalFeature a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:order 5 ; + sh:path rdf:type ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], - [ sh:order 5 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path dct:description ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:iri ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 6 ; sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ] ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:description ] ; sh:targetClass biolink:EnvironmentalFeature . biolink:EnvironmentalFoodContaminant a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:class biolink:ChemicalEntity ; + sh:property [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:trade_name ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:xref ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -7051,73 +7230,62 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 9 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:order 10 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:is_toxic ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 7 ; sh:path biolink:id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:max_tolerated_dose ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:is_toxic ], + sh:order 8 ; + sh:path biolink:iri ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 1 ; sh:path biolink:available_from ], + [ sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:description ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 4 ; - sh:path biolink:has_chemical_role ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:order 10 ; - sh:path rdf:type ] ; + sh:path biolink:has_chemical_role ] ; sh:targetClass biolink:EnvironmentalFoodContaminant . biolink:EnvironmentalProcess a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_attribute ], - [ sh:order 5 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:maxCount 1 ; sh:order 7 ; - sh:path dct:description ], + sh:path biolink:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -7130,7 +7298,24 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 3 ; - sh:path biolink:iri ] ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:order 5 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:EnvironmentalProcess . biolink:EpidemiologicalOutcome a sh:NodeShape ; @@ -7156,129 +7341,103 @@ biolink:Event a sh:NodeShape ; sh:maxCount 1 ; sh:order 6 ; sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_attribute ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 5 ; - sh:path rdf:type ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:iri ], + [ sh:order 5 ; + sh:path rdf:type ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ] ; + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:description ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Event . biolink:ExonToTranscriptRelationship a sh:NodeShape ; sh:closed true ; sh:description "A transcript is formed from multiple exons" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Exon ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], [ sh:class biolink:Transcript ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -7286,11 +7445,6 @@ biolink:ExonToTranscriptRelationship a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -7298,188 +7452,202 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category_closure ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:subject_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:object_namespace ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Exon ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; + sh:order 25 ; + sh:path biolink:id ] ; sh:targetClass biolink:ExonToTranscriptRelationship . biolink:ExposureEventToOutcomeAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between an exposure event and an outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:temporal_context_qualifier ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:population_context_qualifier ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:property [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 30 ; sh:path rdf:type ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_predicate ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 33 ; sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 27 ; - sh:path biolink:id ], - [ sh:class biolink:Outcome ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 3 ; + sh:path rdf:predicate ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 4 ; - sh:path rdf:object ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 5 ; + sh:path biolink:negated ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_object ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_subject ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:object_label_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:population_context_qualifier ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 3 ; - sh:path rdf:predicate ], + sh:order 27 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:subject_closure ], + sh:order 15 ; + sh:path biolink:original_object ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_evidence ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path dct:description ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 22 ; + sh:path biolink:subject_namespace ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 29 ; + sh:path biolink:category ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:object_closure ], + [ sh:description "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:negated ], + sh:order 1 ; + sh:path biolink:temporal_context_qualifier ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 28 ; sh:path biolink:iri ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:object_closure ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:object_category ], + [ sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:description ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 23 ; sh:path biolink:object_namespace ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 29 ; - sh:path biolink:category ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:object_label_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:subject_namespace ], + sh:order 13 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -7487,68 +7655,56 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:subject ], - [ sh:description "a point in time" ; + [ sh:class biolink:Outcome ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 4 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + sh:order 21 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:object_category ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:subject_label_closure ], + sh:order 20 ; + sh:path biolink:subject_category_closure ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 31 ; sh:path rdfs:label ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_predicate ] ; + sh:order 12 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:subject_closure ] ; sh:targetClass biolink:ExposureEventToOutcomeAssociation . biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:subject_namespace ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 29 ; - sh:path rdf:type ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:onset_qualifier ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_label_closure ], + sh:order 22 ; + sh:path biolink:object_namespace ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 30 ; sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category_closure ], + [ sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:has_quotient ], [ sh:class biolink:ExposureEvent ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -7556,279 +7712,286 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path rdf:subject ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 28 ; - sh:path biolink:category ], - [ sh:description "number of things with a particular property" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:has_count ], - [ sh:description "total number of things in a particular reference set" ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:has_total ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 13 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 38 ; + sh:path biolink:onset_qualifier ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 37 ; + sh:path biolink:severity_qualifier ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 27 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:subject_namespace ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 29 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:subject_category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 16 ; + sh:path biolink:object_category ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 11 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], - [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 34 ; + sh:path biolink:has_total ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:has_percentage ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 14 ; + sh:path biolink:original_object ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:description ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], + [ sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:has_count ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 28 ; + sh:path biolink:category ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:object_category ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:severity_qualifier ], + sh:order 15 ; + sh:path biolink:subject_category ], [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:order 39 ; sh:path biolink:frequency_qualifier ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 26 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path dct:description ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:iri ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:object_closure ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_label_closure ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], - [ sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:has_quotient ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], + sh:order 36 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_attribute ], [ sh:class biolink:PhenotypicFeature ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path rdf:object ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ] ; + sh:path rdf:object ] ; sh:targetClass biolink:ExposureEventToPhenotypicFeatureAssociation . biolink:Food a sh:NodeShape ; sh:closed true ; sh:description "A substance consumed by a living organism as a source of nutrition" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], + sh:property [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 9 ; sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:description ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:is_toxic ], + [ sh:order 14 ; + sh:path rdf:type ], [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:highest_FDA_approval_status ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], [ sh:class biolink:ChemicalMixture ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:is_supplement ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:iri ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], + sh:order 4 ; + sh:path biolink:trade_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:xref ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:id ], - [ sh:order 14 ; - sh:path rdf:type ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:trade_name ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 15 ; sh:path rdfs:label ], - [ sh:description "" ; + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ] ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ] ; sh:targetClass biolink:Food . biolink:FoodAdditive a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ], - [ sh:class biolink:ChemicalRole ; + sh:property [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_chemical_role ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:description ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:is_toxic ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:xref ], [ sh:order 10 ; sh:path rdf:type ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 1 ; sh:path biolink:available_from ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 8 ; @@ -7839,26 +8002,24 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:trade_name ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:is_toxic ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 7 ; sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ] ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:max_tolerated_dose ] ; sh:targetClass biolink:FoodAdditive . biolink:FrequencyQualifierMixin a sh:NodeShape ; @@ -7874,65 +8035,98 @@ biolink:FrequencyQualifierMixin a sh:NodeShape ; biolink:FrequencyQuantifier a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:property [ sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:has_percentage ], + sh:order 0 ; + sh:path biolink:has_count ], [ sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:has_total ], + [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:has_percentage ], [ sh:maxCount 1 ; sh:order 2 ; - sh:path biolink:has_quotient ], - [ sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_count ] ; + sh:path biolink:has_quotient ] ; sh:targetClass biolink:FrequencyQuantifier . biolink:FunctionalAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:property [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], [ sh:class biolink:MacromolecularMachineMixin ; sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; @@ -7940,44 +8134,50 @@ biolink:FunctionalAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNode ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 29 ; sh:path rdfs:label ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; @@ -7987,71 +8187,55 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 20 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "class describing the activity, process or localization of the gene product" ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ] ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ] ; sh:targetClass biolink:FunctionalAssociation . biolink:Fungus a sh:NodeShape ; sh:closed true ; sh:description "A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi refer to those that grow as multicellular colonies (mushrooms and molds)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:order 6 ; + sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -8060,212 +8244,203 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:Fungus . + +biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; + sh:order 7 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 7 ; + sh:order 32 ; sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; sh:order 3 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path rdf:subject ], + [ sh:description "The relationship to the disease" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:order 4 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:Fungus . - -biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:path rdf:predicate ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:iri ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:sex_qualifier ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; sh:order 30 ; - sh:path dct:description ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:onset_qualifier ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:path biolink:category ], [ sh:class biolink:Disease ; sh:description "disease" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; + sh:order 5 ; sh:path rdf:object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; + sh:order 1 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 11 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + sh:order 41 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 19 ; + sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:severity_qualifier ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:frequency_qualifier ], + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 31 ; + sh:path rdf:type ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; + sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:has_quotient ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 25 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:publications ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; + sh:path biolink:original_subject ], + [ sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 35 ; + sh:path biolink:has_count ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:onset_qualifier ], + [ sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:has_total ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "a point in time" ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; + sh:order 16 ; sh:path biolink:original_object ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:severity_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "The relationship to the disease" ; + sh:order 34 ; + sh:path biolink:has_attribute ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], + sh:order 28 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ] ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ] ; sh:targetClass biolink:GeneAsAModelOfDiseaseAssociation . biolink:GeneExpressionMixin a sh:NodeShape ; @@ -8278,18 +8453,18 @@ biolink:GeneExpressionMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:quantifier_qualifier ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:phenotypic_state ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:expression_site ], [ sh:class biolink:LifeStage ; sh:description "stage during which gene or protein expression of takes place." ; sh:maxCount 1 ; @@ -8312,530 +8487,599 @@ biolink:GeneGroupingMixin a sh:NodeShape ; biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_label_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; + sh:order 16 ; sh:path biolink:original_predicate ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 26 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category_closure ], [ sh:maxCount 1 ; sh:order 0 ; sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 29 ; - sh:path rdf:type ], - [ sh:class biolink:Disease ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; sh:order 1 ; - sh:path rdf:subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_attribute ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:subject_closure ], + sh:order 9 ; + sh:path biolink:publications ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 29 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; + sh:order 18 ; sh:path biolink:subject_category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:nodeKind sh:IRI ; + sh:order 41 ; + sh:path biolink:onset_qualifier ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:description ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 6 ; + sh:path rdf:object ], + [ sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:has_count ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 28 ; + sh:order 31 ; sh:path biolink:category ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], + [ sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:has_total ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:negated ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; + sh:order 27 ; sh:path biolink:object_label_closure ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:has_quotient ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:object_namespace ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 40 ; + sh:path biolink:severity_qualifier ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 32 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 19 ; - sh:path biolink:subject_category_closure ], + sh:path biolink:object_category ], + [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:has_percentage ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 25 ; + sh:order 28 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 5 ; + sh:order 8 ; sh:path biolink:qualifiers ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 21 ; + sh:order 24 ; sh:path biolink:subject_namespace ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:object_category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:iri ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:minCount 1 ; + sh:order 5 ; + sh:path rdf:predicate ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; + sh:order 11 ; sh:path biolink:knowledge_source ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_attribute ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], - [ sh:description "a human-readable description of an entity" ; + sh:order 33 ; + sh:path rdfs:label ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path dct:description ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ] ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 4 ; + sh:path rdf:subject ] ; sh:targetClass biolink:GeneHasVariantThatContributesToDiseaseAssociation . biolink:GeneProductIsoformMixin a sh:NodeShape ; sh:closed false ; sh:description "This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:order 2 ; sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 0 ; sh:path biolink:synonym ] ; sh:targetClass biolink:GeneProductIsoformMixin . -biolink:GeneToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; +biolink:GeneToDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:onset_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 8 ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 11 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path rdf:subject ], + [ sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:has_quotient ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], + sh:order 28 ; + sh:path biolink:id ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; + sh:order 30 ; sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], + sh:order 5 ; + sh:path rdf:object ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:sex_qualifier ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; + sh:order 16 ; sh:path biolink:original_object ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "a point in time" ; + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:has_total ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:iri ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 20 ; + sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:severity_qualifier ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:description ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], + sh:order 41 ; + sh:path biolink:frequency_qualifier ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 12 ; + sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; + sh:order 31 ; sh:path rdf:type ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ] ; - sh:targetClass biolink:GeneToDiseaseAssociation . - -biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 28 ; - sh:path biolink:id ], - [ sh:description "number of things with a particular property" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:has_count ], + sh:order 6 ; + sh:path biolink:negated ], [ sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:order 38 ; sh:path biolink:has_percentage ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:onset_qualifier ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:has_count ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_attribute ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:GeneToDiseaseAssociation . + +biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:iri ], - [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:has_quotient ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_attribute ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 2 ; + sh:path biolink:sex_qualifier ], + [ sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:description ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 4 ; - sh:path rdf:predicate ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 30 ; - sh:path biolink:category ], - [ sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:has_quotient ], + sh:order 28 ; + sh:path biolink:id ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path rdfs:label ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:severity_qualifier ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], [ sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:object ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 40 ; + sh:path biolink:onset_qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], [ sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:order 36 ; sh:path biolink:has_total ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the phenotypic feature" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:description "a point in time" ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:severity_qualifier ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:has_count ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 31 ; sh:path rdf:type ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:knowledge_source ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:negated ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 33 ; - sh:path dct:description ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:publications ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path rdf:predicate ], + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the phenotypic feature" ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path rdf:subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 5 ; + sh:path rdf:object ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 30 ; + sh:path biolink:category ], + [ sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:sex_qualifier ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 38 ; + sh:path biolink:has_percentage ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ] ; + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ] ; sh:targetClass biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . biolink:GeneToEntityAssociationMixin a sh:NodeShape ; @@ -8847,14 +9091,51 @@ biolink:GeneToExpressionSiteAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:subject_category_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "can be used to indicate magnitude, or also ranking" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:quantifier_qualifier ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 27 ; - sh:path biolink:id ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 30 ; - sh:path rdf:type ], + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path rdf:subject ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:object_namespace ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -8862,200 +9143,132 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 29 ; sh:path biolink:category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_object ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 27 ; + sh:path biolink:id ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 24 ; sh:path biolink:subject_label_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:negated ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 31 ; sh:path rdfs:label ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "can be used to indicate magnitude, or also ranking" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:quantifier_qualifier ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], [ sh:class biolink:LifeStage ; sh:description "stage at which the gene is expressed in the site" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:stage_qualifier ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:object_category ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:subject_category ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_object ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 19 ; sh:path biolink:object_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path rdf:subject ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:object_namespace ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 30 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which the gene is expressed" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 32 ; - sh:path dct:description ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 5 ; + sh:path biolink:negated ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 18 ; sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category_closure ], + sh:order 7 ; + sh:path biolink:publications ], [ sh:description "expression relationship" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:knowledge_source ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 22 ; - sh:path biolink:subject_namespace ] ; + sh:path biolink:subject_namespace ], + [ sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:description ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which the gene is expressed" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:subject_category ] ; sh:targetClass biolink:GeneToExpressionSiteAssociation . biolink:GeneToGeneAssociation a sh:NodeShape ; sh:closed false ; sh:description "abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 16 ; sh:path biolink:subject_closure ], @@ -9064,63 +9277,30 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:object_namespace ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -9132,182 +9312,239 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category_closure ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "a point in time" ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ] ; - sh:targetClass biolink:GeneToGeneAssociation . - -biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Indicates that two genes are co-expressed, generally under the same conditions." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:iri ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:order 18 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNode ; - sh:order 6 ; + sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:LifeStage ; - sh:description "stage during which gene or protein expression of takes place." ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:stage_qualifier ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 14 ; + sh:order 10 ; sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ] ; + sh:targetClass biolink:GeneToGeneAssociation . + +biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Indicates that two genes are co-expressed, generally under the same conditions." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_attribute ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 32 ; + sh:path rdf:type ], [ sh:class biolink:AnatomicalEntity ; sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:expression_site ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:phenotypic_state ], + [ sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:description ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; sh:path rdf:predicate ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNode ; - sh:order 4 ; - sh:path rdf:subject ], + sh:order 6 ; + sh:path rdf:object ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 29 ; sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:LifeStage ; + sh:description "stage during which gene or protein expression of takes place." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], + sh:order 2 ; + sh:path biolink:stage_qualifier ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:iri ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 17 ; sh:path biolink:original_object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:phenotypic_state ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:subject_namespace ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Optional quantitative value indicating degree of expression." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:quantifier_qualifier ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 4 ; + sh:path rdf:subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -9315,201 +9552,60 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 31 ; sh:path biolink:category ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 32 ; - sh:path rdf:type ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:subject_closure ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 33 ; sh:path rdfs:label ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ] ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_source ] ; sh:targetClass biolink:GeneToGeneCoexpressionAssociation . biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; sh:closed true ; sh:description "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], [ sh:description "membership of the gene in the given gene family." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:GeneFamily ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ] ; - sh:targetClass biolink:GeneToGeneFamilyAssociation . - -biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -9517,80 +9613,132 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:knowledge_source ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:subject_namespace ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; sh:path biolink:subject_label_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:class biolink:GeneFamily ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "homology relationship type" ; + [ sh:class biolink:Gene ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "a human-readable description of an entity" ; + sh:order 14 ; + sh:path biolink:subject_category ] ; + sh:targetClass biolink:GeneToGeneFamilyAssociation . + +biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:maxCount 1 ; sh:order 30 ; - sh:path dct:description ], + sh:path biolink:description ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; @@ -9598,82 +9746,146 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:BlankNode ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], + [ sh:description "homology relationship type" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 26 ; sh:path biolink:iri ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "a point in time" ; sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category_closure ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ] ; + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ] ; sh:targetClass biolink:GeneToGeneHomologyAssociation . biolink:GeneToGeneProductRelationship a sh:NodeShape ; sh:closed true ; sh:description "A gene is transcribed and potentially translated to a gene product" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:GeneProductMixin ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -9681,54 +9893,50 @@ biolink:GeneToGeneProductRelationship a sh:NodeShape ; sh:nodeKind sh:BlankNode ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 28 ; sh:path rdf:type ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:subject_category ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:Gene ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -9736,219 +9944,235 @@ biolink:GeneToGeneProductRelationship a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 13 ; + sh:path biolink:original_object ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category_closure ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ] ; + sh:targetClass biolink:GeneToGeneProductRelationship . + +biolink:GeneToGoTermAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:class biolink:Gene ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; - sh:path biolink:retrieval_source_ids ] ; - sh:targetClass biolink:GeneToGeneProductRelationship . - -biolink:GeneToGoTermAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:subject_namespace ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + sh:order 15 ; + sh:path biolink:object_category ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Gene ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + [ sh:class biolink:OntologyClass ; + sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "class describing the activity, process or localization of the gene product" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 29 ; + sh:path rdfs:label ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:path biolink:publications ] ; + sh:targetClass biolink:GeneToGoTermAssociation . + +biolink:GeneToPathwayAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An interaction between a gene or gene product and a biological process or pathway." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -9960,25 +10184,10 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category_closure ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ] ; - sh:targetClass biolink:GeneToGoTermAssociation . - -biolink:GeneToPathwayAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An interaction between a gene or gene product and a biological process or pathway." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -9986,434 +10195,449 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the gene or gene product entity that participates or influences the pathway" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "a human-readable description of an entity" ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the gene or gene product entity that participates or influences the pathway" ; + [ sh:class biolink:Pathway ; + sh:description "the pathway that includes or is affected by the gene or gene product" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 17 ; sh:path biolink:object_closure ], - [ sh:description "a point in time" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:subject_namespace ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], + sh:order 18 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 29 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:GeneToPathwayAssociation . + +biolink:GeneToPhenotypeAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 12 ; + sh:order 15 ; sh:path biolink:original_predicate ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 21 ; + sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:class biolink:Pathway ; - sh:description "the pathway that includes or is affected by the gene or gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 12 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 1 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ] ; - sh:targetClass biolink:GeneToPathwayAssociation . - -biolink:GeneToPhenotypeAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 32 ; + sh:path rdfs:label ], + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], + sh:order 6 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:description ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; + sh:order 18 ; sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], + [ sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:has_count ], [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; + sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; + sh:order 11 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:onset_qualifier ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the phenotypic feature" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path rdf:subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 34 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 4 ; + sh:order 7 ; sh:path biolink:qualifiers ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 26 ; + sh:order 29 ; sh:path biolink:iri ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; + sh:order 21 ; sh:path biolink:subject_category_closure ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; + sh:order 30 ; sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "a point in time" ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:order 4 ; + sh:path rdf:predicate ], + [ sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:severity_qualifier ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 5 ; + sh:order 8 ; sh:path biolink:publications ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 5 ; + sh:path rdf:object ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], + sh:minCount 1 ; + sh:order 28 ; + sh:path biolink:id ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:has_total ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; + sh:order 17 ; sh:path biolink:subject_category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ] ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 31 ; + sh:path rdf:type ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:has_percentage ] ; sh:targetClass biolink:GeneToPhenotypeAssociation . biolink:Genome a sh:NodeShape ; sh:closed true ; sh:description "A genome is the sum of genetic material within a cell or virion." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 7 ; - sh:path rdf:type ], + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; - sh:path biolink:has_biological_sequence ], + sh:path biolink:has_biological_sequence ], + [ sh:order 7 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:Genome . + +biolink:GenomicBackgroundExposure a sh:NodeShape ; + sh:closed true ; + sh:description "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:order 13 ; + sh:path rdf:type ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; + sh:order 11 ; sh:path biolink:xref ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_attribute_type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 10 ; + sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], + sh:order 8 ; + sh:path biolink:has_qualitative_value ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 6 ; + sh:order 12 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 10 ; + sh:path biolink:provided_by ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ] ; - sh:targetClass biolink:Genome . - -biolink:GenomicBackgroundExposure a sh:NodeShape ; - sh:closed true ; - sh:description "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; + [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 7 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_qualitative_value ], + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:in_taxon ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 10 ; - sh:path biolink:provided_by ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 7 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:has_biological_sequence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:description ], [ sh:class biolink:Gene ; sh:description "connects an entity with one or more gene or gene products" ; sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path biolink:has_gene_or_gene_product ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_attribute_type ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path rdfs:label ], - [ sh:order 13 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 11 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ] ; + sh:path biolink:has_gene_or_gene_product ] ; sh:targetClass biolink:GenomicBackgroundExposure . biolink:GenomicEntity a sh:NodeShape ; @@ -10429,25 +10653,53 @@ biolink:GenomicSequenceLocalization a sh:NodeShape ; sh:closed true ; sh:description "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:property [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + sh:order 5 ; + sh:path rdf:subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:description ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:subject_closure ], + [ sh:description "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand)." ; + sh:in ( "+" "-" "." "?" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], + sh:order 3 ; + sh:path biolink:strand ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:object_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:negated ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -10455,127 +10707,68 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 32 ; sh:path biolink:category ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:subject_namespace ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:subject ], [ sh:description "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens." ; sh:in ( "+" "-" "." "?" ) ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:genome_build ], - [ sh:description "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand)." ; - sh:in ( "+" "-" "." "?" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:strand ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], + sh:order 11 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:qualifiers ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 27 ; sh:path biolink:subject_label_closure ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path rdf:predicate ], - [ sh:description "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2." ; - sh:in ( "0" "1" "2" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:phase ], - [ sh:description "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:end_interbase_coordinate ], - [ sh:description "a point in time" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 23 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 19 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:negated ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 25 ; + sh:path biolink:subject_namespace ], + [ sh:description "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 1 ; + sh:path biolink:end_interbase_coordinate ], + [ sh:description "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0)." ; sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:start_interbase_coordinate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:knowledge_source ], + sh:order 10 ; + sh:path biolink:publications ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:class biolink:NucleicAcidEntity ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -10583,36 +10776,59 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 7 ; sh:path rdf:object ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:object_closure ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:object_namespace ], [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 28 ; sh:path biolink:object_label_closure ], - [ sh:description "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0)." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:start_interbase_coordinate ], - [ sh:description "a human-readable description of an entity" ; + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:description "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2." ; + sh:in ( "0" "1" "2" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:phase ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ] ; + sh:order 24 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category ] ; sh:targetClass biolink:GenomicSequenceLocalization . biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; - sh:maxCount 1 ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:severity_qualifier ], + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:Disease ; sh:description "disease" ; sh:maxCount 1 ; @@ -10620,46 +10836,26 @@ biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Genotype ; - sh:description "A genotype that has a role in modeling the disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 33 ; + sh:path biolink:onset_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -10667,215 +10863,188 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:order 32 ; + sh:path biolink:severity_qualifier ], [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 17 ; sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], + sh:order 15 ; + sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:Genotype ; + sh:description "A genotype that has a role in modeling the disease." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "The relationship to the disease" ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "The relationship to the disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:order 34 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:onset_qualifier ] ; + sh:path biolink:frequency_qualifier ] ; sh:targetClass biolink:GenotypeAsAModelOfDiseaseAssociation . biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:Disease ; - sh:description "a disease that is associated with that genotype" ; + sh:property [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Genotype ; + sh:description "a genotype that is associated in some way with a disease state" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 28 ; sh:path rdf:type ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:order 33 ; + sh:path biolink:onset_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:subject_category ], - [ sh:class biolink:Genotype ; - sh:description "a genotype that is associated in some way with a disease state" ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], + sh:order 15 ; + sh:path biolink:object_category ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:onset_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "E.g. is pathogenic for" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -10883,84 +11052,141 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Disease ; + sh:description "a disease that is associated with that genotype" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:SeverityValue ; sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:severity_qualifier ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:frequency_qualifier ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; sh:path biolink:subject_label_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:object_namespace ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "E.g. is pathogenic for" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 16 ; sh:path biolink:subject_closure ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:GenotypeToDiseaseAssociation . + +biolink:GenotypeToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:GenotypeToEntityAssociationMixin . + +biolink:GenotypeToGeneAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ] ; - sh:targetClass biolink:GenotypeToDiseaseAssociation . - -biolink:GenotypeToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:GenotypeToEntityAssociationMixin . - -biolink:GenotypeToGeneAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + sh:order 29 ; + sh:path rdfs:label ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; @@ -10971,24 +11197,21 @@ biolink:GenotypeToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:Gene ; sh:description "gene implicated in genotype" ; sh:maxCount 1 ; @@ -10996,51 +11219,44 @@ biolink:GenotypeToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "the relationship type used to connect genotype to gene" ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:class biolink:Genotype ; sh:description "parent genotype" ; sh:maxCount 1 ; @@ -11048,95 +11264,70 @@ biolink:GenotypeToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "the relationship type used to connect genotype to gene" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "a point in time" ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ] ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ] ; sh:targetClass biolink:GenotypeToGeneAssociation . biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between one genotype and a genotypic entity that is a sub-component of it" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Genotype ; + sh:description "parent genotype" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], [ sh:class biolink:Genotype ; sh:description "child genotype" ; sh:maxCount 1 ; @@ -11144,29 +11335,50 @@ biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Genotype ; - sh:description "parent genotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 31 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -11174,140 +11386,80 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 28 ; sh:path rdf:type ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 16 ; sh:path biolink:subject_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 29 ; sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ] ; + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ] ; sh:targetClass biolink:GenotypeToGenotypePartAssociation . biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:has_percentage ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 29 ; - sh:path rdf:type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "a point in time" ; + sh:property [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:timepoint ], - [ sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:has_quotient ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_label_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -11315,101 +11467,151 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 28 ; sh:path biolink:category ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 26 ; - sh:path biolink:id ], - [ sh:class biolink:Genotype ; - sh:description "genotype that is associated with the phenotypic feature" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:object_category ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path dct:description ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:severity_qualifier ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:object_namespace ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:subject_category_closure ], + [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:has_percentage ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 30 ; sh:path rdfs:label ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:has_total ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 38 ; + sh:path biolink:onset_qualifier ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:subject_category ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_object ], + [ sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:object_category ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 29 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], + [ sh:class biolink:Genotype ; + sh:description "genotype that is associated with the phenotypic feature" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path rdf:predicate ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:iri ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "total number of things in a particular reference set" ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:has_total ], + sh:order 13 ; + sh:path biolink:original_predicate ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_subject ], [ sh:class biolink:PhenotypicFeature ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -11417,199 +11619,172 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 3 ; sh:path rdf:object ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_label_closure ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:object_closure ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + [ sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:description ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:onset_qualifier ], + sh:order 37 ; + sh:path biolink:severity_qualifier ], [ sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:order 33 ; - sh:path biolink:has_count ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ] ; + sh:path biolink:has_count ] ; sh:targetClass biolink:GenotypeToPhenotypicFeatureAssociation . biolink:GenotypeToVariantAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between a genotype and a sequence variant." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; + sh:property [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:class biolink:SequenceVariant ; - sh:description "gene implicated in genotype" ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:object_category ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], - [ sh:description "the relationship type used to connect genotype to gene" ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Genotype ; + sh:description "parent genotype" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:subject_namespace ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "the relationship type used to connect genotype to gene" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Genotype ; - sh:description "parent genotype" ; + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 25 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category_closure ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:SequenceVariant ; + sh:description "gene implicated in genotype" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ] ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ] ; sh:targetClass biolink:GenotypeToVariantAssociation . biolink:GenotypicSex a sh:NodeShape ; @@ -11618,13 +11793,25 @@ biolink:GenotypicSex a sh:NodeShape ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; sh:path biolink:xref ], @@ -11633,13 +11820,19 @@ biolink:GenotypicSex a sh:NodeShape ; sh:nodeKind sh:BlankNode ; sh:order 2 ; sh:path biolink:has_quantitative_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -11649,30 +11842,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ] ; + sh:order 11 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:GenotypicSex . biolink:GeographicExposure a sh:NodeShape ; @@ -11683,11 +11857,10 @@ biolink:GeographicExposure a sh:NodeShape ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -11695,6 +11868,15 @@ biolink:GeographicExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_attribute_type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -11702,77 +11884,78 @@ biolink:GeographicExposure a sh:NodeShape ; sh:path biolink:has_attribute ], [ sh:order 10 ; sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; sh:order 3 ; sh:path biolink:has_quantitative_value ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ] ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ] ; sh:targetClass biolink:GeographicExposure . biolink:GeographicLocation a sh:NodeShape ; sh:closed true ; sh:description "a location that can be described in lat/long coordinates" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "longitude" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:longitude ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "latitude" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], + sh:order 0 ; + sh:path biolink:latitude ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], - [ sh:description "latitude" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:latitude ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 8 ; sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "longitude" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:longitude ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:order 7 ; + sh:path rdf:type ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:description ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -11781,57 +11964,20 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 6 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:order 7 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; sh:targetClass biolink:GeographicLocation . biolink:GeographicLocationAtTime a sh:NodeShape ; sh:closed true ; sh:description "a location that can be described in lat/long coordinates, for a particular time" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:description "longitude" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:longitude ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:property [ sh:maxCount 1 ; sh:order 10 ; - sh:path dct:description ], + sh:path biolink:description ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:timepoint ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:description "latitude" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:latitude ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -11841,21 +11987,60 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 7 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "latitude" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:latitude ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:description "longitude" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:longitude ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], [ sh:order 8 ; sh:path rdf:type ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 9 ; sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ] ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:iri ] ; sh:targetClass biolink:GeographicLocationAtTime . biolink:GrossAnatomicalStructure a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -11864,84 +12049,49 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ] ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ] ; sh:targetClass biolink:GrossAnatomicalStructure . biolink:Haplotype a sh:NodeShape ; sh:closed true ; sh:description "A set of zero or more Alleles on a single instance of a Sequence[VMC]" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 7 ; - sh:path rdf:type ], + sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 4 ; sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ], + [ sh:order 7 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:description ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; @@ -11952,51 +12102,69 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:path biolink:iri ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 3 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:Haplotype . - -biolink:Hospitalization a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 5 ; - sh:path rdf:type ], + sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 4 ; + sh:order 6 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ] ; + sh:targetClass biolink:Haplotype . + +biolink:Hospitalization a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:description ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path dct:description ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 6 ; - sh:path rdfs:label ] ; + sh:path rdfs:label ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:order 5 ; + sh:path rdf:type ] ; sh:targetClass biolink:Hospitalization . biolink:HospitalizationOutcome a sh:NodeShape ; @@ -12009,12 +12177,7 @@ biolink:Human a sh:NodeShape ; sh:closed true ; sh:description "A member of the the species Homo sapiens." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -12023,148 +12186,97 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:order 6 ; - sh:path rdf:type ] ; - sh:targetClass biolink:Human . - -biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:path biolink:has_attribute ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 7 ; + sh:path rdfs:label ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path biolink:id ] ; + sh:targetClass biolink:Human . + +biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], + sh:order 31 ; + sh:path biolink:has_attribute ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 16 ; sh:path biolink:subject_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], + sh:order 26 ; + sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -12172,26 +12284,75 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:object_category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -12199,19 +12360,18 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ] ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ] ; sh:targetClass biolink:InformationContentEntityToNamedThingAssociation . -biolink:InformationResourceCollection a sh:NodeShape ; +biolink:InformationResourceContainer a sh:NodeShape ; sh:closed true ; sh:description "A collection of information resources" ; sh:ignoredProperties ( rdf:type ) ; @@ -12220,27 +12380,28 @@ biolink:InformationResourceCollection a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:information_resources ] ; - sh:targetClass biolink:InformationResourceCollection . + sh:targetClass biolink:InformationResourceContainer . biolink:Invertebrate a sh:NodeShape ; sh:closed true ; sh:description "An animal lacking a vertebral column. This group consists of 98% of all animal species." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:maxCount 1 ; sh:order 8 ; - sh:path dct:description ], + sh:path biolink:description ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -12250,131 +12411,182 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 2 ; sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ] ; + sh:order 7 ; + sh:path rdfs:label ] ; sh:targetClass biolink:Invertebrate . biolink:JournalArticle a sh:NodeShape ; sh:closed true ; sh:description "an article, typically presenting results of research, that is published in an issue of a scientific journal." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "executive summary of a publication" ; + sh:property [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:authors ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 8 ; + sh:path biolink:mesh_terms ], + [ sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:issue ], + [ sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:summary ], - [ sh:description "keywords tagging a publication" ; - sh:order 7 ; - sh:path biolink:keywords ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 14 ; + sh:path biolink:provided_by ], [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:rights ], + sh:order 10 ; + sh:path biolink:license ], + [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 5 ; + sh:path biolink:pages ], + [ sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:published_in ], [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 15 ; sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 9 ; - sh:path biolink:xref ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 8 ; - sh:path biolink:mesh_terms ], + [ sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:volume ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:creation_date ], [ sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:iso_abbreviation ], - [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 9 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:rights ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 19 ; + sh:path rdfs:label ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:order 18 ; + sh:path rdf:type ], + [ sh:description "keywords tagging a publication" ; + sh:order 7 ; + sh:path biolink:keywords ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:description ], + [ sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:format ] ; + sh:targetClass biolink:JournalArticle . + +biolink:LogOddsAnalysisResult a sh:NodeShape ; + sh:closed true ; + sh:description "A result of a log odds ratio analysis." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:order 9 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; - sh:path biolink:pages ], + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 14 ; + sh:order 4 ; sh:path biolink:provided_by ], - [ sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:volume ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:authors ], - [ sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 3 ; - sh:path biolink:issue ], + sh:path biolink:creation_date ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 16 ; + sh:order 7 ; sh:path biolink:iri ], - [ sh:order 18 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path dct:description ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 17 ; + sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:creation_date ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:has_attribute ], - [ sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:published_in ], [ sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:format ], - [ sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:license ] ; - sh:targetClass biolink:JournalArticle . + sh:order 1 ; + sh:path biolink:rights ] ; + sh:targetClass biolink:LogOddsAnalysisResult . biolink:MacromolecularComplex a sh:NodeShape ; sh:closed true ; sh:description "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 7 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; sh:path biolink:provided_by ], @@ -12387,203 +12599,97 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 6 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], + [ sh:order 7 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:in_taxon ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ] ; + sh:order 5 ; + sh:path biolink:iri ] ; sh:targetClass biolink:MacromolecularComplex . biolink:MacromolecularMachineToBiologicalProcessAssociation a sh:NodeShape ; sh:closed true ; sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:BiologicalProcess ; - sh:description "class describing the activity, process or localization of the gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:property [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; sh:order 30 ; - sh:path dct:description ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:path biolink:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:object_category ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category_closure ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ] ; - sh:targetClass biolink:MacromolecularMachineToBiologicalProcessAssociation . - -biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; @@ -12593,63 +12699,30 @@ biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + [ sh:class biolink:BiologicalProcess ; + sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + sh:order 31 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 17 ; sh:path biolink:object_closure ], @@ -12659,29 +12732,92 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:subject_category ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ] ; + sh:targetClass biolink:MacromolecularMachineToBiologicalProcessAssociation . + +biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:object_namespace ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:CellularComponent ; - sh:description "class describing the activity, process or localization of the gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; @@ -12690,41 +12826,105 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ] ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:CellularComponent ; + sh:description "class describing the activity, process or localization of the gene product" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ] ; sh:targetClass biolink:MacromolecularMachineToCellularComponentAssociation . biolink:MacromolecularMachineToEntityAssociationMixin a sh:NodeShape ; @@ -12737,55 +12937,61 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; sh:closed true ; sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:class biolink:MolecularActivity ; + sh:description "class describing the activity, process or localization of the gene product" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], + sh:order 2 ; + sh:path rdf:object ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 28 ; sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:MolecularActivity ; - sh:description "class describing the activity, process or localization of the gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; @@ -12794,118 +13000,93 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 16 ; sh:path biolink:subject_closure ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 26 ; sh:path biolink:iri ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:maxCount 1 ; sh:order 30 ; - sh:path dct:description ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:path biolink:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:subject_category ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:description "a point in time" ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ] ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:MacromolecularMachineToMolecularActivityAssociation . biolink:Mammal a sh:NodeShape ; sh:closed true ; sh:description "A member of the class Mammalia, a clade of endothermic amniotes distinguished from reptiles and birds by the possession of hair, three middle ear bones, mammary glands, and a neocortex" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -12914,29 +13095,40 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 2 ; sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Mammal . biolink:MappingCollection a sh:NodeShape ; @@ -12954,104 +13146,96 @@ biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a material sample and the material entity from which it is derived." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:object_category ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:class biolink:NamedThing ; - sh:description "the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:class biolink:NamedThing ; + sh:description "the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category_closure ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], [ sh:class biolink:MaterialSample ; sh:description "the material sample being described" ; sh:maxCount 1 ; @@ -13059,14 +13243,15 @@ biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; @@ -13078,78 +13263,94 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:description "derivation relationship" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:object_namespace ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ] ; + sh:order 10 ; + sh:path biolink:timepoint ] ; sh:targetClass biolink:MaterialSampleDerivationAssociation . biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a material sample and a disease or phenotype." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:subject_category ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -13157,33 +13358,43 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 16 ; sh:path biolink:subject_closure ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a human-readable description of an entity" ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], [ sh:class biolink:MaterialSample ; sh:description "the material sample being described" ; sh:maxCount 1 ; @@ -13191,50 +13402,30 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 5 ; + sh:path biolink:publications ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "disease or phenotype" ; sh:maxCount 1 ; @@ -13242,24 +13433,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ] ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ] ; sh:targetClass biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . biolink:MaterialSampleToEntityAssociationMixin a sh:NodeShape ; @@ -13271,61 +13449,39 @@ biolink:MaterialSampleToEntityAssociationMixin a sh:NodeShape ; biolink:MicroRNA a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:property [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:max_tolerated_dose ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], [ sh:description "" ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:is_toxic ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; - sh:maxCount 1 ; + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:trade_name ], - [ sh:description "indicates whether a molecular entity is a metabolite" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:is_metabolite ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:order 10 ; + sh:path biolink:has_chemical_role ], + [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], + sh:order 2 ; + sh:path biolink:has_biological_sequence ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_chemical_role ], + sh:order 3 ; + sh:path biolink:in_taxon ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -13335,20 +13491,41 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; + sh:order 15 ; + sh:path rdfs:label ], + [ sh:maxCount 1 ; sh:order 16 ; - sh:path dct:description ], - [ sh:order 14 ; - sh:path rdf:type ], + sh:path biolink:description ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 7 ; - sh:path biolink:available_from ] ; + sh:path biolink:available_from ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:trade_name ], + [ sh:order 14 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], + [ sh:description "indicates whether a molecular entity is a metabolite" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:is_metabolite ] ; sh:targetClass biolink:MicroRNA . biolink:ModelToDiseaseAssociationMixin a sh:NodeShape ; @@ -13361,63 +13538,117 @@ biolink:MolecularActivityToChemicalEntityAssociation a sh:NodeShape ; sh:closed true ; sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:property [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], + sh:order 15 ; + sh:path biolink:object_category ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:object_namespace ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a human-readable description of an entity" ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:MolecularActivity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:ChemicalEntity ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -13425,28 +13656,84 @@ biolink:MolecularActivityToChemicalEntityAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; - sh:path biolink:original_object ], + sh:path biolink:original_object ] ; + sh:targetClass biolink:MolecularActivityToChemicalEntityAssociation . + +biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 16 ; sh:path biolink:subject_closure ], - [ sh:description "a point in time" ; + [ sh:class biolink:MolecularActivity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:subject_category ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -13454,121 +13741,115 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + sh:order 13 ; + sh:path biolink:original_object ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:object_category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ] ; - sh:targetClass biolink:MolecularActivityToChemicalEntityAssociation . - -biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 10 ; + sh:path biolink:timepoint ] ; + sh:targetClass biolink:MolecularActivityToMolecularActivityAssociation . + +biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Association that holds the relationship between a reaction and the pathway it participates in." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -13581,159 +13862,94 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:Pathway ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + sh:order 2 ; + sh:path rdf:object ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ] ; - sh:targetClass biolink:MolecularActivityToMolecularActivityAssociation . - -biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Association that holds the relationship between a reaction and the pathway it participates in." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 28 ; sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a human-readable description of an entity" ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], + sh:order 26 ; + sh:path biolink:iri ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], + sh:order 15 ; + sh:path biolink:object_category ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; @@ -13743,51 +13959,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], [ sh:class biolink:MolecularActivity ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -13795,65 +13966,62 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Pathway ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "a point in time" ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ] ; + sh:order 3 ; + sh:path biolink:negated ] ; sh:targetClass biolink:MolecularActivityToPathwayAssociation . biolink:MolecularMixture a sh:NodeShape ; sh:closed true ; sh:description "A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], + sh:property [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 15 ; sh:path rdfs:label ], - [ sh:order 14 ; - sh:path rdf:type ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:description ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:iri ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:trade_name ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -13863,52 +14031,39 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], + [ sh:order 14 ; + sh:path rdf:type ], [ sh:class biolink:ChemicalMixture ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:is_supplement ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:id ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:trade_name ], + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], [ sh:description "" ; sh:maxCount 1 ; sh:order 7 ; - sh:path biolink:is_toxic ] ; + sh:path biolink:is_toxic ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 9 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:MolecularMixture . biolink:MortalityOutcome a sh:NodeShape ; @@ -13921,39 +14076,41 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape sh:closed true ; sh:description "" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "a point in time" ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], + sh:order 13 ; + sh:path biolink:original_object ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -13961,32 +14118,58 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 17 ; sh:path biolink:object_closure ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -13994,106 +14177,57 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:object_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; sh:path biolink:subject_label_closure ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 16 ; sh:path biolink:subject_closure ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ] ; + sh:path biolink:subject_category_closure ] ; sh:targetClass biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . biolink:NoncodingRNAProduct a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], - [ sh:order 14 ; - sh:path rdf:type ], + sh:order 12 ; + sh:path biolink:iri ], [ sh:description "" ; sh:maxCount 1 ; sh:order 9 ; @@ -14102,28 +14236,47 @@ biolink:NoncodingRNAProduct a sh:NodeShape ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:is_metabolite ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:trade_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], + sh:order 8 ; + sh:path biolink:max_tolerated_dose ], [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:order 15 ; sh:path rdfs:label ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:max_tolerated_dose ], + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:order 14 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:trade_name ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_chemical_role ], + [ sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:description ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 7 ; sh:path biolink:available_from ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:in_taxon ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], @@ -14136,53 +14289,51 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_chemical_role ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], + sh:order 2 ; + sh:path biolink:has_biological_sequence ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 0 ; - sh:path biolink:synonym ] ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:NoncodingRNAProduct . biolink:NucleicAcidSequenceMotif a sh:NodeShape ; sh:closed true ; sh:description "A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:property [ sh:maxCount 1 ; sh:order 8 ; - sh:path dct:description ], + sh:path biolink:description ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -14192,58 +14343,57 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 1 ; sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ] ; + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ] ; sh:targetClass biolink:NucleicAcidSequenceMotif . biolink:NucleosomeModification a sh:NodeShape ; sh:closed true ; sh:description "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:in_taxon ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 11 ; + sh:path biolink:synonym ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:has_biological_sequence ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; + [ sh:order 7 ; + sh:path rdf:type ], + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], + sh:order 8 ; + sh:path rdfs:label ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -14253,32 +14403,35 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 6 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 11 ; - sh:path biolink:synonym ], - [ sh:order 7 ; - sh:path rdf:type ] ; + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:description ] ; sh:targetClass biolink:NucleosomeModification . biolink:ObservedExpectedFrequencyAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a observed expected frequency analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:property [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], [ sh:order 9 ; sh:path rdf:type ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; @@ -14293,32 +14446,23 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], [ sh:maxCount 1 ; sh:order 1 ; sh:path biolink:rights ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], [ sh:maxCount 1 ; sh:order 2 ; sh:path biolink:format ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ] ; + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ] ; sh:targetClass biolink:ObservedExpectedFrequencyAnalysisResult . biolink:Occurrent a sh:NodeShape ; @@ -14331,26 +14475,23 @@ biolink:OrganismAttribute a sh:NodeShape ; sh:closed true ; sh:description "describes a characteristic of an organismal entity." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:property [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + sh:order 0 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_attribute ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -14360,34 +14501,36 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:maxCount 1 ; sh:order 10 ; - sh:path dct:description ], + sh:path biolink:description ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; - sh:path biolink:id ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:order 9 ; - sh:path rdf:type ] ; + sh:path biolink:id ] ; sh:targetClass biolink:OrganismAttribute . biolink:OrganismTaxonToEntityAssociation a sh:NodeShape ; @@ -14399,29 +14542,7 @@ biolink:OrganismTaxonToEntityAssociation a sh:NodeShape ; biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:object_namespace ], @@ -14431,37 +14552,38 @@ biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; sh:order 25 ; sh:path biolink:id ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], [ sh:class biolink:NamedThing ; sh:description "the environment in which the organism occurs" ; sh:maxCount 1 ; @@ -14469,14 +14591,12 @@ biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -14484,20 +14604,39 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:subject_category ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:class biolink:OrganismTaxon ; sh:description "the taxon that is the subject of the association" ; sh:maxCount 1 ; @@ -14505,147 +14644,106 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "predicate describing the relationship between the taxon and the environment" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; - sh:path rdf:predicate ] ; + sh:path rdf:predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ] ; sh:targetClass biolink:OrganismTaxonToEnvironmentAssociation . biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; sh:closed false ; sh:description "A relationship between two organism taxon nodes" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:maxCount 1 ; sh:order 30 ; - sh:path dct:description ], + sh:path biolink:description ], [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; sh:path biolink:object_label_closure ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:subject_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 26 ; sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "organism taxon that is the subject of the association" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:object_namespace ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -14653,454 +14751,349 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:OrganismTaxonToOrganismTaxonAssociation . - -biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; - sh:closed true ; - sh:description "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category_closure ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:object_namespace ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:object_closure ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:object_category ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 26 ; - sh:path biolink:id ], + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 28 ; + sh:order 27 ; sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 19 ; + sh:order 18 ; sh:path biolink:subject_category_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; + sh:order 5 ; sh:path biolink:publications ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:iri ], [ sh:class biolink:OrganismTaxon ; - sh:description "the taxon that is the subject of the association" ; + sh:description "organism taxon that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "a point in time" ; sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 25 ; + sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ] ; + sh:targetClass biolink:OrganismTaxonToOrganismTaxonAssociation . + +biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; + sh:closed true ; + sh:description "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:timepoint ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 29 ; - sh:path rdf:type ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:description "the environment in which the two taxa interact" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:associated_environmental_context ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:maxCount 1 ; sh:order 31 ; - sh:path dct:description ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the taxon that is the subject of the association" ; + sh:path biolink:description ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], + sh:order 2 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; - sh:path biolink:subject_category ] ; - sh:targetClass biolink:OrganismTaxonToOrganismTaxonInteraction . - -biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; - sh:closed true ; - sh:description "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], + sh:path biolink:subject_category ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 3 ; + sh:order 4 ; sh:path biolink:negated ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the more specific taxon" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:subject_namespace ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; + sh:order 16 ; sh:path biolink:object_category ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_object ], [ sh:class biolink:OrganismTaxon ; - sh:description "the more general taxon" ; + sh:description "the taxon that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; + sh:order 3 ; sh:path rdf:object ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 26 ; + sh:order 27 ; sh:path biolink:iri ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 13 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a point in time" ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 30 ; + sh:path rdfs:label ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink:knowledge_source ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; - sh:path biolink:original_predicate ], + sh:path biolink:original_subject ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; + sh:order 28 ; sh:path biolink:category ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 29 ; + sh:path rdf:type ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OrganismTaxon ; + sh:description "the taxon that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], + sh:order 1 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 19 ; + sh:order 20 ; sh:path biolink:object_category_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ] ; + sh:targetClass biolink:OrganismTaxonToOrganismTaxonInteraction . + +biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; + sh:closed true ; + sh:description "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:order 29 ; + sh:path rdfs:label ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 17 ; sh:path biolink:object_closure ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:subject_category ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OrganismTaxon ; + sh:description "the more specific taxon" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ] ; - sh:targetClass biolink:OrganismTaxonToOrganismTaxonSpecialization . - -biolink:OrganismToOrganismAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + sh:order 26 ; + sh:path biolink:iri ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:IndividualOrganism ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], + sh:order 31 ; + sh:path biolink:has_attribute ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:IndividualOrganism ; - sh:description "An association between two individual organisms." ; + [ sh:class biolink:OrganismTaxon ; + sh:description "the more general taxon" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -15108,343 +15101,328 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:OrganismToOrganismAssociation . + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ] ; + sh:targetClass biolink:OrganismTaxonToOrganismTaxonSpecialization . -biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; +biolink:OrganismToOrganismAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:class biolink:IndividualOrganism ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:IndividualOrganism ; + sh:description "An association between two individual organisms." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category_closure ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; sh:path biolink:object_label_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:severity_qualifier ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:onset_qualifier ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], - [ sh:class biolink:OrganismalEntity ; - sh:description "A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease." ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Disease ; - sh:description "disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 29 ; sh:path rdfs:label ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "The relationship to the disease" ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:OrganismalEntityAsAModelOfDiseaseAssociation . + sh:order 11 ; + sh:path biolink:original_subject ] ; + sh:targetClass biolink:OrganismToOrganismAssociation . -biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; +biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; - sh:description "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], + sh:order 29 ; + sh:path rdfs:label ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:severity_qualifier ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:description "interaction relationship type" ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "The relationship to the disease" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:order 33 ; + sh:path biolink:onset_qualifier ], + [ sh:class biolink:OrganismalEntity ; + sh:description "A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; + sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; sh:path biolink:object_label_closure ], @@ -15452,164 +15430,191 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:has_evidence ] ; + sh:targetClass biolink:OrganismalEntityAsAModelOfDiseaseAssociation . + +biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; + sh:closed true ; + sh:description "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:PairwiseGeneToGeneInteraction . - -biolink:PairwiseMolecularInteraction a sh:NodeShape ; - sh:closed true ; - sh:description "An interaction at the molecular level between two physical entities" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 22 ; + sh:order 21 ; sh:path biolink:object_namespace ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category_closure ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; + sh:order 5 ; sh:path biolink:publications ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], - [ sh:description "identifier for the interaction. This may come from an interaction database such as IMEX." ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:order 26 ; - sh:path biolink:id ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:retrieval_source_ids ], + sh:path biolink:iri ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 21 ; + sh:order 20 ; sh:path biolink:subject_namespace ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:description "interaction relationship type" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 2 ; + sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:object_closure ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:interacting_molecules_category ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; - sh:path biolink:subject_label_closure ], - [ sh:description "a human-readable description of an entity" ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path dct:description ], + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:object_category ], + sh:order 18 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 32 ; + sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ] ; + sh:targetClass biolink:PairwiseGeneToGeneInteraction . + +biolink:PairwiseMolecularInteraction a sh:NodeShape ; + sh:closed true ; + sh:description "An interaction at the molecular level between two physical entities" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:MolecularEntity ; sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; @@ -15617,13 +15622,6 @@ biolink:PairwiseMolecularInteraction a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path rdf:object ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path rdfs:label ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_label_closure ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -15631,6 +15629,18 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 28 ; sh:path biolink:category ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:description "identifier for the interaction. This may come from an interaction database such as IMEX." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ], [ sh:class biolink:MolecularEntity ; sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; @@ -15638,57 +15648,127 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 1 ; sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:subject_category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_predicate ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:timepoint ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_subject ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 27 ; sh:path biolink:iri ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 29 ; - sh:path rdf:type ] ; - sh:targetClass biolink:PairwiseMolecularInteraction . - -biolink:Patent a sh:NodeShape ; - sh:closed true ; - sh:description "a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time. " ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:description ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], - [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:order 21 ; + sh:path biolink:subject_namespace ], + [ sh:description "interaction relationship type" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:id ], + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:interacting_molecules_category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 17 ; + sh:order 32 ; sh:path biolink:has_attribute ], - [ sh:order 14 ; - sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:license ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:PairwiseMolecularInteraction . + +biolink:Patent a sh:NodeShape ; + sh:closed true ; + sh:description "a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time. " ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 10 ; + sh:path biolink:provided_by ], + [ sh:description "keywords tagging a publication" ; + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 1 ; + sh:path biolink:pages ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -15698,48 +15778,54 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:rights ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:format ], + [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:id ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:creation_date ], + [ sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:summary ], [ sh:class biolink:Agent ; sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:authors ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 10 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; sh:order 16 ; - sh:path dct:description ], - [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], + sh:path biolink:description ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:rights ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:iri ], [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:order 15 ; sh:path rdfs:label ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:creation_date ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:format ], + [ sh:order 14 ; + sh:path rdf:type ], [ sh:description "mesh terms tagging a publication" ; sh:order 4 ; sh:path biolink:mesh_terms ], - [ sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:summary ], - [ sh:description "keywords tagging a publication" ; - sh:order 3 ; - sh:path biolink:keywords ] ; + [ sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:license ] ; sh:targetClass biolink:Patent . biolink:PathognomonicityQuantifier a sh:NodeShape ; @@ -15758,6 +15844,9 @@ biolink:PathologicalAnatomicalExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -15765,8 +15854,13 @@ biolink:PathologicalAnatomicalExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_attribute_type ], - [ sh:order 10 ; - sh:path rdf:type ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -15776,43 +15870,34 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 9 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 1 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; sh:order 3 ; sh:path biolink:has_quantitative_value ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ] ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:order 10 ; + sh:path rdf:type ] ; sh:targetClass biolink:PathologicalAnatomicalExposure . biolink:PathologicalAnatomicalOutcome a sh:NodeShape ; @@ -15825,18 +15910,38 @@ biolink:PathologicalAnatomicalStructure a sh:NodeShape ; sh:closed true ; sh:description "An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 7 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -15847,28 +15952,7 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:order 6 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ] ; + sh:path rdf:type ] ; sh:targetClass biolink:PathologicalAnatomicalStructure . biolink:PathologicalEntityMixin a sh:NodeShape ; @@ -15881,42 +15965,9 @@ biolink:PathologicalProcess a sh:NodeShape ; sh:closed true ; sh:description "A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:property [ sh:maxCount 1 ; sh:order 11 ; - sh:path dct:description ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], + sh:path biolink:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -15926,6 +15977,15 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; @@ -15935,11 +15995,34 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_input ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ] ; sh:targetClass biolink:PathologicalProcess . biolink:PathologicalProcessExposure a sh:NodeShape ; @@ -15950,17 +16033,6 @@ biolink:PathologicalProcessExposure a sh:NodeShape ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:timepoint ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -15970,6 +16042,24 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 9 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -15977,17 +16067,15 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_attribute_type ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 7 ; sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -15995,18 +16083,12 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:path biolink:id ], [ sh:order 10 ; sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ] ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ] ; sh:targetClass biolink:PathologicalProcessExposure . biolink:PathologicalProcessOutcome a sh:NodeShape ; @@ -16019,171 +16101,168 @@ biolink:Phenomenon a sh:NodeShape ; sh:closed true ; sh:description "a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:order 5 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 6 ; sh:path rdfs:label ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:maxCount 1 ; sh:order 7 ; - sh:path dct:description ], + sh:path biolink:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_attribute ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:Phenomenon . + +biolink:PhenotypicQuality a sh:NodeShape ; + sh:closed true ; + sh:description "A property of a phenotype" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 4 ; + sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 5 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:Phenomenon . - -biolink:PhenotypicQuality a sh:NodeShape ; - sh:closed true ; - sh:description "A property of a phenotype" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_attribute ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 0 ; sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:maxCount 1 ; sh:order 10 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:path biolink:description ] ; sh:targetClass biolink:PhenotypicQuality . biolink:PhenotypicSex a sh:NodeShape ; sh:closed true ; sh:description "An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:property [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 0 ; sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; sh:path biolink:id ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:order 9 ; - sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ] ; + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; sh:targetClass biolink:PhenotypicSex . biolink:PhysicalEssence a sh:NodeShape ; @@ -16201,48 +16280,45 @@ biolink:PhysicalEssenceOrOccurrent a sh:NodeShape ; biolink:PhysiologicalProcess a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 1 ; + sh:path biolink:has_input ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_output ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:in_taxon ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16255,28 +16331,20 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 6 ; sh:path biolink:xref ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ] ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ] ; sh:targetClass biolink:PhysiologicalProcess . biolink:PlanetaryEntity a sh:NodeShape ; sh:closed true ; sh:description "Any entity or process that exists at the level of the whole planet" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 6 ; sh:path rdfs:label ], @@ -16285,17 +16353,13 @@ biolink:PlanetaryEntity a sh:NodeShape ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path dct:description ], - [ sh:order 5 ; - sh:path rdf:type ], + sh:order 3 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16304,68 +16368,86 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 4 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:order 5 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:description ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:PlanetaryEntity . biolink:Plant a sh:NodeShape ; sh:closed true ; sh:description "" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], [ sh:order 6 ; sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], + sh:order 5 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ] ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ] ; sh:targetClass biolink:Plant . biolink:Polypeptide a sh:NodeShape ; sh:closed true ; sh:description "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16384,194 +16466,200 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; - sh:path biolink:has_attribute ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ] ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Polypeptide . biolink:PopulationToPopulationAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a two populations" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "the population that form the object of the association" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; + sh:property [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 26 ; sh:path biolink:iri ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "the population that form the subject of the association" ; + sh:description "the population that form the object of the association" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:order 2 ; + sh:path rdf:object ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category_closure ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:description "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "a human-readable description of an entity" ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ] ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "the population that form the subject of the association" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ] ; sh:targetClass biolink:PopulationToPopulationAssociation . biolink:PosttranslationalModification a sh:NodeShape ; sh:closed true ; sh:description "A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16581,144 +16669,135 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:order 7 ; sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ] ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:PosttranslationalModification . biolink:PreprintPublication a sh:NodeShape ; sh:closed true ; sh:description "a document reresenting an early version of an author's original scholarly work, such as a research paper or a review, prior to formal peer review and publication in a peer-reviewed scholarly or scientific journal." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "mesh terms tagging a publication" ; + sh:property [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], + [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:description "mesh terms tagging a publication" ; sh:order 4 ; sh:path biolink:mesh_terms ], - [ sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:summary ], - [ sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:license ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:rights ], - [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; - sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:description ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:id ], + sh:order 13 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:creation_date ], + [ sh:order 14 ; + sh:path rdf:type ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], - [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], + [ sh:description "keywords tagging a publication" ; + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:summary ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:iri ], + [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:id ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 10 ; sh:path biolink:provided_by ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:creation_date ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], [ sh:maxCount 1 ; sh:order 8 ; sh:path biolink:format ], - [ sh:description "keywords tagging a publication" ; - sh:order 3 ; - sh:path biolink:keywords ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], - [ sh:order 14 ; - sh:path rdf:type ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ] ; + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:rights ], + [ sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:license ] ; sh:targetClass biolink:PreprintPublication . biolink:ProcessedMaterial a sh:NodeShape ; sh:closed true ; sh:description "A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:id ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:maxCount 1 ; sh:order 16 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:description ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], + [ sh:class biolink:ChemicalMixture ; + sh:description "" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], - [ sh:order 14 ; - sh:path rdf:type ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:is_supplement ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 9 ; sh:path biolink:provided_by ], @@ -16726,26 +16805,23 @@ biolink:ProcessedMaterial a sh:NodeShape ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:is_toxic ], - [ sh:class biolink:ChemicalMixture ; - sh:description "" ; + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:is_supplement ], + sh:order 15 ; + sh:path rdfs:label ], + [ sh:order 14 ; + sh:path rdf:type ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 10 ; sh:path biolink:xref ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:id ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:trade_name ], + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16755,37 +16831,24 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:order 4 ; + sh:path biolink:trade_name ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ] ; + sh:order 12 ; + sh:path biolink:iri ] ; sh:targetClass biolink:ProcessedMaterial . biolink:Protein a sh:NodeShape ; sh:closed true ; sh:description "A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], + sh:property [ sh:order 7 ; + sh:path rdf:type ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; @@ -16800,46 +16863,58 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 6 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:description ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:iri ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:order 8 ; sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:order 7 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ] ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:Protein . biolink:ProteinDomain a sh:NodeShape ; sh:closed true ; sh:description "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], + sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16849,38 +16924,26 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 6 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:order 7 ; - sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:maxCount 1 ; sh:order 9 ; - sh:path dct:description ], + sh:path biolink:description ], [ sh:class biolink:Gene ; sh:description "connects an entity with one or more gene or gene products" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:has_gene_or_gene_product ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:in_taxon ], + [ sh:order 7 ; + sh:path rdf:type ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ] ; @@ -16889,70 +16952,61 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t biolink:ProteinFamily a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:class biolink:Gene ; sh:description "connects an entity with one or more gene or gene products" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:has_gene_or_gene_product ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:order 7 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 8 ; sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:order 7 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:description ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ] ; + sh:order 10 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:ProteinFamily . biolink:ProteinIsoform a sh:NodeShape ; sh:closed true ; sh:description "Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -16961,33 +17015,40 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 6 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:order 7 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:order 7 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; sh:order 9 ; - sh:path dct:description ], + sh:path biolink:description ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:order 8 ; sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 0 ; sh:path biolink:synonym ] ; @@ -17001,43 +17062,21 @@ biolink:RNAProduct a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:in_taxon ], - [ sh:description "indicates whether a molecular entity is a metabolite" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:is_metabolite ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:trade_name ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], - [ sh:order 14 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 15 ; + sh:path rdfs:label ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_chemical_role ], + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -17048,47 +17087,64 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 7 ; - sh:path biolink:available_from ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], + sh:order 9 ; + sh:path biolink:is_toxic ], [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:max_tolerated_dose ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_chemical_role ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path biolink:iri ], [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 7 ; + sh:path biolink:available_from ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:description ], + [ sh:order 14 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:has_biological_sequence ], + [ sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:is_toxic ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 11 ; - sh:path biolink:provided_by ] ; + sh:order 5 ; + sh:path biolink:is_metabolite ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:RNAProduct . biolink:RNAProductIsoform a sh:NodeShape ; sh:closed true ; sh:description "Represents a protein that is a specific isoform of the canonical or reference RNA" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -17098,205 +17154,95 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], [ sh:order 14 ; sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], + sh:order 8 ; + sh:path biolink:max_tolerated_dose ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 0 ; sh:path biolink:synonym ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_chemical_role ], - [ sh:description "" ; + [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:is_toxic ], + sh:order 2 ; + sh:path biolink:has_biological_sequence ], + [ sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:in_taxon ], + [ sh:description "indicates whether a molecular entity is a metabolite" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:is_metabolite ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 11 ; sh:path biolink:provided_by ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 7 ; - sh:path biolink:available_from ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], + sh:order 12 ; + sh:path biolink:iri ], [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:trade_name ], - [ sh:description "indicates whether a molecular entity is a metabolite" ; + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 7 ; + sh:path biolink:available_from ], + [ sh:description "" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:is_metabolite ] ; + sh:order 9 ; + sh:path biolink:is_toxic ], + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path rdfs:label ] ; sh:targetClass biolink:RNAProductIsoform . biolink:ReactionToCatalystAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:MolecularEntity ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:subject ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 31 ; - sh:path rdf:type ], - [ sh:description "the side of a reaction being modeled (ie: left or right)" ; - sh:in ( "left" "right" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:reaction_side ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path rdf:predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path dct:description ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 28 ; - sh:path biolink:id ], - [ sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:stoichiometry ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:reaction_direction ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 0 ; + sh:path biolink:stoichiometry ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "the chemical element that is the target of the statement" ; sh:maxCount 1 ; @@ -17304,79 +17250,123 @@ biolink:ReactionToCatalystAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNode ; sh:order 5 ; sh:path rdf:object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 30 ; - sh:path biolink:category ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; - sh:path biolink:subject_category ] ; - sh:targetClass biolink:ReactionToCatalystAssociation . - -biolink:ReactionToParticipantAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:qualifiers ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "the side of a reaction being modeled (ie: left or right)" ; + sh:in ( "left" "right" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:reaction_side ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:publications ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_attribute ], - [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; - sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:reaction_direction ], - [ sh:description "the side of a reaction being modeled (ie: left or right)" ; - sh:in ( "left" "right" ) ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:MolecularEntity ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:reaction_side ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:subject ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 28 ; sh:path biolink:id ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:description ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 31 ; - sh:path rdf:type ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path rdfs:label ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_attribute ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 31 ; + sh:path rdf:type ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -17384,89 +17374,102 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 30 ; sh:path biolink:category ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:path biolink:retrieval_source_ids ] ; + sh:targetClass biolink:ReactionToCatalystAssociation . + +biolink:ReactionToParticipantAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a human-readable description of an entity" ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 33 ; - sh:path dct:description ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 30 ; + sh:path biolink:category ], [ sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:stoichiometry ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 34 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:MolecularEntity ; sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; @@ -17474,18 +17477,22 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 3 ; sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:description ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:qualifiers ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 4 ; - sh:path rdf:predicate ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 28 ; + sh:path biolink:id ], [ sh:class biolink:ChemicalEntity ; sh:description "the chemical element that is the target of the statement" ; sh:maxCount 1 ; @@ -17493,58 +17500,95 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 5 ; sh:path rdf:object ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ] ; + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path rdfs:label ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:description "the side of a reaction being modeled (ie: left or right)" ; + sh:in ( "left" "right" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:reaction_side ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 31 ; + sh:path rdf:type ], + [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; + sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:reaction_direction ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:iri ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ] ; sh:targetClass biolink:ReactionToParticipantAssociation . biolink:ReagentTargetedGene a sh:NodeShape ; sh:closed true ; sh:description "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 8 ; sh:path rdfs:label ], + [ sh:order 7 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:id ], + [ sh:maxCount 1 ; sh:order 9 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + sh:path biolink:description ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 4 ; sh:path biolink:xref ], - [ sh:order 7 ; - sh:path rdf:type ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 3 ; sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:has_biological_sequence ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; @@ -17556,29 +17600,14 @@ biolink:RegulatoryRegion a sh:NodeShape ; sh:closed true ; sh:description "A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:order 7 ; - sh:path rdf:type ], + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 8 ; sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; @@ -17588,13 +17617,12 @@ biolink:RegulatoryRegion a sh:NodeShape ; sh:minCount 1 ; sh:order 1 ; sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:description ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 4 ; sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -17603,7 +17631,22 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 6 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:order 7 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:RegulatoryRegion . biolink:RelationshipQuantifier a sh:NodeShape ; @@ -17626,30 +17669,7 @@ biolink:RelativeFrequencyAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a relative frequency analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -17658,26 +17678,48 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], [ sh:maxCount 1 ; sh:order 1 ; sh:path biolink:rights ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ] ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ] ; sh:targetClass biolink:RelativeFrequencyAnalysisResult . biolink:SensitivityQuantifier a sh:NodeShape ; @@ -17689,26 +17731,23 @@ biolink:SequenceAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a sequence feature and a nucleic acid entity it is localized to." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], + sh:property [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -17716,199 +17755,167 @@ biolink:SequenceAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "a point in time" ; + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], + sh:order 31 ; + sh:path biolink:has_attribute ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:subject_namespace ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ] ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ] ; sh:targetClass biolink:SequenceAssociation . biolink:SequenceFeatureRelationship a sh:NodeShape ; sh:closed true ; sh:description "For example, a particular exon is part of a particular transcript or gene" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; + sh:property [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 20 ; @@ -17920,261 +17927,290 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:maxCount 1 ; sh:order 30 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:path biolink:description ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "a point in time" ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ] ; + sh:path biolink:subject_closure ] ; sh:targetClass biolink:SequenceFeatureRelationship . biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; sh:closed false ; sh:description "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:class biolink:Treatment ; + sh:description "treatment whose efficacy is modulated by the subject variant" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 29 ; sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:SequenceVariant ; + sh:description "variant that modulates the treatment of some disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:object_category ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:SequenceVariant ; - sh:description "variant that modulates the treatment of some disease" ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 13 ; + sh:path biolink:original_object ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Treatment ; - sh:description "treatment whose efficacy is modulated by the subject variant" ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], + sh:order 18 ; + sh:path biolink:subject_category_closure ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:subject_namespace ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:subject_category ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ] ; + sh:path biolink:publications ] ; sh:targetClass biolink:SequenceVariantModulatesTreatmentAssociation . biolink:Serial a sh:NodeShape ; sh:closed true ; sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 13 ; - sh:path biolink:provided_by ], - [ sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:property [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:format ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:volume ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 18 ; + sh:path rdfs:label ], + [ sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], + sh:order 2 ; + sh:path biolink:issue ], [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:creation_date ], + [ sh:description "keywords tagging a publication" ; + sh:order 6 ; + sh:path biolink:keywords ], + [ sh:description "Serials (journals) should have industry-standard identifier such as from ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 19 ; + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:iri ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 7 ; + sh:path biolink:mesh_terms ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -18184,25 +18220,10 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 16 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:format ], - [ sh:description "Should generally be set to an ontology class defined term for 'serial' or 'journal'." ; - sh:order 17 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + [ sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], + sh:order 1 ; + sh:path biolink:volume ], [ sh:class biolink:Agent ; sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; @@ -18212,94 +18233,107 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 4 ; sh:path biolink:pages ], [ sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:license ], - [ sh:description "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:iso_abbreviation ], + sh:order 10 ; + sh:path biolink:rights ], [ sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:summary ], - [ sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:rights ], - [ sh:description "keywords tagging a publication" ; - sh:order 6 ; - sh:path biolink:keywords ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 7 ; - sh:path biolink:mesh_terms ], - [ sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:issue ], - [ sh:description "Serials (journals) should have industry-standard identifier such as from ISSN." ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:description "Should generally be set to an ontology class defined term for 'serial' or 'journal'." ; + sh:order 17 ; + sh:path rdf:type ], + [ sh:description "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ] ; + sh:order 0 ; + sh:path biolink:iso_abbreviation ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 13 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:license ] ; sh:targetClass biolink:Serial . biolink:SiRNA a sh:NodeShape ; sh:closed true ; sh:description "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_chemical_role ], + sh:property [ sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:description ], + [ sh:order 14 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:iri ], + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path rdfs:label ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:is_toxic ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; - sh:maxCount 1 ; + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 7 ; + sh:path biolink:available_from ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:trade_name ], + sh:order 10 ; + sh:path biolink:has_chemical_role ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:in_taxon ], - [ sh:order 14 ; - sh:path rdf:type ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:has_biological_sequence ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:is_metabolite ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 7 ; - sh:path biolink:available_from ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 11 ; - sh:path biolink:provided_by ], + sh:order 8 ; + sh:path biolink:max_tolerated_dose ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:trade_name ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -18308,29 +18342,49 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 13 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:is_toxic ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; sh:targetClass biolink:SiRNA . biolink:SmallMolecule a sh:NodeShape ; sh:closed true ; sh:description "A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:description ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:is_toxic ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:description "indicates whether a molecular entity is a metabolite" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:is_metabolite ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -18339,76 +18393,51 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 10 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:has_chemical_role ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 2 ; - sh:path biolink:available_from ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], [ sh:order 11 ; sh:path rdf:type ], [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:max_tolerated_dose ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:is_toxic ], - [ sh:description "indicates whether a molecular entity is a metabolite" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:is_metabolite ], [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:trade_name ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ] ; + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 2 ; + sh:path biolink:available_from ] ; sh:targetClass biolink:SmallMolecule . biolink:Snv a sh:NodeShape ; sh:closed true ; sh:description "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], [ sh:description "The state of the sequence w.r.t a reference sequence" ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:has_biological_sequence ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 6 ; @@ -18422,39 +18451,27 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 7 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:maxCount 1 ; sh:order 10 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], + sh:path biolink:description ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:in_taxon ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path rdfs:label ], + [ sh:order 8 ; + sh:path rdf:type ], [ sh:class biolink:Gene ; sh:description "Each allele can be associated with any number of genes" ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:has_gene ], - [ sh:order 8 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ] ; + sh:path biolink:has_gene ] ; sh:targetClass biolink:Snv . biolink:SocioeconomicExposure a sh:NodeShape ; @@ -18467,19 +18484,23 @@ biolink:SocioeconomicExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:order 10 ; + sh:path rdf:type ], [ sh:class biolink:SocioeconomicAttribute ; sh:description "connects any entity to an attribute" ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -18487,42 +18508,37 @@ biolink:SocioeconomicExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_attribute_type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:timepoint ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 1 ; sh:path rdfs:label ], - [ sh:order 10 ; - sh:path rdf:type ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], + sh:order 6 ; + sh:path biolink:id ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 5 ; - sh:path biolink:iri ] ; + sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ] ; sh:targetClass biolink:SocioeconomicExposure . biolink:SocioeconomicOutcome a sh:NodeShape ; @@ -18540,15 +18556,7 @@ biolink:Study a sh:NodeShape ; sh:closed true ; sh:description "a detailed investigation and/or analysis" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -18562,53 +18570,43 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], + sh:order 3 ; + sh:path biolink:iri ], [ sh:order 5 ; sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ] ; + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ] ; sh:targetClass biolink:Study . biolink:StudyPopulation a sh:NodeShape ; sh:closed true ; sh:description "A group of people banded together or treated as a group as participants in a research study." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -18618,48 +18616,40 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 6 ; - sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ] ; + sh:order 7 ; + sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ] ; sh:targetClass biolink:StudyPopulation . biolink:StudyResult a sh:NodeShape ; sh:closed false ; sh:description "A collection of data items from a study that are about a particular study subject or experimental unit (the 'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation of this data as evidence." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -18668,58 +18658,87 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:maxCount 1 ; sh:order 1 ; sh:path biolink:rights ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], [ sh:maxCount 1 ; sh:order 2 ; sh:path biolink:format ], - [ sh:order 9 ; - sh:path rdf:type ], [ sh:maxCount 1 ; sh:order 0 ; - sh:path biolink:license ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ] ; + sh:path biolink:license ] ; sh:targetClass biolink:StudyResult . biolink:StudyVariable a sh:NodeShape ; sh:closed true ; sh:description "a variable that is used as a measure in the investigation of a study" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -18729,22 +18748,15 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 9 ; - sh:path rdf:type ], [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ] ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ] ; sh:targetClass biolink:StudyVariable . biolink:SubjectOfInvestigation a sh:NodeShape ; @@ -18756,39 +18768,69 @@ biolink:SubjectOfInvestigation a sh:NodeShape ; biolink:TaxonToTaxonAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "An association between individuals of different taxa." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; - sh:description "An association between individuals of different taxa." ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -18796,116 +18838,79 @@ biolink:TaxonToTaxonAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; sh:path biolink:subject_label_closure ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], + sh:order 15 ; + sh:path biolink:object_category ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a point in time" ; + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category_closure ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:maxCount 1 ; sh:order 30 ; - sh:path dct:description ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ] ; + sh:path biolink:description ] ; sh:targetClass biolink:TaxonToTaxonAssociation . biolink:TaxonomicRank a sh:NodeShape ; @@ -18923,27 +18928,19 @@ biolink:TextMiningResult a sh:NodeShape ; sh:closed true ; sh:description "A result of text mining." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:maxCount 1 ; + sh:property [ sh:maxCount 1 ; sh:order 0 ; sh:path biolink:license ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 1 ; + sh:path biolink:rights ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -18953,28 +18950,35 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:creation_date ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ] ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ] ; sh:targetClass biolink:TextMiningResult . biolink:ThingWithTaxon a sh:NodeShape ; @@ -18987,89 +18991,62 @@ biolink:ThingWithTaxon a sh:NodeShape ; sh:order 0 ; sh:path biolink:in_taxon ] ; sh:targetClass biolink:ThingWithTaxon . - -biolink:TranscriptToGeneRelationship a sh:NodeShape ; - sh:closed true ; - sh:description "A gene is a collection of transcripts" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + +biolink:TranscriptToGeneRelationship a sh:NodeShape ; + sh:closed true ; + sh:description "A gene is a collection of transcripts" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 26 ; sh:path biolink:iri ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + sh:order 18 ; + sh:path biolink:subject_category_closure ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -19077,22 +19054,13 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:Transcript ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -19100,33 +19068,61 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:object_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -19136,52 +19132,54 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ] ; + sh:order 13 ; + sh:path biolink:original_object ] ; sh:targetClass biolink:TranscriptToGeneRelationship . biolink:TranscriptionFactorBindingSite a sh:NodeShape ; sh:closed true ; sh:description "A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:has_biological_sequence ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 4 ; sh:path biolink:xref ], + [ sh:order 7 ; + sh:path rdf:type ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 8 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:order 7 ; - sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -19191,159 +19189,140 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 6 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ] ; + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:description ] ; sh:targetClass biolink:TranscriptionFactorBindingSite . biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "a human-readable description of an entity" ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "The relationship to the disease" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:order 32 ; + sh:path biolink:severity_qualifier ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:severity_qualifier ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], + sh:order 29 ; + sh:path rdfs:label ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + sh:order 18 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:Onset ; sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 33 ; sh:path biolink:onset_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], [ sh:class biolink:SequenceVariant ; sh:description "A variant that has a role in modeling the disease." ; sh:maxCount 1 ; @@ -19351,15 +19330,25 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "The relationship to the disease" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:class biolink:Disease ; sh:description "disease" ; sh:maxCount 1 ; @@ -19372,61 +19361,31 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t biolink:VariantToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:SeverityValue ; + sh:property [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:SeverityValue ; sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:severity_qualifier ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:object_category ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], [ sh:class biolink:SequenceVariant ; sh:description "a sequence variant in which the allele state is associated in some way with the disease state" ; sh:maxCount 1 ; @@ -19434,124 +19393,80 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:description "E.g. is pathogenic for" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; - sh:maxCount 1 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:onset_qualifier ], + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 29 ; sh:path rdfs:label ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Disease ; - sh:description "a disease that is associated with that variant" ; + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ] ; - sh:targetClass biolink:VariantToDiseaseAssociation . - -biolink:VariantToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:VariantToEntityAssociationMixin . - -biolink:VariantToGeneAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 17 ; sh:path biolink:object_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:onset_qualifier ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; @@ -19562,20 +19477,6 @@ biolink:VariantToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:subject_category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -19583,81 +19484,104 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated with some other entity" ; + [ sh:class biolink:Disease ; + sh:description "a disease that is associated with that variant" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ] ; + sh:targetClass biolink:VariantToDiseaseAssociation . + +biolink:VariantToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:VariantToEntityAssociationMixin . + +biolink:VariantToGeneAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:subject_namespace ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:Gene ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -19665,166 +19589,113 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a point in time" ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ] ; - sh:targetClass biolink:VariantToGeneAssociation . - -biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a variant and expression of a gene (i.e. e-QTL)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:LifeStage ; - sh:description "stage during which gene or protein expression of takes place." ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:stage_qualifier ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:path biolink:object_namespace ], + [ sh:maxCount 1 ; sh:order 30 ; - sh:path biolink:iri ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink:description ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], + sh:order 29 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:description "a human-readable description of an entity" ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path dct:description ], + sh:order 26 ; + sh:path biolink:iri ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 28 ; + sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 32 ; + sh:order 28 ; sh:path rdf:type ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; - sh:description "Optional quantitative value indicating degree of expression." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:quantifier_qualifier ], + sh:order 15 ; + sh:path biolink:object_category ], [ sh:class biolink:SequenceVariant ; sh:description "a sequence variant in which the allele state is associated with some other entity" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; + sh:order 0 ; sh:path rdf:subject ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path biolink:phenotypic_state ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:path biolink:negated ] ; + sh:targetClass biolink:VariantToGeneAssociation . + +biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between a variant and expression of a gene (i.e. e-QTL)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path rdf:object ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 29 ; - sh:path biolink:id ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + sh:order 33 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], + sh:order 25 ; + sh:path biolink:object_namespace ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 26 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -19832,321 +19703,402 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 31 ; sh:path biolink:category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 1 ; + sh:path biolink:expression_site ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path rdf:predicate ], + [ sh:class biolink:LifeStage ; + sh:description "stage during which gene or protein expression of takes place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 2 ; + sh:path biolink:stage_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path rdf:object ], + [ sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:description ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 32 ; + sh:path rdf:type ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:negated ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated with some other entity" ; sh:maxCount 1 ; - sh:order 33 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 4 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path rdf:predicate ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 19 ; + sh:path biolink:object_category ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 17 ; sh:path biolink:original_object ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ] ; - sh:targetClass biolink:VariantToGeneExpressionAssociation . - -biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated in some way with the phenotype state" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 29 ; - sh:path rdf:type ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 28 ; - sh:path biolink:category ], - [ sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:has_quotient ], + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:subject_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 32 ; + sh:order 35 ; sh:path biolink:has_attribute ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:onset_qualifier ], + sh:order 3 ; + sh:path biolink:phenotypic_state ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:object_category ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], - [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:has_percentage ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 23 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Optional quantitative value indicating degree of expression." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:subject_category ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_label_closure ], + sh:order 0 ; + sh:path biolink:quantifier_qualifier ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_source ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 27 ; + sh:order 30 ; sh:path biolink:iri ], - [ sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:has_count ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:subject_closure ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 26 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + sh:order 29 ; + sh:path biolink:id ] ; + sh:targetClass biolink:VariantToGeneExpressionAssociation . + +biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path dct:description ], - [ sh:description "total number of things in a particular reference set" ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:has_total ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 37 ; + sh:path biolink:severity_qualifier ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 14 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 19 ; + sh:path biolink:subject_category_closure ], [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:order 39 ; sh:path biolink:frequency_qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:has_percentage ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:object_namespace ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 30 ; sh:path rdfs:label ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:has_total ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 16 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], + sh:order 21 ; + sh:path biolink:subject_namespace ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 29 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category_closure ], + [ sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:has_count ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:sex_qualifier ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:has_quotient ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated in some way with the phenotype state" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:severity_qualifier ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ] ; - sh:targetClass biolink:VariantToPhenotypicFeatureAssociation . - -biolink:VariantToPopulationAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a variant and a population, where the variant has particular frequency in the population" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:object_label_closure ], + sh:order 13 ; + sh:path biolink:original_predicate ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 30 ; + sh:order 26 ; sh:path biolink:id ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:object_namespace ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 8 ; + sh:order 4 ; sh:path biolink:negated ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:description ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:timepoint ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 28 ; + sh:path biolink:category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:iri ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; + sh:order 15 ; sh:path biolink:subject_category ], - [ sh:description "number in object population that carry a particular allele, aka allele count" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_count ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:onset_qualifier ] ; + sh:targetClass biolink:VariantToPhenotypicFeatureAssociation . + +biolink:VariantToPopulationAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between a variant and a population, where the variant has particular frequency in the population" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:has_quotient ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:order 31 ; + sh:path biolink:iri ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:InformationResource ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:SequenceVariant ; + sh:description "an allele that has a certain frequency in a given population" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], + sh:order 5 ; + sh:path rdf:subject ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; sh:path biolink:object_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:description "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency" ; + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "the population that is observed to have the frequency" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], + sh:order 7 ; + sh:path rdf:object ], + [ sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:description ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 21 ; sh:path biolink:subject_closure ], - [ sh:description "number all populations that carry a particular allele, aka allele number" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:has_total ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], + sh:order 29 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -20154,108 +20106,137 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 32 ; sh:path biolink:category ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:subject_namespace ], - [ sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:has_percentage ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:object_label_closure ], [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:frequency_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], + sh:order 19 ; + sh:path biolink:subject_category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:has_attribute ], - [ sh:class biolink:InformationResource ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "the population that is observed to have the frequency" ; + sh:order 9 ; + sh:path biolink:qualifiers ], + [ sh:description "number all populations that carry a particular allele, aka allele number" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:has_total ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:object_namespace ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path rdf:object ], + sh:order 30 ; + sh:path biolink:id ], + [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:has_percentage ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 25 ; + sh:path biolink:subject_namespace ], + [ sh:description "number in object population that carry a particular allele, aka allele count" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:has_count ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_subject ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path rdf:predicate ], - [ sh:class biolink:SequenceVariant ; - sh:description "an allele that has a certain frequency in a given population" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:subject ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:InformationResource ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:subject_label_closure ] ; + sh:order 34 ; + sh:path rdfs:label ] ; sh:targetClass biolink:VariantToPopulationAssociation . biolink:Vertebrate a sh:NodeShape ; sh:closed true ; sh:description "A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 1 ; sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -20266,66 +20247,40 @@ biolink:Vertebrate a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:maxCount 1 ; sh:order 8 ; - sh:path dct:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:path biolink:description ] ; sh:targetClass biolink:Vertebrate . biolink:Virus a sh:NodeShape ; sh:closed true ; sh:description "A virus is a microorganism that replicates itself as a microRNA and infects the host cell." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 6 ; + sh:property [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:order 6 ; sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 2 ; sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -20335,27 +20290,72 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ] ; + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Virus . biolink:WebPage a sh:NodeShape ; sh:closed true ; sh:description "a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, and/or other features." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:property [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path rdfs:label ], + [ sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:summary ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 4 ; + sh:path biolink:mesh_terms ], + [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:description "keywords tagging a publication" ; + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:rights ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:license ], + [ sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:description ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 10 ; sh:path biolink:provided_by ], + [ sh:order 14 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:format ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -20365,105 +20365,26 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:format ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:description "keywords tagging a publication" ; - sh:order 3 ; - sh:path biolink:keywords ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:creation_date ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; - sh:path biolink:id ], - [ sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:summary ], - [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], - [ sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:rights ], - [ sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:license ], - [ sh:order 14 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ] ; + sh:path biolink:id ] ; sh:targetClass biolink:WebPage . biolink:Behavior a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 5 ; sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -20473,6 +20394,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; @@ -20483,43 +20409,70 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:enabled_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; - sh:path biolink:iri ] ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Behavior . biolink:BehavioralFeature a sh:NodeShape ; sh:closed true ; sh:description "A phenotypic feature which is behavioral in nature." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 1 ; sh:path biolink:provided_by ], - [ sh:order 6 ; - sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -20529,49 +20482,58 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ] ; + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ] ; sh:targetClass biolink:BehavioralFeature . biolink:BiologicalProcess a sh:NodeShape ; sh:closed true ; sh:description "One or more causally connected executions of molecular functions" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], + sh:order 1 ; + sh:path biolink:has_input ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; - sh:path biolink:iri ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:path biolink:iri ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:order 0 ; + sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:xref ], [ sh:order 9 ; sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:maxCount 1 ; sh:order 11 ; - sh:path dct:description ], + sh:path biolink:description ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 5 ; sh:path biolink:provided_by ], @@ -20579,43 +20541,32 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ] ; + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; sh:targetClass biolink:BiologicalProcess . biolink:Case a sh:NodeShape ; sh:closed true ; sh:description "An individual (human) organism that has a patient role in some clinical context." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 2 ; sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -20625,17 +20576,21 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:order 6 ; - sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 7 ; @@ -20643,44 +20598,13 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:iri ] ; sh:targetClass biolink:Case . biolink:CellLine a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; + sh:property [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; @@ -20693,40 +20617,53 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 2 ; - sh:path biolink:xref ] ; + sh:path biolink:xref ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; sh:targetClass biolink:CellLine . biolink:CellularComponent a sh:NodeShape ; sh:closed true ; sh:description "A location in or around a cell" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -20736,28 +20673,52 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ] ; sh:targetClass biolink:CellularComponent . biolink:ClinicalAttribute a sh:NodeShape ; sh:closed true ; sh:description "Attributes relating to a clinical manifestation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -20766,12 +20727,18 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:description ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + sh:order 11 ; + sh:path biolink:has_attribute ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -20780,54 +20747,31 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; sh:path biolink:xref ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:has_quantitative_value ] ; sh:targetClass biolink:ClinicalAttribute . biolink:Dataset a sh:NodeShape ; sh:closed true ; sh:description "an item that refers to a collection of data from a data source." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:order 9 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -20837,38 +20781,37 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:creation_date ], [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 11 ; + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:order 9 ; - sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:maxCount 1 ; sh:order 0 ; sh:path biolink:license ] ; @@ -20878,88 +20821,71 @@ biolink:DatasetDistribution a sh:NodeShape ; sh:closed true ; sh:description "an item that holds distribution level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:property [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:creation_date ], - [ sh:order 10 ; - sh:path rdf:type ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:license ], + sh:order 12 ; + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], [ sh:maxCount 1 ; sh:order 3 ; sh:path biolink:format ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:order 10 ; + sh:path rdf:type ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 6 ; sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:rights ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 11 ; sh:path rdfs:label ], [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:rights ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 0 ; + sh:path biolink:distribution_download_url ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 7 ; + sh:path biolink:id ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:distribution_download_url ] ; + sh:order 1 ; + sh:path biolink:license ] ; sh:targetClass biolink:DatasetDistribution . biolink:Device a sh:NodeShape ; sh:closed true ; sh:description "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 5 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -20969,35 +20895,37 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:order 5 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:description ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 3 ; - sh:path biolink:iri ] ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ] ; sh:targetClass biolink:Device . biolink:Exon a sh:NodeShape ; sh:closed true ; sh:description "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path dct:description ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -21006,86 +20934,116 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 12 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:description "indicates whether a molecular entity is a metabolite" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:is_metabolite ], + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:has_attribute ], - [ sh:order 13 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 5 ; sh:path biolink:available_from ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:description "indicates whether a molecular entity is a metabolite" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:is_metabolite ], [ sh:description "" ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:is_toxic ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path rdfs:label ], [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:trade_name ], + [ sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:order 13 ; + sh:path rdf:type ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; - sh:path biolink:has_biological_sequence ] ; + sh:path biolink:has_biological_sequence ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:iri ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ] ; sh:targetClass biolink:Exon . biolink:GeneFamily a sh:NodeShape ; sh:closed true ; sh:description "any grouping of multiple genes or gene products related by common descent" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], + sh:order 8 ; + sh:path rdfs:label ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:description ], [ sh:order 7 ; sh:path rdf:type ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -21094,39 +21052,20 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 6 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; sh:targetClass biolink:GeneFamily . biolink:GeneProductMixin a sh:NodeShape ; sh:closed false ; sh:description "The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA molecules." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:order 2 ; sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ] ; @@ -21136,7 +21075,18 @@ biolink:GeneticInheritance a sh:NodeShape ; sh:closed true ; sh:description "The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -21145,71 +21095,44 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:maxCount 1 ; sh:order 8 ; - sh:path dct:description ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ] ; + sh:path biolink:description ] ; sh:targetClass biolink:GeneticInheritance . biolink:InformationContentEntity a sh:NodeShape ; sh:closed false ; sh:description "a piece of information that typically describes some topic of discourse or is used as support." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -21219,55 +21142,105 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:order 9 ; + sh:path rdf:type ] ; + sh:targetClass biolink:InformationContentEntity . + +biolink:InformationResource a sh:NodeShape ; + sh:closed true ; + sh:description "A database or knowledgebase and its supporting ecosystem of interfaces and services that deliver content to consumers (e.g. web portals, APIs, query endpoints, streaming services, data downloads, etc.). A single Information Resource by this definition may span many different datasets or databases, and include many access endpoints and user interfaces. Information Resources include project-specific resources such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 4 ; + sh:path biolink:synonym ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; + sh:order 2 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "the status of the infores identifier, the default is \"released\"" ; + sh:in ( "released" "deprecated" "draft" "modified" ) ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + sh:order 0 ; + sh:path biolink:status ], [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ] ; - sh:targetClass biolink:InformationContentEntity . + sh:order 5 ; + sh:path biolink:description ] ; + sh:targetClass biolink:InformationResource . biolink:OrganismalEntity a sh:NodeShape ; sh:closed false ; sh:description "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 7 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 1 ; sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -21277,17 +21250,9 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:maxCount 1 ; sh:order 8 ; - sh:path dct:description ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ] ; + sh:path biolink:description ] ; sh:targetClass biolink:OrganismalEntity . biolink:Outcome a sh:NodeShape ; @@ -21300,19 +21265,26 @@ biolink:PredicateMapping a sh:NodeShape ; sh:closed true ; sh:description "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:object_derivative_qualifier ], + sh:property [ sh:class biolink:NamedThing ; + sh:description "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:broad_match ], + [ sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:object_aspect_qualifier ], [ sh:class biolink:NamedThing ; sh:description "holds between two entities that have strictly equivalent meanings, with a high degree of confidence" ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:exact_match ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:causal_mechanism_qualifier ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:maxCount 1 ; sh:order 3 ; sh:path biolink:subject_form_or_variant_qualifier ], @@ -21322,82 +21294,87 @@ biolink:PredicateMapping a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:species_context_qualifier ], - [ sh:description "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:mapped_predicate ], - [ sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:subject_context_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path rdf:predicate ], - [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; - sh:in [ rdf:rest () ] ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:anatomical_context_qualifier ], [ sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:qualified_predicate ], + [ sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:object_part_qualifier ], + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; + sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:causal_mechanism_qualifier ], [ sh:class biolink:NamedThing ; - sh:description "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree." ; + sh:description "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree." ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:broad_match ], + sh:order 19 ; + sh:path biolink:narrow_match ], [ sh:maxCount 1 ; sh:order 14 ; sh:path biolink:object_context_qualifier ], - [ sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:object_part_qualifier ], - [ sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:object_aspect_qualifier ], [ sh:maxCount 1 ; sh:order 5 ; sh:path biolink:subject_derivative_qualifier ], + [ sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:subject_context_qualifier ], [ sh:maxCount 1 ; sh:order 11 ; sh:path biolink:object_form_or_variant_qualifier ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 7 ; + sh:path rdf:predicate ], [ sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:subject_part_qualifier ], + sh:order 13 ; + sh:path biolink:object_derivative_qualifier ], + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:subject_direction_qualifier ], [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:object_direction_qualifier ], + [ sh:description "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:mapped_predicate ], [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:narrow_match ] ; + sh:order 4 ; + sh:path biolink:subject_part_qualifier ] ; sh:targetClass biolink:PredicateMapping . biolink:Procedure a sh:NodeShape ; sh:closed true ; sh:description "A series of actions conducted in a certain order or manner" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_attribute ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 6 ; sh:path rdfs:label ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -21407,33 +21384,35 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path dct:description ], [ sh:order 5 ; sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_attribute ] ; + sh:order 3 ; + sh:path biolink:iri ] ; sh:targetClass biolink:Procedure . biolink:SocioeconomicAttribute a sh:NodeShape ; sh:closed true ; sh:description "Attributes relating to a socioeconomic manifestation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -21442,28 +21421,19 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -21471,40 +21441,57 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:maxCount 1 ; sh:order 10 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:order 9 ; - sh:path rdf:type ] ; + sh:path biolink:description ] ; sh:targetClass biolink:SocioeconomicAttribute . biolink:Treatment a sh:NodeShape ; sh:closed true ; sh:description "A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Device ; - sh:description "connects an entity to one or more (medical) devices" ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:class biolink:Procedure ; + sh:description "connects an entity to one or more (medical) procedures" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_device ], + sh:order 2 ; + sh:path biolink:has_procedure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:timepoint ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Drug ; + sh:description "connects an entity to one or more drugs" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_drug ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -21519,87 +21506,50 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:class biolink:Procedure ; - sh:description "connects an entity to one or more (medical) procedures" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_procedure ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Drug ; - sh:description "connects an entity to one or more drugs" ; + [ sh:class biolink:Device ; + sh:description "connects an entity to one or more (medical) devices" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_drug ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ] ; + sh:order 1 ; + sh:path biolink:has_device ] ; sh:targetClass biolink:Treatment . biolink:Zygosity a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:QuantityValue ; + sh:property [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; sh:order 2 ; sh:path biolink:has_quantitative_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; sh:path biolink:id ], - [ sh:order 9 ; - sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:description ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -21607,101 +21557,110 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ] ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:Zygosity . biolink:Drug a sh:NodeShape ; sh:closed true ; sh:description "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 6 ; - sh:path biolink:available_from ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 11 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_chemical_role ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 4 ; - sh:path biolink:routes_of_delivery ], + sh:order 13 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:class biolink:ChemicalMixture ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:is_supplement ], + [ sh:order 14 ; + sh:path rdf:type ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 6 ; + sh:path biolink:available_from ], [ sh:description "" ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:is_toxic ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 10 ; - sh:path biolink:provided_by ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 4 ; + sh:path biolink:routes_of_delivery ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:order 14 ; - sh:path rdf:type ], + sh:order 2 ; + sh:path biolink:highest_FDA_approval_status ], [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:trade_name ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 0 ; + sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:iri ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], + sh:order 9 ; + sh:path biolink:has_chemical_role ], [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:max_tolerated_dose ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 10 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:highest_FDA_approval_status ] ; + sh:order 15 ; + sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 11 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:description ] ; sh:targetClass biolink:Drug . biolink:ExposureEvent a sh:NodeShape ; @@ -21723,16 +21682,13 @@ biolink:IndividualOrganism a sh:NodeShape ; sh:closed true ; sh:description "An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -21742,59 +21698,68 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], - [ sh:order 6 ; - sh:path rdf:type ] ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:IndividualOrganism . biolink:MaterialSample a sh:NodeShape ; sh:closed true ; sh:description "A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO]" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 5 ; - sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 6 ; sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], + [ sh:order 5 ; + sh:path rdf:type ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -21803,127 +21768,128 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 4 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; sh:targetClass biolink:MaterialSample . biolink:Transcript a sh:NodeShape ; sh:closed true ; sh:description "An RNA synthesized on a DNA or RNA template by an RNA polymerase." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "" ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:description "indicates whether a molecular entity is a metabolite" ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:is_metabolite ], + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:iri ], [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:is_toxic ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:in_taxon ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], + sh:order 14 ; + sh:path rdfs:label ], [ sh:order 13 ; sh:path rdf:type ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path rdfs:label ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_chemical_role ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:iri ], + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:trade_name ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 9 ; - sh:path biolink:provided_by ] ; + sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:description ], + [ sh:description "indicates whether a molecular entity is a metabolite" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:is_metabolite ] ; sh:targetClass biolink:Transcript . biolink:Pathway a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_output ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -21933,45 +21899,39 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; sh:path biolink:id ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:maxCount 1 ; sh:order 11 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ] ; + sh:path biolink:description ] ; sh:targetClass biolink:Pathway . biolink:LifeStage a sh:NodeShape ; sh:closed true ; sh:description "A stage of development or growth of an organism, including post-natal adult stages" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -21985,20 +21945,14 @@ biolink:LifeStage a sh:NodeShape ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 6 ; - sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; @@ -22013,45 +21967,60 @@ biolink:NucleicAcidEntity a sh:NodeShape ; sh:closed true ; sh:description "A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "indicates whether a molecular entity is a metabolite" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:is_metabolite ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path rdfs:label ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:order 13 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 9 ; + sh:path biolink:provided_by ], [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:trade_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:has_biological_sequence ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path rdfs:label ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:is_toxic ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], + [ sh:description "indicates whether a molecular entity is a metabolite" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:is_metabolite ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -22061,65 +22030,50 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 12 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:order 13 ; - sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ] ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:description ] ; sh:targetClass biolink:NucleicAcidEntity . biolink:PopulationOfIndividualOrganisms a sh:NodeShape ; sh:closed true ; sh:description "A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], + sh:order 7 ; + sh:path rdfs:label ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; @@ -22133,11 +22087,9 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ] ; + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ] ; sh:targetClass biolink:PopulationOfIndividualOrganisms . biolink:ChemicalEntityOrGeneOrGeneProduct a sh:NodeShape ; @@ -22150,19 +22102,19 @@ biolink:MolecularActivity a sh:NodeShape ; sh:closed true ; sh:description "An execution of a molecular function carried out by a gene product or macromolecular complex." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "The gene product, gene, or complex that catalyzes the reaction" ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path biolink:enabled_by ], + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -22172,128 +22124,104 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:MolecularEntity ; - sh:description "A chemical entity that is the input for the reaction" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], - [ sh:order 9 ; - sh:path rdf:type ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:id ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 6 ; sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], + sh:order 10 ; + sh:path rdfs:label ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "The gene product, gene, or complex that catalyzes the reaction" ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path biolink:enabled_by ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], [ sh:class biolink:MolecularEntity ; sh:description "A chemical entity that is the output for the reaction" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_output ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:class biolink:MolecularEntity ; + sh:description "A chemical entity that is the input for the reaction" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ] ; + sh:order 1 ; + sh:path biolink:has_input ] ; sh:targetClass biolink:MolecularActivity . -biolink:PhenotypicFeature a sh:NodeShape ; +biolink:ChemicalMixture a sh:NodeShape ; sh:closed true ; - sh:description "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment." ; + sh:description "A chemical mixture is a chemical entity composed of two or more molecular entities." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 7 ; + sh:order 15 ; sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:ChemicalMixture ; + sh:description "" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:path biolink:is_supplement ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; + sh:order 10 ; sh:path biolink:xref ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 9 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:PhenotypicFeature . - -biolink:ChemicalMixture a sh:NodeShape ; - sh:closed true ; - sh:description "A chemical mixture is a chemical entity composed of two or more molecular entities." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:ChemicalEntity ; - sh:description "" ; + sh:path biolink:provided_by ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:trade_name ], + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:is_toxic ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:iri ], - [ sh:class biolink:ChemicalMixture ; + [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:is_supplement ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], + sh:order 4 ; + sh:path biolink:trade_name ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -22303,48 +22231,20 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], [ sh:order 14 ; sh:path rdf:type ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:maxCount 1 ; sh:order 16 ; - sh:path dct:description ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], + sh:path biolink:description ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; - sh:path biolink:id ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ] ; + sh:path biolink:id ] ; sh:targetClass biolink:ChemicalMixture . biolink:MacromolecularMachineMixin a sh:NodeShape ; @@ -22361,16 +22261,13 @@ biolink:MolecularEntity a sh:NodeShape ; sh:closed true ; sh:description "A molecular entity is a chemical entity composed of individual or covalently bonded atoms." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], + sh:property [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:max_tolerated_dose ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; sh:path biolink:xref ], - [ sh:order 11 ; - sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -22385,245 +22282,250 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 8 ; sh:path biolink:id ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "indicates whether a molecular entity is a metabolite" ; + [ sh:description "" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:is_metabolite ], + sh:order 4 ; + sh:path biolink:is_toxic ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:has_chemical_role ], - [ sh:description "" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:is_toxic ], + sh:order 12 ; + sh:path rdfs:label ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:trade_name ], + [ sh:maxCount 1 ; sh:order 13 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:path biolink:description ], + [ sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 0 ; + sh:path biolink:is_metabolite ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:order 11 ; + sh:path rdf:type ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 2 ; - sh:path biolink:available_from ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:trade_name ] ; + sh:path biolink:available_from ] ; sh:targetClass biolink:MolecularEntity . -biolink:PhysicalEntity a sh:NodeShape ; +biolink:PhenotypicFeature a sh:NodeShape ; sh:closed true ; - sh:description "An entity that has material reality (a.k.a. physical essence)." ; + sh:description "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 5 ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:order 6 ; sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 4 ; + sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 7 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:path rdfs:label ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; sh:order 3 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:PhysicalEntity . + sh:path biolink:id ] ; + sh:targetClass biolink:PhenotypicFeature . -biolink:Genotype a sh:NodeShape ; +biolink:PhysicalEntity a sh:NodeShape ; sh:closed true ; - sh:description "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background" ; + sh:description "An entity that has material reality (a.k.a. physical essence)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 7 ; + sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Zygosity ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:order 5 ; + sh:path rdf:type ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; - sh:path biolink:has_zygosity ], + sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:description ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 6 ; + sh:order 3 ; sh:path biolink:iri ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:PhysicalEntity . + +biolink:Genotype a sh:NodeShape ; + sh:closed true ; + sh:description "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path rdfs:label ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:in_taxon ], - [ sh:order 8 ; - sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:has_biological_sequence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path rdfs:label ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:Zygosity ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_zygosity ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], + [ sh:order 8 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; sh:order 10 ; - sh:path dct:description ] ; - sh:targetClass biolink:Genotype . - -biolink:BiologicalSex a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 6 ; + sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:targetClass biolink:Genotype . + +biolink:SequenceVariant a sh:NodeShape ; + sh:closed true ; + sh:description "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:order 9 ; - sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_attribute ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 0 ; + sh:order 9 ; sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:description "The state of the sequence w.r.t a reference sequence" ; sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:has_biological_sequence ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path biolink:has_qualitative_value ] ; - sh:targetClass biolink:BiologicalSex . - -biolink:SequenceVariant a sh:NodeShape ; - sh:closed true ; - sh:description "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:path biolink:in_taxon ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:description ], [ sh:class biolink:Gene ; sh:description "Each allele can be associated with any number of genes" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:has_gene ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], - [ sh:order 8 ; - sh:path rdf:type ], - [ sh:description "The state of the sequence w.r.t a reference sequence" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 6 ; + sh:path biolink:iri ], + [ sh:order 8 ; + sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -22632,50 +22534,14 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 7 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; sh:targetClass biolink:SequenceVariant . biolink:Agent a sh:NodeShape ; sh:closed true ; sh:description "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:order 7 ; - sh:path rdf:type ], - [ sh:description "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?)." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:address ], - [ sh:description "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations." ; - sh:order 0 ; - sh:path biolink:affiliation ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -22684,39 +22550,67 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 6 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:description ], + [ sh:description "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?)." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:address ], [ sh:description "Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], + [ sh:order 7 ; + sh:path rdf:type ], + [ sh:description "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations." ; + sh:order 0 ; + sh:path biolink:affiliation ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ] ; + sh:order 5 ; + sh:path biolink:iri ] ; sh:targetClass biolink:Agent . -biolink:Disease a sh:NodeShape ; +biolink:DiseaseOrPhenotypicFeature a sh:NodeShape ; sh:closed true ; - sh:description "A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." ; + sh:description "Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:order 6 ; sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 9 ; + sh:path biolink:has_attribute ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -22726,112 +22620,148 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 2 ; sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 7 ; sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ] ; - sh:targetClass biolink:Disease . + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ] ; + sh:targetClass biolink:DiseaseOrPhenotypicFeature . -biolink:DiseaseOrPhenotypicFeature a sh:NodeShape ; +biolink:Disease a sh:NodeShape ; sh:closed true ; - sh:description "Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature." ; + sh:description "A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], + sh:property [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:order 6 ; sh:path rdf:type ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 1 ; sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "a human-readable description of an entity" ; + sh:path biolink:in_taxon ] ; + sh:targetClass biolink:Disease . + +biolink:BiologicalSex a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 7 ; + sh:order 0 ; sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:description ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 5 ; + sh:order 8 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; - sh:targetClass biolink:DiseaseOrPhenotypicFeature . + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ] ; + sh:targetClass biolink:BiologicalSex . biolink:Gene a sh:NodeShape ; sh:closed true ; sh:description "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 1 ; - sh:path biolink:synonym ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:in_taxon ], + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -22841,37 +22771,54 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:in_taxon ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 2 ; sh:path biolink:xref ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:has_biological_sequence ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], [ sh:description "Symbol for a particular thing" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:symbol ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 1 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:has_biological_sequence ] ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Gene . biolink:AnatomicalEntity a sh:NodeShape ; sh:closed true ; sh:description "A subcellular location, cell type or gross anatomical part" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -22880,48 +22827,55 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], [ sh:order 6 ; sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 2 ; sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ] ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ] ; sh:targetClass biolink:AnatomicalEntity . -biolink:Onset a sh:NodeShape ; +biolink:ChemicalRole a sh:NodeShape ; sh:closed true ; - sh:description "The age group in which (disease) symptom manifestations appear" ; + sh:description " A role played by the molecular entity or part thereof within a chemical context." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -22930,79 +22884,59 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; sh:order 2 ; sh:path biolink:has_quantitative_value ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; sh:order 10 ; - sh:path dct:description ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:path biolink:description ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:order 9 ; - sh:path rdf:type ] ; - sh:targetClass biolink:Onset . + sh:order 3 ; + sh:path biolink:has_qualitative_value ] ; + sh:targetClass biolink:ChemicalRole . -biolink:SeverityValue a sh:NodeShape ; +biolink:GeneOrGeneProduct a sh:NodeShape ; + sh:closed false ; + sh:description "A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:GeneOrGeneProduct . + +biolink:Onset a sh:NodeShape ; sh:closed true ; - sh:description "describes the severity of a phenotypic feature or disease" ; + sh:description "The age group in which (disease) symptom manifestations appear" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; sh:path biolink:id ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -23010,69 +22944,84 @@ biolink:SeverityValue a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; sh:order 2 ; sh:path biolink:has_quantitative_value ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:description ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 9 ; - sh:path rdf:type ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 0 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:SeverityValue . - -biolink:GeneOrGeneProduct a sh:NodeShape ; - sh:closed false ; - sh:description "A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:GeneOrGeneProduct . + sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ] ; + sh:targetClass biolink:Onset . -biolink:ChemicalRole a sh:NodeShape ; +biolink:SeverityValue a sh:NodeShape ; sh:closed true ; - sh:description " A role played by the molecular entity or part thereof within a chemical context." ; + sh:description "describes the severity of a phenotypic feature or disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 9 ; - sh:path rdf:type ], + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:description ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 0 ; + sh:path rdfs:label ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -23082,23 +23031,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -23106,87 +23038,85 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ] ; - sh:targetClass biolink:ChemicalRole . + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:SeverityValue . biolink:QuantityValue a sh:NodeShape ; sh:closed true ; sh:description "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "connects a quantity value to a unit" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_unit ], - [ sh:description "connects a quantity value to a number" ; + sh:property [ sh:description "connects a quantity value to a number" ; sh:maxCount 1 ; sh:order 1 ; - sh:path biolink:has_numeric_value ] ; + sh:path biolink:has_numeric_value ], + [ sh:description "connects a quantity value to a unit" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:has_unit ] ; sh:targetClass biolink:QuantityValue . biolink:ChemicalEntity a sh:NodeShape ; sh:closed true ; sh:description "A chemical entity is a physical entity that pertains to chemistry or biochemistry." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:description "" ; + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:is_toxic ], - [ sh:description "a human-readable description of an entity" ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 7 ; + sh:path biolink:id ], + [ sh:maxCount 1 ; sh:order 12 ; - sh:path dct:description ], + sh:path biolink:description ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 11 ; sh:path rdfs:label ], - [ sh:order 10 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:trade_name ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ], + sh:order 3 ; + sh:path biolink:is_toxic ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_chemical_role ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:trade_name ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:id ], + sh:order 2 ; + sh:path biolink:max_tolerated_dose ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -23195,30 +23125,26 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 9 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:order 10 ; + sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:xref ] ; sh:targetClass biolink:ChemicalEntity . biolink:NamedThing a sh:NodeShape ; sh:closed true ; sh:description "a databased entity or concept/class" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:description ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; sh:path biolink:provided_by ], @@ -23226,12 +23152,12 @@ biolink:NamedThing a sh:NodeShape ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path dct:description ], [ sh:order 5 ; sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -23240,17 +23166,7 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 4 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; - sh:targetClass biolink:NamedThing . - -biolink:OrganismTaxon a sh:NodeShape ; - sh:closed true ; - sh:description "A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -23258,25 +23174,38 @@ biolink:OrganismTaxon a sh:NodeShape ; sh:path biolink:has_attribute ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:path biolink:xref ] ; + sh:targetClass biolink:NamedThing . + +biolink:OrganismTaxon a sh:NodeShape ; + sh:closed true ; + sh:description "A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:order 5 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path dct:description ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:description ], + [ sh:order 5 ; + sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_attribute ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -23285,37 +23214,19 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 4 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ] ; sh:targetClass biolink:OrganismTaxon . biolink:EvidenceType a sh:NodeShape ; sh:closed true ; sh:description "Class of evidence that supports an association" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:order 9 ; + sh:property [ sh:order 9 ; sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], @@ -23324,6 +23235,11 @@ biolink:EvidenceType a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -23333,42 +23249,64 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:creation_date ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ] ; + sh:order 2 ; + sh:path biolink:format ] ; sh:targetClass biolink:EvidenceType . biolink:Publication a sh:NodeShape ; sh:closed true ; sh:description "Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP). " ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 14 ; - sh:path rdf:type ], - [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; - sh:maxCount 1 ; + sh:property [ sh:description "mesh terms tagging a publication" ; + sh:order 4 ; + sh:path biolink:mesh_terms ], + [ sh:description "keywords tagging a publication" ; + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], + sh:order 13 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:license ], [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:creation_date ], + [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 1 ; + sh:path biolink:pages ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 12 ; @@ -23378,70 +23316,63 @@ biolink:Publication a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], - [ sh:description "executive summary of a publication" ; + [ sh:order 14 ; + sh:path rdf:type ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:summary ], + sh:order 15 ; + sh:path rdfs:label ], [ sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:rights ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 10 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], + sh:order 16 ; + sh:path biolink:description ], [ sh:class biolink:Agent ; sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:authors ], - [ sh:description "keywords tagging a publication" ; - sh:order 3 ; - sh:path biolink:keywords ], + [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 10 ; + sh:path biolink:provided_by ], [ sh:maxCount 1 ; sh:order 8 ; sh:path biolink:format ], - [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], + [ sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:summary ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:license ] ; + sh:order 7 ; + sh:path biolink:rights ] ; sh:targetClass biolink:Publication . biolink:RetrievalSource a sh:NodeShape ; sh:closed true ; sh:description "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 8 ; - sh:path biolink:provided_by ], - [ sh:description "The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:upstream_resource_ids ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:format ], + [ sh:description "The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:id ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:creation_date ], + sh:order 0 ; + sh:path biolink:resource_id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -23451,98 +23382,71 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 11 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge." ; - sh:in ( "primary_knowledge_source" "aggregator_knowledge_source" "supporting_data_source" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:resource_role ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 8 ; + sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:rights ], [ sh:maxCount 1 ; sh:order 4 ; sh:path biolink:license ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], [ sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:format ], + sh:order 14 ; + sh:path biolink:description ], [ sh:order 12 ; sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge." ; + sh:in ( "primary_knowledge_source" "aggregator_knowledge_source" "supporting_data_source" ) ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:resource_role ], + [ sh:description "The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], + sh:order 2 ; + sh:path biolink:upstream_resource_ids ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 13 ; sh:path rdfs:label ], - [ sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:rights ], - [ sh:description "The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:creation_date ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:resource_id ] ; + sh:order 9 ; + sh:path biolink:id ] ; sh:targetClass biolink:RetrievalSource . biolink:Attribute a sh:NodeShape ; sh:closed true ; sh:description "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:property [ sh:maxCount 1 ; sh:order 10 ; - sh:path dct:description ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], + sh:path biolink:description ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; sh:path biolink:id ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; @@ -23550,79 +23454,38 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:path biolink:has_quantitative_value ], [ sh:order 9 ; sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ] ; - sh:targetClass biolink:Attribute . - -biolink:InformationResource a sh:NodeShape ; - sh:closed true ; - sh:description "A database or knowledgebase and its supporting ecosystem of interfaces and services that deliver content to consumers (e.g. web portals, APIs, query endpoints, streaming services, data downloads, etc.). A single Information Resource by this definition may span many different datasets or databases, and include many access endpoints and user interfaces. Information Resources include project-specific resources such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; sh:order 1 ; - sh:path rdfs:label ], - [ sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:rights ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:path biolink:has_attribute_type ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 0 ; + sh:path rdfs:label ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 12 ; + sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:format ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:creation_date ], - [ sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:license ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 14 ; + sh:order 11 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path dct:description ], - [ sh:description "the status of the infores identifier, default is released" ; - sh:in ( "released" "deprecated" "draft" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:information_resource_status ], - [ sh:order 13 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 4 ; - sh:path biolink:synonym ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 10 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:InformationResource . + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ] ; + sh:targetClass biolink:Attribute . biolink:OntologyClass a sh:NodeShape ; sh:closed false ; diff --git a/biolink-model.shexj b/biolink-model.shexj index 06da52561b..7f3c3199e4 100644 --- a/biolink-model.shexj +++ b/biolink-model.shexj @@ -1,5 +1,5 @@ # metamodel_version: 1.7.0 -# version: 3.3.2 +# version: 3.4.0 { "type": "Schema", "@context": [ @@ -868,21 +868,21 @@ { "type": "TripleConstraint", "predicate": "https://w3id.org/biolink/vocab/knowledge_source", - "valueExpr": "https://w3id.org/biolink/vocab/InformationResource", + "valueExpr": "https://w3id.org/linkml/String", "min": 0, "max": 1 }, { "type": "TripleConstraint", "predicate": "https://w3id.org/biolink/vocab/primary_knowledge_source", - "valueExpr": "https://w3id.org/biolink/vocab/InformationResource", + "valueExpr": "https://w3id.org/linkml/String", "min": 0, "max": 1 }, { "type": "TripleConstraint", "predicate": "https://w3id.org/biolink/vocab/aggregator_knowledge_source", - "valueExpr": "https://w3id.org/biolink/vocab/InformationResource", + "valueExpr": "https://w3id.org/linkml/String", "min": 0, "max": -1 }, @@ -1044,13 +1044,11 @@ "https://w3id.org/biolink/vocab/ExposureEventToOutcomeAssociation", "https://w3id.org/biolink/vocab/ExposureEventToPhenotypicFeatureAssociation", "https://w3id.org/biolink/vocab/FunctionalAssociation", - "https://w3id.org/biolink/vocab/GeneToDiseaseAssociation", "https://w3id.org/biolink/vocab/GeneToDiseaseOrPhenotypicFeatureAssociation", "https://w3id.org/biolink/vocab/GeneToExpressionSiteAssociation", "https://w3id.org/biolink/vocab/GeneToGeneAssociation", "https://w3id.org/biolink/vocab/GeneToGeneFamilyAssociation", "https://w3id.org/biolink/vocab/GeneToPathwayAssociation", - "https://w3id.org/biolink/vocab/GeneToPhenotypeAssociation", "https://w3id.org/biolink/vocab/GenotypeToDiseaseAssociation", "https://w3id.org/biolink/vocab/GenotypeToGeneAssociation", "https://w3id.org/biolink/vocab/GenotypeToGenotypePartAssociation", @@ -2193,6 +2191,83 @@ ] } }, + { + "type": "Shape", + "id": "https://w3id.org/biolink/vocab/CausalGeneToDiseaseAssociation", + "closed": true, + "expression": { + "type": "EachOf", + "expressions": [ + { + "type": "EachOf", + "id": "https://w3id.org/biolink/vocab/CausalGeneToDiseaseAssociation_tes", + "expressions": [ + "https://w3id.org/biolink/vocab/GeneToDiseaseAssociation_tes", + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/GeneToDiseaseAssociation" + ] + }, + "min": 0 + }, + "https://w3id.org/biolink/vocab/EntityToDiseaseAssociationMixin_tes", + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/EntityToDiseaseAssociationMixin" + ] + }, + "min": 0 + }, + "https://w3id.org/biolink/vocab/GeneToEntityAssociationMixin_tes", + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/GeneToEntityAssociationMixin" + ] + }, + "min": 0 + }, + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#subject", + "valueExpr": "https://w3id.org/biolink/vocab/GeneOrGeneProduct", + "min": 1, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#object", + "valueExpr": "https://w3id.org/biolink/vocab/Disease", + "min": 1, + "max": 1 + } + ] + }, + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/CausalGeneToDiseaseAssociation" + ] + }, + "min": 1 + } + ] + } + }, { "type": "Shape", "id": "https://w3id.org/biolink/vocab/Cell", @@ -4640,6 +4715,83 @@ ] } }, + { + "type": "Shape", + "id": "https://w3id.org/biolink/vocab/CorrelatedGeneToDiseaseAssociation", + "closed": true, + "expression": { + "type": "EachOf", + "expressions": [ + { + "type": "EachOf", + "id": "https://w3id.org/biolink/vocab/CorrelatedGeneToDiseaseAssociation_tes", + "expressions": [ + "https://w3id.org/biolink/vocab/GeneToDiseaseAssociation_tes", + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/GeneToDiseaseAssociation" + ] + }, + "min": 0 + }, + "https://w3id.org/biolink/vocab/EntityToDiseaseAssociationMixin_tes", + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/EntityToDiseaseAssociationMixin" + ] + }, + "min": 0 + }, + "https://w3id.org/biolink/vocab/GeneToEntityAssociationMixin_tes", + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/GeneToEntityAssociationMixin" + ] + }, + "min": 0 + }, + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#subject", + "valueExpr": "https://w3id.org/biolink/vocab/GeneOrGeneProduct", + "min": 1, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#object", + "valueExpr": "https://w3id.org/biolink/vocab/Disease", + "min": 1, + "max": 1 + } + ] + }, + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/CorrelatedGeneToDiseaseAssociation" + ] + }, + "min": 1 + } + ] + } + }, { "type": "Shape", "id": "https://w3id.org/biolink/vocab/Dataset", @@ -5875,27 +6027,6 @@ "valueExpr": "https://w3id.org/biolink/vocab/DruggableGeneCategoryEnum", "min": 0, "max": -1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/frequency_qualifier", - "valueExpr": "https://w3id.org/biolink/vocab/FrequencyValue", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/severity_qualifier", - "valueExpr": "https://w3id.org/biolink/vocab/SeverityValue", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/onset_qualifier", - "valueExpr": "https://w3id.org/biolink/vocab/Onset", - "min": 0, - "max": 1 } ] }, @@ -7479,27 +7610,6 @@ "valueExpr": "https://w3id.org/biolink/vocab/GeneOrGeneProduct", "min": 1, "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/frequency_qualifier", - "valueExpr": "https://w3id.org/biolink/vocab/FrequencyValue", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/severity_qualifier", - "valueExpr": "https://w3id.org/biolink/vocab/SeverityValue", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/onset_qualifier", - "valueExpr": "https://w3id.org/biolink/vocab/Onset", - "min": 0, - "max": 1 } ] }, @@ -7895,17 +8005,55 @@ "type": "EachOf", "id": "https://w3id.org/biolink/vocab/GeneToDiseaseAssociation_tes", "expressions": [ - "https://w3id.org/biolink/vocab/Association_tes", + "https://w3id.org/biolink/vocab/GeneToDiseaseOrPhenotypicFeatureAssociation_tes", { "type": "TripleConstraint", "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", "valueExpr": { "type": "NodeConstraint", "values": [ - "https://w3id.org/biolink/vocab/Association" + "https://w3id.org/biolink/vocab/GeneToDiseaseOrPhenotypicFeatureAssociation" + ] + }, + "min": 0 + }, + "https://w3id.org/biolink/vocab/EntityToDiseaseAssociationMixin_tes", + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/EntityToDiseaseAssociationMixin" ] }, "min": 0 + }, + "https://w3id.org/biolink/vocab/GeneToEntityAssociationMixin_tes", + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/GeneToEntityAssociationMixin" + ] + }, + "min": 0 + }, + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#subject", + "valueExpr": "https://w3id.org/biolink/vocab/GeneOrGeneProduct", + "min": 1, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#object", + "valueExpr": "https://w3id.org/biolink/vocab/Disease", + "min": 1, + "max": 1 } ] }, @@ -7923,164 +8071,173 @@ ] } }, + "https://w3id.org/biolink/vocab/CausalGeneToDiseaseAssociation", + "https://w3id.org/biolink/vocab/CorrelatedGeneToDiseaseAssociation", "https://w3id.org/biolink/vocab/DruggableGeneToDiseaseAssociation", "https://w3id.org/biolink/vocab/GeneAsAModelOfDiseaseAssociation", "https://w3id.org/biolink/vocab/GeneHasVariantThatContributesToDiseaseAssociation" ] }, { - "type": "Shape", + "type": "ShapeOr", "id": "https://w3id.org/biolink/vocab/GeneToDiseaseOrPhenotypicFeatureAssociation", - "closed": true, - "expression": { - "type": "EachOf", - "expressions": [ - { + "shapeExprs": [ + { + "type": "Shape", + "closed": true, + "expression": { "type": "EachOf", - "id": "https://w3id.org/biolink/vocab/GeneToDiseaseOrPhenotypicFeatureAssociation_tes", "expressions": [ - "https://w3id.org/biolink/vocab/Association_tes", - { - "type": "TripleConstraint", - "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", - "valueExpr": { - "type": "NodeConstraint", - "values": [ - "https://w3id.org/biolink/vocab/Association" - ] - }, - "min": 0 - }, - "https://w3id.org/biolink/vocab/EntityToPhenotypicFeatureAssociationMixin_tes", { - "type": "TripleConstraint", - "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", - "valueExpr": { - "type": "NodeConstraint", - "values": [ - "https://w3id.org/biolink/vocab/EntityToPhenotypicFeatureAssociationMixin" - ] - }, - "min": 0 + "type": "EachOf", + "id": "https://w3id.org/biolink/vocab/GeneToDiseaseOrPhenotypicFeatureAssociation_tes", + "expressions": [ + "https://w3id.org/biolink/vocab/Association_tes", + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/Association" + ] + }, + "min": 0 + }, + "https://w3id.org/biolink/vocab/EntityToPhenotypicFeatureAssociationMixin_tes", + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/EntityToPhenotypicFeatureAssociationMixin" + ] + }, + "min": 0 + }, + "https://w3id.org/biolink/vocab/GeneToEntityAssociationMixin_tes", + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/GeneToEntityAssociationMixin" + ] + }, + "min": 0 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/subject_aspect_qualifier", + "valueExpr": "https://w3id.org/biolink/vocab/GeneOrGeneProductOrChemicalEntityAspectEnum", + "min": 0, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/object_direction_qualifier", + "valueExpr": "https://w3id.org/biolink/vocab/DirectionQualifierEnum", + "min": 0, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#subject", + "valueExpr": "https://w3id.org/biolink/vocab/GeneOrGeneProduct", + "min": 1, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#object", + "valueExpr": "https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeature", + "min": 1, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#predicate", + "valueExpr": "https://w3id.org/biolink/vocab/PredicateType", + "min": 1, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/frequency_qualifier", + "valueExpr": "https://w3id.org/biolink/vocab/FrequencyValue", + "min": 0, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/severity_qualifier", + "valueExpr": "https://w3id.org/biolink/vocab/SeverityValue", + "min": 0, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/onset_qualifier", + "valueExpr": "https://w3id.org/biolink/vocab/Onset", + "min": 0, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/sex_qualifier", + "valueExpr": "https://w3id.org/biolink/vocab/BiologicalSex", + "min": 0, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/has_count", + "valueExpr": "https://w3id.org/linkml/Integer", + "min": 0, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/has_total", + "valueExpr": "https://w3id.org/linkml/Integer", + "min": 0, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/has_quotient", + "valueExpr": "https://w3id.org/linkml/Double", + "min": 0, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/has_percentage", + "valueExpr": "https://w3id.org/linkml/Double", + "min": 0, + "max": 1 + } + ] }, - "https://w3id.org/biolink/vocab/GeneToEntityAssociationMixin_tes", { "type": "TripleConstraint", "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", "valueExpr": { "type": "NodeConstraint", "values": [ - "https://w3id.org/biolink/vocab/GeneToEntityAssociationMixin" + "https://w3id.org/biolink/vocab/GeneToDiseaseOrPhenotypicFeatureAssociation" ] }, - "min": 0 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/subject_aspect_qualifier", - "valueExpr": "https://w3id.org/biolink/vocab/GeneOrGeneProductOrChemicalEntityAspectEnum", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/object_direction_qualifier", - "valueExpr": "https://w3id.org/biolink/vocab/DirectionQualifierEnum", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#subject", - "valueExpr": "https://w3id.org/biolink/vocab/GeneOrGeneProduct", - "min": 1, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#object", - "valueExpr": "https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeature", - "min": 1, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#predicate", - "valueExpr": "https://w3id.org/biolink/vocab/PredicateType", - "min": 1, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/frequency_qualifier", - "valueExpr": "https://w3id.org/biolink/vocab/FrequencyValue", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/severity_qualifier", - "valueExpr": "https://w3id.org/biolink/vocab/SeverityValue", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/onset_qualifier", - "valueExpr": "https://w3id.org/biolink/vocab/Onset", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/sex_qualifier", - "valueExpr": "https://w3id.org/biolink/vocab/BiologicalSex", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/has_count", - "valueExpr": "https://w3id.org/linkml/Integer", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/has_total", - "valueExpr": "https://w3id.org/linkml/Integer", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/has_quotient", - "valueExpr": "https://w3id.org/linkml/Double", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/has_percentage", - "valueExpr": "https://w3id.org/linkml/Double", - "min": 0, - "max": 1 + "min": 1 } ] - }, - { - "type": "TripleConstraint", - "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", - "valueExpr": { - "type": "NodeConstraint", - "values": [ - "https://w3id.org/biolink/vocab/GeneToDiseaseOrPhenotypicFeatureAssociation" - ] - }, - "min": 1 } - ] - } + }, + "https://w3id.org/biolink/vocab/GeneToDiseaseAssociation", + "https://w3id.org/biolink/vocab/GeneToPhenotypeAssociation" + ] }, { "type": "Shape", @@ -8642,17 +8799,55 @@ "type": "EachOf", "id": "https://w3id.org/biolink/vocab/GeneToPhenotypeAssociation_tes", "expressions": [ - "https://w3id.org/biolink/vocab/Association_tes", + "https://w3id.org/biolink/vocab/GeneToDiseaseOrPhenotypicFeatureAssociation_tes", { "type": "TripleConstraint", "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", "valueExpr": { "type": "NodeConstraint", "values": [ - "https://w3id.org/biolink/vocab/Association" + "https://w3id.org/biolink/vocab/GeneToDiseaseOrPhenotypicFeatureAssociation" ] }, "min": 0 + }, + "https://w3id.org/biolink/vocab/EntityToPhenotypicFeatureAssociationMixin_tes", + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/EntityToPhenotypicFeatureAssociationMixin" + ] + }, + "min": 0 + }, + "https://w3id.org/biolink/vocab/GeneToEntityAssociationMixin_tes", + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/GeneToEntityAssociationMixin" + ] + }, + "min": 0 + }, + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#subject", + "valueExpr": "https://w3id.org/biolink/vocab/GeneOrGeneProduct", + "min": 1, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#object", + "valueExpr": "https://w3id.org/biolink/vocab/PhenotypicFeature", + "min": 1, + "max": 1 } ] }, @@ -10179,7 +10374,6 @@ "https://w3id.org/biolink/vocab/DatasetSummary", "https://w3id.org/biolink/vocab/DatasetVersion", "https://w3id.org/biolink/vocab/EvidenceType", - "https://w3id.org/biolink/vocab/InformationResource", "https://w3id.org/biolink/vocab/Publication", "https://w3id.org/biolink/vocab/RetrievalSource", "https://w3id.org/biolink/vocab/StudyResult", @@ -10315,40 +10509,26 @@ }, { "type": "Shape", - "id": "https://w3id.org/biolink/vocab/InformationResource", + "id": "https://w3id.org/biolink/vocab/Invertebrate", "closed": true, "expression": { "type": "EachOf", "expressions": [ { "type": "EachOf", - "id": "https://w3id.org/biolink/vocab/InformationResource_tes", + "id": "https://w3id.org/biolink/vocab/Invertebrate_tes", "expressions": [ - "https://w3id.org/biolink/vocab/InformationContentEntity_tes", + "https://w3id.org/biolink/vocab/CellularOrganism_tes", { "type": "TripleConstraint", "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", "valueExpr": { "type": "NodeConstraint", "values": [ - "https://w3id.org/biolink/vocab/InformationContentEntity" + "https://w3id.org/biolink/vocab/CellularOrganism" ] }, "min": 0 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/information_resource_status", - "valueExpr": "https://w3id.org/biolink/vocab/InformationResourceStatusEnum", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/synonym", - "valueExpr": "https://w3id.org/biolink/vocab/LabelType", - "min": 0, - "max": -1 } ] }, @@ -10358,7 +10538,7 @@ "valueExpr": { "type": "NodeConstraint", "values": [ - "https://w3id.org/biolink/vocab/InformationResource" + "https://w3id.org/biolink/vocab/Invertebrate" ] }, "min": 1 @@ -10368,52 +10548,23 @@ }, { "type": "Shape", - "id": "https://w3id.org/biolink/vocab/InformationResourceCollection", - "closed": true, - "expression": { - "type": "EachOf", - "expressions": [ - { - "type": "TripleConstraint", - "id": "https://w3id.org/biolink/vocab/InformationResourceCollection_tes", - "predicate": "https://w3id.org/biolink/vocab/information_resources", - "valueExpr": "https://w3id.org/biolink/vocab/InformationResource", - "min": 0, - "max": -1 - }, - { - "type": "TripleConstraint", - "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", - "valueExpr": { - "type": "NodeConstraint", - "values": [ - "https://w3id.org/biolink/vocab/InformationResourceCollection" - ] - }, - "min": 0 - } - ] - } - }, - { - "type": "Shape", - "id": "https://w3id.org/biolink/vocab/Invertebrate", + "id": "https://w3id.org/biolink/vocab/JournalArticle", "closed": true, "expression": { "type": "EachOf", "expressions": [ { "type": "EachOf", - "id": "https://w3id.org/biolink/vocab/Invertebrate_tes", + "id": "https://w3id.org/biolink/vocab/JournalArticle_tes", "expressions": [ - "https://w3id.org/biolink/vocab/CellularOrganism_tes", + "https://w3id.org/biolink/vocab/Article_tes", { "type": "TripleConstraint", "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", "valueExpr": { "type": "NodeConstraint", "values": [ - "https://w3id.org/biolink/vocab/CellularOrganism" + "https://w3id.org/biolink/vocab/Article" ] }, "min": 0 @@ -10426,7 +10577,7 @@ "valueExpr": { "type": "NodeConstraint", "values": [ - "https://w3id.org/biolink/vocab/Invertebrate" + "https://w3id.org/biolink/vocab/JournalArticle" ] }, "min": 1 @@ -10436,23 +10587,23 @@ }, { "type": "Shape", - "id": "https://w3id.org/biolink/vocab/JournalArticle", + "id": "https://w3id.org/biolink/vocab/LifeStage", "closed": true, "expression": { "type": "EachOf", "expressions": [ { "type": "EachOf", - "id": "https://w3id.org/biolink/vocab/JournalArticle_tes", + "id": "https://w3id.org/biolink/vocab/LifeStage_tes", "expressions": [ - "https://w3id.org/biolink/vocab/Article_tes", + "https://w3id.org/biolink/vocab/OrganismalEntity_tes", { "type": "TripleConstraint", "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", "valueExpr": { "type": "NodeConstraint", "values": [ - "https://w3id.org/biolink/vocab/Article" + "https://w3id.org/biolink/vocab/OrganismalEntity" ] }, "min": 0 @@ -10465,7 +10616,7 @@ "valueExpr": { "type": "NodeConstraint", "values": [ - "https://w3id.org/biolink/vocab/JournalArticle" + "https://w3id.org/biolink/vocab/LifeStage" ] }, "min": 1 @@ -10475,23 +10626,23 @@ }, { "type": "Shape", - "id": "https://w3id.org/biolink/vocab/LifeStage", + "id": "https://w3id.org/biolink/vocab/LogOddsAnalysisResult", "closed": true, "expression": { "type": "EachOf", "expressions": [ { "type": "EachOf", - "id": "https://w3id.org/biolink/vocab/LifeStage_tes", + "id": "https://w3id.org/biolink/vocab/LogOddsAnalysisResult_tes", "expressions": [ - "https://w3id.org/biolink/vocab/OrganismalEntity_tes", + "https://w3id.org/biolink/vocab/StudyResult_tes", { "type": "TripleConstraint", "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", "valueExpr": { "type": "NodeConstraint", "values": [ - "https://w3id.org/biolink/vocab/OrganismalEntity" + "https://w3id.org/biolink/vocab/StudyResult" ] }, "min": 0 @@ -10504,7 +10655,7 @@ "valueExpr": { "type": "NodeConstraint", "values": [ - "https://w3id.org/biolink/vocab/LifeStage" + "https://w3id.org/biolink/vocab/LogOddsAnalysisResult" ] }, "min": 1 @@ -14177,7 +14328,7 @@ { "type": "TripleConstraint", "predicate": "https://w3id.org/biolink/vocab/anatomical_context_qualifier", - "valueExpr": "https://w3id.org/biolink/vocab/AnatomicalContextQualifierEnum", + "valueExpr": "https://w3id.org/linkml/String", "min": 0, "max": 1 }, @@ -14682,7 +14833,7 @@ "predicate": "http://purl.org/dc/terms/type", "valueExpr": "https://w3id.org/linkml/String", "min": 1, - "max": 1 + "max": -1 } ] }, @@ -16150,6 +16301,7 @@ "shapeExprs": [ "https://w3id.org/biolink/vocab/ChiSquaredAnalysisResult", "https://w3id.org/biolink/vocab/ConceptCountAnalysisResult", + "https://w3id.org/biolink/vocab/LogOddsAnalysisResult", "https://w3id.org/biolink/vocab/ObservedExpectedFrequencyAnalysisResult", "https://w3id.org/biolink/vocab/RelativeFrequencyAnalysisResult", "https://w3id.org/biolink/vocab/TextMiningResult" diff --git a/biolink-model.ttl b/biolink-model.ttl index 63049b5eeb..9ec3feb5d7 100644 --- a/biolink-model.ttl +++ b/biolink-model.ttl @@ -12,7 +12,7 @@ a linkml:SchemaDefinition ; dcterms:license "https://creativecommons.org/publicdomain/zero/1.0/" ; - pav:version "3.3.2" ; + pav:version "3.4.0" ; skos:definition "Entity and association taxonomy and datamodel for life-sciences data" ; linkml:classes , , @@ -43,6 +43,7 @@ , , , + , , , , @@ -86,6 +87,7 @@ , , , + , , , , @@ -183,11 +185,10 @@ , , , - , - , , , , + , , , , @@ -327,8 +328,7 @@ "rdfs", "skos", "xsd" ; - linkml:enums , - , + linkml:enums , , , , @@ -339,7 +339,6 @@ , , , - , , , , @@ -347,268 +346,269 @@ , , ; - linkml:generation_date "2023-05-04T23:01:51"^^xsd:dateTime ; + linkml:generation_date "2023-05-23T23:05:03"^^xsd:dateTime ; linkml:id ; - linkml:imports linkml:types ; + linkml:imports , + linkml:types ; linkml:metamodel_version "1.7.0" ; - linkml:prefixes [ linkml:prefix_prefix "isni" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "gtpo" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "doi" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GTOPDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GTEx" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "foodb.food" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-FORMAT" ; - linkml:prefix_reference ], + linkml:prefixes [ linkml:prefix_prefix "ScopusID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.RCLASS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.BRITE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "INO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "os" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "biolink" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SPDI" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GOP" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "linkml" ; + linkml:prefix_reference linkml: ], [ linkml:prefix_prefix "MI" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "ComplexPortal" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "DGIdb" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CTD.CHEMICAL" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "RXNORM" ; - linkml:prefix_reference ], [ linkml:prefix_prefix "WBbt" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "dct" ; - linkml:prefix_reference dcterms: ], - [ linkml:prefix_prefix "WBls" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "gtpo" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "foaf" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "COG" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ICD9" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RXNORM" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "isbn" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-DATA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "gpi" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SIO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MSigDB" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "foodb.compound" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "MmusDv" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MESH" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "METANETX.REACTION" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CHEMBL.MECHANISM" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PomBase" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "gff3" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "SEMMEDDB" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "WBls" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "doi" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "CTD.GENE" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "VANDF" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "prov" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PHARMGKB.CHEMICAL" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "orphanet" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UBERGRAPH" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PHAROS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "issn" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "ncats.drug" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CLINVAR" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "PANTHER.FAMILY" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "PomBase" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "mmmp.biomaps" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "XPO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ResearchID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "FYPO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PHARMGKB.DISEASE" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "metacyc.reaction" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "qud" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "Xenbase" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "ICD10" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WBVocab" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ORCID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "RO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NBO-PROPERTY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "INO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ECTO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "gff3" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "wgs" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "LOINC" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "bioschemas" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "NCIT-OBO" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "MESH" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NLMID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CLINVAR" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PHARMGKB.VARIANT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ExO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "schema" ; - linkml:prefix_reference schema: ], - [ linkml:prefix_prefix "CPT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GOREL" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UO-PROPERTY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "REPODB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MSigDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ScopusID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "apollo" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WIKIDATA_PROPERTY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SEED.REACTION" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "linkml" ; - linkml:prefix_reference linkml: ], - [ linkml:prefix_prefix "EDAM-OPERATION" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "HANCESTRO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SIO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "mirbase" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NDDF" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "DrugCentral" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-DATA" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PathWhiz" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CHADO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PMC" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "isni" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "HsapDv" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "gpi" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UBERON_NONAMESPACE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "OMIM.PS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "DOID-PROPERTY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-TOPIC" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "FYECO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EFO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SNOMEDCT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UNIPROT.ISOFORM" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "PHARMGKB.PATHWAYS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.PATHWAY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PHARMGKB.DISEASE" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "COAR_RESOURCE" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "prov" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SNOMEDCT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NBO-PROPERTY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GTOPDB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NCBIGene" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "VMC" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "SPDI" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "fabio" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "medgen" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "FYPO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CTD" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ResearchID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "AspGD" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UBERGRAPH" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WIKIDATA_PROPERTY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ICD10" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-TOPIC" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "OMIM.PS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UBERON_CORE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "apollo" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "interpro" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ExO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NLMID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PHARMGKB.GENE" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "ChemBank" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.RCLASS" ; - linkml:prefix_reference ], [ linkml:prefix_prefix "UniProtKB" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "isbn" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "metacyc.reaction" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "DGIdb" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CHADO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MAXO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "DrugCentral" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PHARMGKB.VARIANT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GTEx" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CPT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NDDF" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "dct" ; + linkml:prefix_reference dcterms: ], + [ linkml:prefix_prefix "ECTO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CAID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "VANDF" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UMLSSG" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "foodb.food" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "fabio" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ComplexPortal" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "dcat" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "DOID-PROPERTY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "pav" ; + linkml:prefix_reference pav: ], + [ linkml:prefix_prefix "UO-PROPERTY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-OPERATION" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "HCPCS" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "AGRKB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PHARMGKB.GENE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "OBAN" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "interpro" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ncats.drug" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UBERON_CORE" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "CTD.CHEMICAL" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "XPO" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "RXCUI" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "foaf" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "qud" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "dcat" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "ORCID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PMC" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "CTD.DISEASE" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "pav" ; - linkml:prefix_reference pav: ], - [ linkml:prefix_prefix "CHEMBL.MECHANISM" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "COG" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ncats.bioplanet" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "biolink" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "METANETX.REACTION" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "AspGD" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GSID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "LOINC" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NCBIGene" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "os" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "wgs" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.PATHWAY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "bioschemas" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CAID" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "PHAROS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "schema" ; + linkml:prefix_reference schema: ], [ linkml:prefix_prefix "WIKIDATA" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.BRITE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MAXO" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "mmmp.biomaps" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.GENES" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "FYECO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "orphanet" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "STY" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "GOP" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CTD" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MmusDv" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PHARMGKB.PATHWAYS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "medgen" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UMLSSG" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "dcid" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "AGRKB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SEED.REACTION" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ncats.bioplanet" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-FORMAT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EFO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GSID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "mirbase" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "issn" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PHARMGKB.CHEMICAL" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "HANCESTRO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "REPODB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GOREL" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "OBAN" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "CID" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.GENES" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ICD9" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "dcid" ; - linkml:prefix_reference ] ; + [ linkml:prefix_prefix "UBERON_NONAMESPACE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PathWhiz" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WBVocab" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UNIPROT.ISOFORM" ; + linkml:prefix_reference ] ; linkml:slots , , , @@ -682,6 +682,8 @@ , , , + , + , , , , @@ -765,9 +767,12 @@ , , , + , + , , , , + , , , , @@ -839,6 +844,8 @@ , , , + , + , , , , @@ -866,6 +873,8 @@ , , , + , + , , , , @@ -987,8 +996,6 @@ , , , - , - , , , , @@ -1030,6 +1037,8 @@ , , , + , + , , , , @@ -1268,6 +1277,7 @@ , , , + , , , , @@ -1301,8 +1311,8 @@ , ; linkml:source_file "biolink-model.yaml" ; - linkml:source_file_date "2023-05-04T23:00:24"^^xsd:dateTime ; - linkml:source_file_size 355095 ; + linkml:source_file_date "2023-05-23T23:03:00"^^xsd:dateTime ; + linkml:source_file_size 356228 ; linkml:subsets , , , @@ -1979,6 +1989,51 @@ linkml:slot_uri rdf:subject ; linkml:usage_slot_name "subject" . + a linkml:SlotDefinition ; + skos:definition "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + skos:exactMatch , + owl:annotatedTarget ; + skos:inScheme ; + skos:mappingRelation rdf:object ; + linkml:alias "object" ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:is_a ; + linkml:is_usage_slot true ; + linkml:local_names [ linkml:ga4gh [ skos:altLabel "descriptor" ; + linkml:local_name_source "ga4gh" ] ; + linkml:neo4j [ skos:altLabel "node with incoming relationship" ; + linkml:local_name_source "neo4j" ] ] ; + linkml:owner ; + linkml:range ; + linkml:required true ; + linkml:slot_uri rdf:object ; + linkml:usage_slot_name "object" . + + a linkml:SlotDefinition ; + skos:definition "gene in which variation is shown to cause the disease." ; + skos:exactMatch , + owl:annotatedSource ; + skos:inScheme ; + skos:mappingRelation rdf:subject ; + linkml:alias "subject" ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:inlined true ; + linkml:is_a ; + linkml:is_usage_slot true ; + linkml:local_names [ linkml:ga4gh [ skos:altLabel "annotation subject" ; + linkml:local_name_source "ga4gh" ] ; + linkml:neo4j [ skos:altLabel "node with outgoing relationship" ; + linkml:local_name_source "neo4j" ] ] ; + linkml:owner ; + linkml:range ; + linkml:required true ; + linkml:slot_uri rdf:subject ; + linkml:usage_slot_name "subject" . + a linkml:SlotDefinition ; skos:definition "A cell line derived from an organismal entity with a disease state that is used as a model of that disease." ; skos:exactMatch , @@ -3061,6 +3116,51 @@ linkml:slot_uri rdf:subject ; linkml:usage_slot_name "subject" . + a linkml:SlotDefinition ; + skos:definition "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + skos:exactMatch , + owl:annotatedTarget ; + skos:inScheme ; + skos:mappingRelation rdf:object ; + linkml:alias "object" ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:is_a ; + linkml:is_usage_slot true ; + linkml:local_names [ linkml:ga4gh [ skos:altLabel "descriptor" ; + linkml:local_name_source "ga4gh" ] ; + linkml:neo4j [ skos:altLabel "node with incoming relationship" ; + linkml:local_name_source "neo4j" ] ] ; + linkml:owner ; + linkml:range ; + linkml:required true ; + linkml:slot_uri rdf:object ; + linkml:usage_slot_name "object" . + + a linkml:SlotDefinition ; + skos:definition "gene in which variation is shown to correlate with the disease." ; + skos:exactMatch , + owl:annotatedSource ; + skos:inScheme ; + skos:mappingRelation rdf:subject ; + linkml:alias "subject" ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:inlined true ; + linkml:is_a ; + linkml:is_usage_slot true ; + linkml:local_names [ linkml:ga4gh [ skos:altLabel "annotation subject" ; + linkml:local_name_source "ga4gh" ] ; + linkml:neo4j [ skos:altLabel "node with outgoing relationship" ; + linkml:local_name_source "neo4j" ] ] ; + linkml:owner ; + linkml:range ; + linkml:required true ; + linkml:slot_uri rdf:subject ; + linkml:usage_slot_name "subject" . + a linkml:SlotDefinition ; skos:definition "disease or phenotype" ; skos:exactMatch , @@ -3310,7 +3410,7 @@ linkml:definition_uri ; linkml:domain ; linkml:domain_of ; - linkml:is_a ; + linkml:is_a ; linkml:is_usage_slot true ; linkml:local_names [ linkml:ga4gh [ skos:altLabel "annotation predicate" ; linkml:local_name_source "ga4gh" ] ; @@ -3333,7 +3433,7 @@ linkml:domain ; linkml:domain_of ; linkml:inlined true ; - linkml:is_a ; + linkml:is_a ; linkml:is_usage_slot true ; linkml:local_names [ linkml:ga4gh [ skos:altLabel "annotation subject" ; linkml:local_name_source "ga4gh" ] ; @@ -3562,7 +3662,7 @@ linkml:domain ; linkml:domain_of ; linkml:inlined true ; - linkml:is_a ; + linkml:is_a ; linkml:is_usage_slot true ; linkml:local_names [ linkml:ga4gh [ skos:altLabel "annotation subject" ; linkml:local_name_source "ga4gh" ] ; @@ -3584,7 +3684,7 @@ linkml:definition_uri ; linkml:domain ; linkml:domain_of ; - linkml:is_a ; + linkml:is_a ; linkml:is_usage_slot true ; linkml:local_names [ linkml:ga4gh [ skos:altLabel "descriptor" ; linkml:local_name_source "ga4gh" ] ; @@ -3608,7 +3708,7 @@ linkml:definition_uri ; linkml:domain ; linkml:domain_of ; - linkml:is_a ; + linkml:is_a ; linkml:is_usage_slot true ; linkml:local_names [ linkml:ga4gh [ skos:altLabel "annotation predicate" ; linkml:local_name_source "ga4gh" ] ; @@ -3631,7 +3731,7 @@ linkml:domain ; linkml:domain_of ; linkml:inlined true ; - linkml:is_a ; + linkml:is_a ; linkml:is_usage_slot true ; linkml:local_names [ linkml:ga4gh [ skos:altLabel "annotation subject" ; linkml:local_name_source "ga4gh" ] ; @@ -3643,79 +3743,16 @@ linkml:slot_uri rdf:subject ; linkml:usage_slot_name "subject" . - a linkml:SlotDefinition ; - skos:definition "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - skos:exactMatch , - owl:annotatedTarget ; - skos:inScheme ; - skos:mappingRelation rdf:object ; - linkml:alias "object" ; - linkml:definition_uri ; - linkml:domain ; - linkml:domain_of ; - linkml:is_a ; - linkml:is_usage_slot true ; - linkml:local_names [ linkml:ga4gh [ skos:altLabel "descriptor" ; - linkml:local_name_source "ga4gh" ] ; - linkml:neo4j [ skos:altLabel "node with incoming relationship" ; - linkml:local_name_source "neo4j" ] ] ; - linkml:owner ; - linkml:range ; - linkml:required true ; - linkml:slot_uri rdf:object ; - linkml:usage_slot_name "object" . - - a linkml:SlotDefinition ; - OIO:inSubset ; - skos:inScheme ; - linkml:alias "object direction qualifier" ; - linkml:definition_uri ; - linkml:domain ; - linkml:domain_of ; - linkml:is_a ; - linkml:is_usage_slot true ; - linkml:owner ; - linkml:range ; - linkml:slot_uri ; - linkml:usage_slot_name "object direction qualifier" . - - a linkml:SlotDefinition ; - rdfs:subPropertyOf ; - skos:definition "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - skos:editorialNote "Has a value from the Biolink related_to hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; - skos:exactMatch , - owl:annotatedProperty ; - skos:inScheme ; - skos:mappingRelation rdf:predicate ; - linkml:alias "predicate" ; - linkml:definition_uri ; - linkml:domain ; - linkml:domain_of ; - linkml:is_a ; - linkml:is_usage_slot true ; - linkml:local_names [ linkml:ga4gh [ skos:altLabel "annotation predicate" ; - linkml:local_name_source "ga4gh" ] ; - linkml:translator [ skos:altLabel "predicate" ; - linkml:local_name_source "translator" ] ] ; - linkml:owner ; - linkml:range ; - linkml:required true ; - linkml:slot_uri rdf:predicate ; - linkml:usage_slot_name "predicate" . - - a linkml:SlotDefinition ; - skos:definition "gene in which variation is correlated with the phenotypic feature" ; + a linkml:SlotDefinition ; + skos:definition "gene that is the subject of the association" ; skos:exactMatch , owl:annotatedSource ; skos:inScheme ; skos:mappingRelation rdf:subject ; linkml:alias "subject" ; linkml:definition_uri ; - linkml:domain ; - linkml:domain_of ; - linkml:examples [ a linkml:Example ; - skos:definition "COL1A1 (Human)" ; - skos:example "HGNC:2197" ] ; + linkml:domain ; + linkml:domain_of ; linkml:inlined true ; linkml:is_a ; linkml:is_usage_slot true ; @@ -3723,26 +3760,12 @@ linkml:local_name_source "ga4gh" ] ; linkml:neo4j [ skos:altLabel "node with outgoing relationship" ; linkml:local_name_source "neo4j" ] ] ; - linkml:owner ; + linkml:owner ; linkml:range ; linkml:required true ; linkml:slot_uri rdf:subject ; linkml:usage_slot_name "subject" . - a linkml:SlotDefinition ; - OIO:inSubset ; - skos:inScheme ; - linkml:alias "subject aspect qualifier" ; - linkml:definition_uri ; - linkml:domain ; - linkml:domain_of ; - linkml:is_a ; - linkml:is_usage_slot true ; - linkml:owner ; - linkml:range ; - linkml:slot_uri ; - linkml:usage_slot_name "subject aspect qualifier" . - a linkml:SlotDefinition ; skos:definition "location in which the gene is expressed" ; skos:exactMatch , @@ -4130,52 +4153,100 @@ linkml:local_name_source "ga4gh" ] ; linkml:neo4j [ skos:altLabel "node with outgoing relationship" ; linkml:local_name_source "neo4j" ] ] ; - linkml:owner ; - linkml:range ; + linkml:owner ; + linkml:range ; + linkml:required true ; + linkml:slot_uri rdf:subject ; + linkml:usage_slot_name "subject" . + + a linkml:SlotDefinition ; + skos:definition "the pathway that includes or is affected by the gene or gene product" ; + skos:exactMatch , + owl:annotatedTarget ; + skos:inScheme ; + skos:mappingRelation rdf:object ; + linkml:alias "object" ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:is_a ; + linkml:is_usage_slot true ; + linkml:local_names [ linkml:ga4gh [ skos:altLabel "descriptor" ; + linkml:local_name_source "ga4gh" ] ; + linkml:neo4j [ skos:altLabel "node with incoming relationship" ; + linkml:local_name_source "neo4j" ] ] ; + linkml:owner ; + linkml:range ; + linkml:required true ; + linkml:slot_uri rdf:object ; + linkml:usage_slot_name "object" . + + a linkml:SlotDefinition ; + skos:definition "the gene or gene product entity that participates or influences the pathway" ; + skos:exactMatch , + owl:annotatedSource ; + skos:inScheme ; + skos:mappingRelation rdf:subject ; + linkml:alias "subject" ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:inlined true ; + linkml:is_a ; + linkml:is_usage_slot true ; + linkml:local_names [ linkml:ga4gh [ skos:altLabel "annotation subject" ; + linkml:local_name_source "ga4gh" ] ; + linkml:neo4j [ skos:altLabel "node with outgoing relationship" ; + linkml:local_name_source "neo4j" ] ] ; + linkml:owner ; + linkml:range ; linkml:required true ; linkml:slot_uri rdf:subject ; linkml:usage_slot_name "subject" . - a linkml:SlotDefinition ; - skos:definition "the pathway that includes or is affected by the gene or gene product" ; + a linkml:SlotDefinition ; + skos:definition "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; skos:exactMatch , owl:annotatedTarget ; skos:inScheme ; skos:mappingRelation rdf:object ; linkml:alias "object" ; linkml:definition_uri ; - linkml:domain ; - linkml:domain_of ; - linkml:is_a ; + linkml:domain ; + linkml:domain_of ; + linkml:is_a ; linkml:is_usage_slot true ; linkml:local_names [ linkml:ga4gh [ skos:altLabel "descriptor" ; linkml:local_name_source "ga4gh" ] ; linkml:neo4j [ skos:altLabel "node with incoming relationship" ; linkml:local_name_source "neo4j" ] ] ; - linkml:owner ; - linkml:range ; + linkml:owner ; + linkml:range ; linkml:required true ; linkml:slot_uri rdf:object ; linkml:usage_slot_name "object" . - a linkml:SlotDefinition ; - skos:definition "the gene or gene product entity that participates or influences the pathway" ; + a linkml:SlotDefinition ; + skos:definition "gene in which variation is correlated with the phenotypic feature" ; skos:exactMatch , owl:annotatedSource ; skos:inScheme ; skos:mappingRelation rdf:subject ; linkml:alias "subject" ; linkml:definition_uri ; - linkml:domain ; - linkml:domain_of ; + linkml:domain ; + linkml:domain_of ; + linkml:examples [ a linkml:Example ; + skos:definition "COL1A1 (Human)" ; + skos:example "HGNC:2197" ] ; linkml:inlined true ; - linkml:is_a ; + linkml:is_a ; linkml:is_usage_slot true ; linkml:local_names [ linkml:ga4gh [ skos:altLabel "annotation subject" ; linkml:local_name_source "ga4gh" ] ; linkml:neo4j [ skos:altLabel "node with outgoing relationship" ; linkml:local_name_source "neo4j" ] ] ; - linkml:owner ; + linkml:owner ; linkml:range ; linkml:required true ; linkml:slot_uri rdf:subject ; @@ -4822,6 +4893,28 @@ linkml:slot_uri rdf:predicate ; linkml:usage_slot_name "predicate" . + a linkml:SlotDefinition ; + skos:definition "The entity that serves as the model of the disease. This may be an organism, a strain of organism, a genotype or variant that exhibits similar features, or a gene that when mutated exhibits features of the disease" ; + skos:exactMatch , + owl:annotatedSource ; + skos:inScheme ; + skos:mappingRelation rdf:subject ; + linkml:alias "subject" ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:is_a ; + linkml:is_usage_slot true ; + linkml:local_names [ linkml:ga4gh [ skos:altLabel "annotation subject" ; + linkml:local_name_source "ga4gh" ] ; + linkml:neo4j [ skos:altLabel "node with outgoing relationship" ; + linkml:local_name_source "neo4j" ] ] ; + linkml:owner ; + linkml:range ; + linkml:required true ; + linkml:slot_uri rdf:subject ; + linkml:usage_slot_name "subject" . + a linkml:SlotDefinition ; OIO:inSubset ; skos:definition "The gene product, gene, or complex that catalyzes the reaction" ; @@ -6259,12 +6352,6 @@ , . - skos:inScheme ; - linkml:definition_uri ; - linkml:reachable_from [ linkml:relationship_types "rdfs:subClassOf" ; - linkml:source_nodes "UBERON:0001062" ; - linkml:source_ontology "bioregistry:uberon" ] . - a linkml:ClassDefinition ; skos:definition "A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and are often motile." ; skos:exactMatch , @@ -6978,47 +7065,6 @@ , . - a linkml:ClassDefinition ; - skos:inScheme ; - linkml:class_uri ; - linkml:definition_uri ; - linkml:deprecated "True" ; - linkml:deprecated_element_has_exact_replacement ; - linkml:is_a ; - linkml:slot_usage [ ] ; - linkml:slots , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - . - a linkml:ClassDefinition ; OIO:inSubset ; skos:closeMatch ; @@ -7238,12 +7284,6 @@ , . - skos:inScheme ; - linkml:definition_uri ; - linkml:permissible_values , - , - . - a linkml:ClassDefinition ; skos:definition "An animal lacking a vertebral column. This group consists of 98% of all animal species." ; skos:exactMatch , @@ -7303,6 +7343,27 @@ , . + a linkml:ClassDefinition ; + skos:definition "A result of a log odds ratio analysis." ; + skos:inScheme ; + linkml:class_uri ; + linkml:definition_uri ; + linkml:is_a ; + linkml:slot_usage [ ] ; + linkml:slots , + , + , + , + , + , + , + , + , + , + , + , + . + skos:inScheme ; linkml:definition_uri ; linkml:permissible_values , @@ -8390,29 +8451,6 @@ linkml:range ; linkml:slot_uri . - a linkml:SlotDefinition ; - skos:definition "gene that is the subject of the association" ; - skos:exactMatch , - owl:annotatedSource ; - skos:inScheme ; - skos:mappingRelation rdf:subject ; - linkml:alias "subject" ; - linkml:definition_uri ; - linkml:domain ; - linkml:domain_of ; - linkml:inlined true ; - linkml:is_a ; - linkml:is_usage_slot true ; - linkml:local_names [ linkml:ga4gh [ skos:altLabel "annotation subject" ; - linkml:local_name_source "ga4gh" ] ; - linkml:neo4j [ skos:altLabel "node with outgoing relationship" ; - linkml:local_name_source "neo4j" ] ] ; - linkml:owner ; - linkml:range ; - linkml:required true ; - linkml:slot_uri rdf:subject ; - linkml:usage_slot_name "subject" . - a linkml:SlotDefinition ; skos:definition "a disease that is associated with that genotype" ; skos:exactMatch , @@ -8533,28 +8571,6 @@ linkml:range ; linkml:slot_uri pav:version . - a linkml:SlotDefinition ; - skos:definition "The entity that serves as the model of the disease. This may be an organism, a strain of organism, a genotype or variant that exhibits similar features, or a gene that when mutated exhibits features of the disease" ; - skos:exactMatch , - owl:annotatedSource ; - skos:inScheme ; - skos:mappingRelation rdf:subject ; - linkml:alias "subject" ; - linkml:definition_uri ; - linkml:domain ; - linkml:domain_of ; - linkml:is_a ; - linkml:is_usage_slot true ; - linkml:local_names [ linkml:ga4gh [ skos:altLabel "annotation subject" ; - linkml:local_name_source "ga4gh" ] ; - linkml:neo4j [ skos:altLabel "node with outgoing relationship" ; - linkml:local_name_source "neo4j" ] ] ; - linkml:owner ; - linkml:range ; - linkml:required true ; - linkml:slot_uri rdf:subject ; - linkml:usage_slot_name "subject" . - a linkml:SlotDefinition ; skos:definition "A list of terms from different schemas or terminology systems that have a narrower meaning. Such terms often describe a more specific concept from different ontological perspectives." ; skos:inScheme ; @@ -8658,11 +8674,11 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:definition "ti282a allele from ZFIN" ; - skos:example "ZFIN:ZDB-ALT-980203-1091" ], - [ a linkml:Example ; skos:definition "NM_007294.3(BRCA1):c.2521C>T (p.Arg841Trp)" ; - skos:example "CLINVAR:17681" ] ; + skos:example "CLINVAR:17681" ], + [ a linkml:Example ; + skos:definition "ti282a allele from ZFIN" ; + skos:example "ZFIN:ZDB-ALT-980203-1091" ] ; linkml:identifier true ; linkml:is_a ; linkml:is_usage_slot true ; @@ -10056,6 +10072,54 @@ linkml:slot_uri ; linkml:symmetric true . + a linkml:SlotDefinition ; + skos:definition "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + skos:exactMatch , + owl:annotatedTarget ; + skos:inScheme ; + skos:mappingRelation rdf:object ; + linkml:alias "object" ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:is_a ; + linkml:is_usage_slot true ; + linkml:local_names [ linkml:ga4gh [ skos:altLabel "descriptor" ; + linkml:local_name_source "ga4gh" ] ; + linkml:neo4j [ skos:altLabel "node with incoming relationship" ; + linkml:local_name_source "neo4j" ] ] ; + linkml:owner ; + linkml:range ; + linkml:required true ; + linkml:slot_uri rdf:object ; + linkml:usage_slot_name "object" . + + a linkml:SlotDefinition ; + skos:definition "gene in which variation is correlated with the phenotypic feature" ; + skos:exactMatch , + owl:annotatedSource ; + skos:inScheme ; + skos:mappingRelation rdf:subject ; + linkml:alias "subject" ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:examples [ a linkml:Example ; + skos:definition "COL1A1 (Human)" ; + skos:example "HGNC:2197" ] ; + linkml:inlined true ; + linkml:is_a ; + linkml:is_usage_slot true ; + linkml:local_names [ linkml:ga4gh [ skos:altLabel "annotation subject" ; + linkml:local_name_source "ga4gh" ] ; + linkml:neo4j [ skos:altLabel "node with outgoing relationship" ; + linkml:local_name_source "neo4j" ] ] ; + linkml:owner ; + linkml:range ; + linkml:required true ; + linkml:slot_uri rdf:subject ; + linkml:usage_slot_name "subject" . + a linkml:SlotDefinition ; skos:inScheme ; linkml:definition_uri ; @@ -10350,29 +10414,6 @@ linkml:slot_uri ; linkml:symmetric true . - a linkml:SlotDefinition ; - skos:definition "the status of the infores identifier, default is released" ; - skos:inScheme ; - linkml:definition_uri ; - linkml:domain ; - linkml:domain_of ; - linkml:is_a ; - linkml:owner ; - linkml:range ; - linkml:slot_uri . - - a linkml:SlotDefinition ; - skos:definition "a collection of information resources" ; - skos:inScheme ; - linkml:definition_uri ; - linkml:domain_of ; - linkml:inlined true ; - linkml:inlined_as_list true ; - linkml:multivalued true ; - linkml:owner ; - linkml:range ; - linkml:slot_uri . - a linkml:SlotDefinition ; skos:exactMatch ; skos:inScheme ; @@ -10412,6 +10453,26 @@ linkml:range ; linkml:slot_uri . + a linkml:SlotDefinition ; + skos:definition "The logarithm of the odds ratio, or the ratio of the odds of event Y occurring in an exposed group versus the odds of event Y occurring in a non-exposed group." ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:is_a ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + + a linkml:SlotDefinition ; + skos:definition "The ninety-five percent confidence range in which the true log odds ratio for the sample population falls." ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:is_a ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + a linkml:SlotDefinition ; skos:exactMatch ; skos:inScheme ; @@ -10636,6 +10697,7 @@ skos:inScheme ; skos:mappingRelation dcterms:type ; linkml:definition_uri ; + linkml:multivalued true ; linkml:range ; linkml:slot_uri dcterms:type ; linkml:values_from , @@ -10847,7 +10909,7 @@ linkml:is_a ; linkml:multivalued true ; linkml:owner ; - linkml:range ; + linkml:range ; linkml:slot_uri . a linkml:SlotDefinition ; @@ -10991,6 +11053,16 @@ linkml:typeof ; linkml:uri xsd:time . + a linkml:SlotDefinition ; + skos:definition "The total number of patients or participants within a sample population." ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:is_a ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + a linkml:SlotDefinition ; skos:definition "date on which an entity was updated. This can be applied to nodes or edges" ; skos:inScheme ; @@ -11169,15 +11241,6 @@ linkml:range ; linkml:slot_uri . - a linkml:ClassDefinition ; - skos:definition "A collection of information resources" ; - skos:inScheme ; - linkml:class_uri ; - linkml:definition_uri ; - linkml:slot_usage [ ] ; - linkml:slots ; - linkml:tree_root true . - a linkml:ClassDefinition ; OIO:inSubset ; skos:definition "A stage of development or growth of an organism, including post-natal adult stages" ; @@ -11840,6 +11903,18 @@ linkml:range ; linkml:slot_uri . + a linkml:SlotDefinition ; + skos:definition "The total number of instances (e.g., number of patients, number of rows, etc) in a dataset/cohort." ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:examples [ a linkml:Example ; + skos:example "100000" ] ; + linkml:is_a ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + a linkml:SlotDefinition ; owl:inverseOf ; skos:inScheme ; @@ -11888,11 +11963,11 @@ skos:inScheme ; skos:narrowMatch ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "increases response to" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -12050,11 +12125,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "prevents" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "prevents" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -12180,11 +12255,11 @@ skos:inScheme ; skos:mappingRelation ; linkml:annotations [ a linkml:Annotation ; - skos:example "is excipient of" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "is excipient of" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -12338,11 +12413,11 @@ skos:inScheme ; skos:narrowMatch ; linkml:annotations [ a linkml:Annotation ; - skos:example "has decreased amount" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "has decreased amount" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -13368,11 +13443,11 @@ skos:inScheme ; skos:narrowMatch ; linkml:annotations [ a linkml:Annotation ; - skos:example "predisposes" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "predisposes" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -13666,7 +13741,7 @@ linkml:is_a ; linkml:multivalued true ; linkml:owner ; - linkml:range ; + linkml:range ; linkml:slot_uri . a linkml:SlotDefinition ; @@ -14288,14 +14363,21 @@ , , , + , + , + , + , , + , , + , + , + , , , , , , - , , , , @@ -14305,53 +14387,12 @@ , , , - , , , , , , - , - , - , - , - , - . - - a linkml:ClassDefinition ; - skos:inScheme ; - linkml:class_uri ; - linkml:definition_uri ; - linkml:deprecated "True" ; - linkml:deprecated_element_has_exact_replacement ; - linkml:is_a ; - linkml:slot_usage [ ] ; - linkml:slots , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , + , , , , @@ -15115,11 +15156,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "exacerbates" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "exacerbates" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -15138,11 +15179,11 @@ linkml:definition_uri ; linkml:domain ; linkml:examples [ a linkml:Example ; - skos:example "stability" ], + skos:example "abundance" ], [ a linkml:Example ; skos:example "exposure" ], [ a linkml:Example ; - skos:example "abundance" ], + skos:example "stability" ], [ a linkml:Example ; skos:example "expression" ] ; linkml:is_a ; @@ -15250,11 +15291,11 @@ , ; linkml:annotations [ a linkml:Annotation ; - skos:example "prevents" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "prevents" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -15272,9 +15313,9 @@ linkml:definition_uri ; linkml:domain ; linkml:examples [ a linkml:Example ; - skos:example "cohort x (e.g. a specific population, referenced by an identifier)" ], + skos:example "gut microbiome" ], [ a linkml:Example ; - skos:example "gut microbiome" ] ; + skos:example "cohort x (e.g. a specific population, referenced by an identifier)" ] ; linkml:is_a ; linkml:owner ; linkml:range ; @@ -15401,15 +15442,15 @@ linkml:definition_uri ; linkml:domain ; linkml:examples [ a linkml:Example ; - skos:example "severe" ], + skos:example "chemical analog" ], [ a linkml:Example ; skos:example "mutation" ], [ a linkml:Example ; - skos:example "late stage" ], + skos:example "severe" ], [ a linkml:Example ; - skos:example "transplant" ], + skos:example "late stage" ], [ a linkml:Example ; - skos:example "chemical analog" ] ; + skos:example "transplant" ] ; linkml:is_a ; linkml:owner ; linkml:range ; @@ -15426,11 +15467,11 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:definition "kinase activity" ; - skos:example "GO:0016301" ], - [ a linkml:Example ; skos:definition "postsynaptic membrane" ; - skos:example "GO:0045211" ] ; + skos:example "GO:0045211" ], + [ a linkml:Example ; + skos:definition "kinase activity" ; + skos:example "GO:0016301" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:local_names [ linkml:ga4gh [ skos:altLabel "descriptor" ; @@ -15956,9 +15997,9 @@ linkml:definition_uri ; linkml:domain ; linkml:examples [ a linkml:Example ; - skos:example "polyA tail" ], + skos:example "upstream control region" ], [ a linkml:Example ; - skos:example "upstream control region" ] ; + skos:example "polyA tail" ] ; linkml:is_a ; linkml:owner ; linkml:range ; @@ -16534,6 +16575,51 @@ linkml:imported_from "linkml:types" ; linkml:uri xsd:double . + a linkml:SlotDefinition ; + skos:definition "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + skos:exactMatch , + owl:annotatedTarget ; + skos:inScheme ; + skos:mappingRelation rdf:object ; + linkml:alias "object" ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:is_a ; + linkml:is_usage_slot true ; + linkml:local_names [ linkml:ga4gh [ skos:altLabel "descriptor" ; + linkml:local_name_source "ga4gh" ] ; + linkml:neo4j [ skos:altLabel "node with incoming relationship" ; + linkml:local_name_source "neo4j" ] ] ; + linkml:owner ; + linkml:range ; + linkml:required true ; + linkml:slot_uri rdf:object ; + linkml:usage_slot_name "object" . + + a linkml:SlotDefinition ; + skos:definition "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model" ; + skos:exactMatch , + owl:annotatedSource ; + skos:inScheme ; + skos:mappingRelation rdf:subject ; + linkml:alias "subject" ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:inlined true ; + linkml:is_a ; + linkml:is_usage_slot true ; + linkml:local_names [ linkml:ga4gh [ skos:altLabel "annotation subject" ; + linkml:local_name_source "ga4gh" ] ; + linkml:neo4j [ skos:altLabel "node with outgoing relationship" ; + linkml:local_name_source "neo4j" ] ] ; + linkml:owner ; + linkml:range ; + linkml:required true ; + linkml:slot_uri rdf:subject ; + linkml:usage_slot_name "subject" . + a linkml:SlotDefinition ; OIO:inSubset ; skos:definition "" ; @@ -16915,29 +17001,6 @@ , . - a linkml:ClassDefinition ; - skos:definition "A collection of data items from a study that are about a particular study subject or experimental unit (the 'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation of this data as evidence." ; - skos:editorialNote "The data/metadata included in a Study Result object are typically a subset of data from a larger study data set, that are selected by a curator because they may be useful as evidence for deriving knowledge about a specific focus of the study. The notion of a 'study' here is defined broadly to include any research activity at any scale that is aimed at generating knowledge or hypotheses. This may include a single assay or computational analyses, or a larger scale clinical trial or experimental research investigation." ; - skos:inScheme ; - linkml:abstract true ; - linkml:class_uri ; - linkml:definition_uri ; - linkml:is_a ; - linkml:slot_usage [ ] ; - linkml:slots , - , - , - , - , - , - , - , - , - , - , - , - . - a linkml:SlotDefinition ; owl:inverseOf ; skos:exactMatch ; @@ -17291,23 +17354,121 @@ , . + a linkml:ClassDefinition ; + skos:inScheme ; + linkml:class_uri ; + linkml:defining_slots , + ; + linkml:definition_uri ; + linkml:is_a ; + linkml:mixins , + ; + linkml:slot_usage [ ] ; + linkml:slots , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + . + a linkml:ClassDefinition ; skos:definition "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect." ; skos:inScheme ; - linkml:class_uri ; + linkml:class_uri ; + linkml:defining_slots , + , + ; + linkml:definition_uri ; + linkml:is_a ; + linkml:mixins , + ; + linkml:slot_usage [ ] ; + linkml:slots , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + . + + a linkml:ClassDefinition ; + skos:definition "An interaction between a chemical entity and a biological process or pathway." ; + skos:exactMatch ; + skos:inScheme ; + linkml:class_uri ; linkml:defining_slots , - , ; - linkml:definition_uri ; + linkml:definition_uri ; linkml:is_a ; - linkml:mixins , - ; + linkml:mixins ; linkml:slot_usage [ ] ; - linkml:slots , - , + linkml:slots , , , - , + , + , , , , @@ -17316,7 +17477,6 @@ , , , - , , , , @@ -17325,11 +17485,11 @@ , , , + , , , , , - , , , , @@ -17337,25 +17497,32 @@ , . - a linkml:ClassDefinition ; - skos:definition "An interaction between a chemical entity and a biological process or pathway." ; - skos:exactMatch ; + a linkml:ClassDefinition ; skos:inScheme ; - linkml:class_uri ; + linkml:class_uri ; linkml:defining_slots , ; - linkml:definition_uri ; - linkml:is_a ; - linkml:mixins ; + linkml:definition_uri ; + linkml:is_a ; + linkml:mixins , + ; linkml:slot_usage [ ] ; linkml:slots , , , - , - , + , + , , + , + , + , + , , + , , + , + , + , , , , @@ -17366,14 +17533,16 @@ , , , + , , , , - , , , , , + , + , , , , @@ -17529,15 +17698,6 @@ , . - a linkml:ClassDefinition ; - skos:inScheme ; - linkml:class_uri ; - linkml:defining_slots ; - linkml:definition_uri ; - linkml:mixin true ; - linkml:slot_usage [ ] ; - linkml:slots . - a linkml:ClassDefinition ; skos:altLabel "functional association" ; skos:exactMatch ; @@ -17624,6 +17784,60 @@ , . + a linkml:ClassDefinition ; + skos:exactMatch ; + skos:inScheme ; + linkml:class_uri ; + linkml:defining_slots , + ; + linkml:definition_uri ; + linkml:is_a ; + linkml:mixins , + ; + linkml:slot_usage [ ] ; + linkml:slots , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + . + a linkml:ClassDefinition ; skos:definition "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ; skos:inScheme ; @@ -17859,6 +18073,29 @@ , . + a linkml:ClassDefinition ; + skos:definition "A collection of data items from a study that are about a particular study subject or experimental unit (the 'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation of this data as evidence." ; + skos:editorialNote "The data/metadata included in a Study Result object are typically a subset of data from a larger study data set, that are selected by a curator because they may be useful as evidence for deriving knowledge about a specific focus of the study. The notion of a 'study' here is defined broadly to include any research activity at any scale that is aimed at generating knowledge or hypotheses. This may include a single assay or computational analyses, or a larger scale clinical trial or experimental research investigation." ; + skos:inScheme ; + linkml:abstract true ; + linkml:class_uri ; + linkml:definition_uri ; + linkml:is_a ; + linkml:slot_usage [ ] ; + linkml:slots , + , + , + , + , + , + , + , + , + , + , + , + . + a linkml:ClassDefinition ; skos:inScheme ; linkml:class_uri ; @@ -17975,6 +18212,58 @@ linkml:range ; linkml:slot_uri . + a linkml:SlotDefinition ; + OIO:inSubset ; + skos:inScheme ; + linkml:alias "object direction qualifier" ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:is_a ; + linkml:is_usage_slot true ; + linkml:owner ; + linkml:range ; + linkml:slot_uri ; + linkml:usage_slot_name "object direction qualifier" . + + a linkml:SlotDefinition ; + rdfs:subPropertyOf ; + skos:definition "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + skos:editorialNote "Has a value from the Biolink related_to hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats" ; + skos:exactMatch , + owl:annotatedProperty ; + skos:inScheme ; + skos:mappingRelation rdf:predicate ; + linkml:alias "predicate" ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:is_a ; + linkml:is_usage_slot true ; + linkml:local_names [ linkml:ga4gh [ skos:altLabel "annotation predicate" ; + linkml:local_name_source "ga4gh" ] ; + linkml:translator [ skos:altLabel "predicate" ; + linkml:local_name_source "translator" ] ] ; + linkml:owner ; + linkml:range ; + linkml:required true ; + linkml:slot_uri rdf:predicate ; + linkml:usage_slot_name "predicate" . + + a linkml:SlotDefinition ; + OIO:inSubset ; + skos:inScheme ; + linkml:alias "subject aspect qualifier" ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:is_a ; + linkml:is_usage_slot true ; + linkml:owner ; + linkml:range ; + linkml:slot_uri ; + linkml:usage_slot_name "subject aspect qualifier" . + a linkml:SlotDefinition ; owl:inverseOf ; skos:inScheme ; @@ -18044,118 +18333,54 @@ linkml:range ; linkml:slot_uri . - a linkml:SlotDefinition ; - OIO:inSubset ; - skos:definition "stage during which gene or protein expression of takes place." ; - skos:inScheme ; - linkml:definition_uri ; - linkml:domain ; - linkml:domain_of , - ; - linkml:examples [ a linkml:Example ; - skos:definition "larval stage" ; - skos:example "UBERON:0000069" ] ; - linkml:is_a ; - linkml:owner ; - linkml:range ; - linkml:slot_uri . - - a linkml:ClassDefinition ; - skos:definition "an item that holds summary level information about a dataset." ; - skos:inScheme ; - linkml:class_uri ; - linkml:definition_uri ; - linkml:is_a ; - linkml:slot_usage [ ] ; - linkml:slots , - , - , - , - , - , - , - , - , - , - , - , - , - , - . - - a linkml:ClassDefinition ; - skos:definition "any grouping of multiple genes or gene products" ; - skos:inScheme ; - linkml:class_uri ; - linkml:definition_uri ; - linkml:mixin true ; - linkml:slot_usage [ ] ; - linkml:slots . - - a linkml:ClassDefinition ; - OIO:inSubset ; - skos:altLabel "endophenotype", - "phenotype", - "sign", - "symptom", - "trait" ; - skos:broadMatch , - ; - skos:definition "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment." ; - skos:exactMatch , - , - , - , - , - , - ; - skos:inScheme ; - skos:narrowMatch , - , - , - , - , - , - , - , - , - , - , - ; - linkml:class_uri ; - linkml:definition_uri ; + a linkml:SlotDefinition ; + OIO:inSubset ; + skos:definition "stage during which gene or protein expression of takes place." ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of , + ; linkml:examples [ a linkml:Example ; - skos:definition "decreased body weight" ; - skos:example "MP:0001262" ] ; - linkml:id_prefixes "APO", - "EFO", - "FBcv", - "FYPO", - "HP", - "MEDDRA", - "MESH", - "MP", - "NCIT", - "SNOMEDCT", - "TO", - "UMLS", - "UPHENO", - "WBPhenotype", - "XPO", - "ZP" ; - linkml:is_a ; + skos:definition "larval stage" ; + skos:example "UBERON:0000069" ] ; + linkml:is_a ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + + a linkml:ClassDefinition ; + skos:definition "an item that holds summary level information about a dataset." ; + skos:inScheme ; + linkml:class_uri ; + linkml:definition_uri ; + linkml:is_a ; linkml:slot_usage [ ] ; - linkml:slots , + linkml:slots , + , + , , , - , , + , , , , + , + , + , , . + a linkml:ClassDefinition ; + skos:definition "any grouping of multiple genes or gene products" ; + skos:inScheme ; + linkml:class_uri ; + linkml:definition_uri ; + linkml:mixin true ; + linkml:slot_usage [ ] ; + linkml:slots . + a linkml:ClassDefinition ; skos:definition "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value" ; skos:inScheme ; @@ -18298,7 +18523,7 @@ skos:example "cerebral cortext" ] ; linkml:is_a ; linkml:owner ; - linkml:range ; + linkml:range ; linkml:slot_uri . a linkml:SlotDefinition ; @@ -18355,15 +18580,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:slot_uri ; linkml:symmetric true . - a linkml:TypeDefinition ; - skos:definition "A real number that conforms to the xsd:float specification" ; - skos:exactMatch schema:Float ; - skos:inScheme linkml:types ; - linkml:base "float" ; - linkml:definition_uri linkml:Float ; - linkml:imported_from "linkml:types" ; - linkml:uri xsd:float . - a linkml:SlotDefinition ; skos:definition "connects an entity with one or more gene or gene products" ; skos:inScheme ; @@ -18415,11 +18631,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , ; linkml:annotations [ a linkml:Annotation ; - skos:example "lacks part" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "lacks part" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -18825,6 +19041,70 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , . + a linkml:ClassDefinition ; + OIO:inSubset ; + skos:altLabel "endophenotype", + "phenotype", + "sign", + "symptom", + "trait" ; + skos:broadMatch , + ; + skos:definition "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment." ; + skos:exactMatch , + , + , + , + , + , + ; + skos:inScheme ; + skos:narrowMatch , + , + , + , + , + , + , + , + , + , + , + ; + linkml:class_uri ; + linkml:definition_uri ; + linkml:examples [ a linkml:Example ; + skos:definition "decreased body weight" ; + skos:example "MP:0001262" ] ; + linkml:id_prefixes "APO", + "EFO", + "FBcv", + "FYPO", + "HP", + "MEDDRA", + "MESH", + "MP", + "NCIT", + "SNOMEDCT", + "TO", + "UMLS", + "UPHENO", + "WBPhenotype", + "XPO", + "ZP" ; + linkml:is_a ; + linkml:slot_usage [ ] ; + linkml:slots , + , + , + , + , + , + , + , + , + . + a linkml:ClassDefinition ; skos:definition "A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; genes, their products and other molecular entities; body parts; biological processes" ; skos:inScheme ; @@ -19001,6 +19281,7 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:domain_of ; linkml:is_a ; linkml:is_usage_slot true ; + linkml:multivalued true ; linkml:owner ; linkml:range ; linkml:required true ; @@ -19012,18 +19293,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , . - a linkml:SlotDefinition ; - OIO:inSubset ; - skos:definition "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - skos:inScheme ; - linkml:definition_uri ; - linkml:domain ; - linkml:domain_of ; - linkml:is_a ; - linkml:owner ; - linkml:range ; - linkml:slot_uri . - a linkml:SlotDefinition ; OIO:inSubset ; skos:inScheme ; @@ -19177,62 +19446,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:slot_usage [ ] ; linkml:slots . - a linkml:ClassDefinition ; - OIO:inSubset , - ; - skos:altLabel "condition", - "disorder", - "medical condition" ; - skos:definition "A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." ; - skos:exactMatch , - , - , - , - , - , - , - ; - skos:inScheme ; - skos:narrowMatch , - , - , - , - , - , - ; - linkml:class_uri ; - linkml:definition_uri ; - linkml:id_prefixes "DOID", - "EFO", - "HP", - "ICD10", - "ICD9", - "KEGG.DISEASE", - "MEDDRA", - "MESH", - "MONDO", - "MP", - "NCIT", - "OMIM", - "OMIM.PS", - "PHARMGKB.DISEASE", - "SNOMEDCT", - "UMLS", - "medgen", - "orphanet" ; - linkml:is_a ; - linkml:slot_usage [ ] ; - linkml:slots , - , - , - , - , - , - , - , - , - . - a linkml:ClassDefinition ; skos:inScheme ; linkml:class_uri ; @@ -19252,13 +19465,19 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , + , , + , + , + , + , , , , , , - , , , , @@ -19273,6 +19492,7 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , , , , @@ -19943,6 +20163,15 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:range ; linkml:slot_uri . + a linkml:TypeDefinition ; + skos:definition "A real number that conforms to the xsd:float specification" ; + skos:exactMatch schema:Float ; + skos:inScheme linkml:types ; + linkml:base "float" ; + linkml:definition_uri linkml:Float ; + linkml:imported_from "linkml:types" ; + linkml:uri xsd:float . + a linkml:SlotDefinition ; owl:inverseOf ; skos:inScheme ; @@ -20140,6 +20369,15 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , . + a linkml:ClassDefinition ; + skos:inScheme ; + linkml:class_uri ; + linkml:defining_slots ; + linkml:definition_uri ; + linkml:mixin true ; + linkml:slot_usage [ ] ; + linkml:slots . + a linkml:ClassDefinition ; skos:inScheme ; skos:note "TODO decide no how to model pathogenicity" ; @@ -20326,11 +20564,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , ; linkml:annotations [ a linkml:Annotation ; - skos:example "has input" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "has input" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:domain_of ; @@ -20338,19 +20576,8 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:is_a ; linkml:multivalued true ; linkml:owner ; - linkml:range ; - linkml:slot_uri . - - a linkml:SlotDefinition ; - skos:definition "equivalent to has quotient multiplied by 100" ; - skos:inScheme ; - linkml:definition_uri ; - linkml:domain ; - linkml:domain_of ; - linkml:is_a ; - linkml:owner ; - linkml:range ; - linkml:slot_uri . + linkml:range ; + linkml:slot_uri . a linkml:SlotDefinition ; skos:definition "keywords tagging a publication" ; @@ -20448,20 +20675,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , . - a linkml:ClassDefinition ; - skos:definition "mixin class for any association whose object (target node) is a disease" ; - skos:inScheme ; - linkml:class_uri ; - linkml:defining_slots ; - linkml:definition_uri ; - linkml:is_a ; - linkml:mixin true ; - linkml:slot_usage [ ] ; - linkml:slots , - , - , - . - a linkml:ClassDefinition ; skos:definition "Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs." ; skos:inScheme ; @@ -20487,11 +20700,18 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , , , , + , + , , + , , + , + , + , , , , @@ -20502,6 +20722,7 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , , , , @@ -20509,6 +20730,8 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , + , + , , , , @@ -20517,6 +20740,62 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , . + a linkml:ClassDefinition ; + skos:closeMatch ; + skos:exactMatch ; + skos:inScheme ; + skos:note "NCIT:R176 refers to the inverse relationship" ; + linkml:class_uri ; + linkml:defining_slots , + ; + linkml:definition_uri ; + linkml:is_a ; + linkml:mixins , + ; + linkml:slot_usage [ ] ; + linkml:slots , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + . + a linkml:ClassDefinition ; skos:definition "A union of gene locus, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this." ; skos:inScheme ; @@ -20583,11 +20862,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "has output" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:domain_of ; @@ -20692,24 +20971,61 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , . - a linkml:ClassDefinition ; + a linkml:ClassDefinition ; + OIO:inSubset , + ; + skos:altLabel "condition", + "disorder", + "medical condition" ; + skos:definition "A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." ; + skos:exactMatch , + , + , + , + , + , + , + ; skos:inScheme ; - linkml:class_uri ; - linkml:defining_slots ; - linkml:definition_uri ; - linkml:is_a ; - linkml:mixin true ; - linkml:mixins ; + skos:narrowMatch , + , + , + , + , + , + ; + linkml:class_uri ; + linkml:definition_uri ; + linkml:id_prefixes "DOID", + "EFO", + "HP", + "ICD10", + "ICD9", + "KEGG.DISEASE", + "MEDDRA", + "MESH", + "MONDO", + "MP", + "NCIT", + "OMIM", + "OMIM.PS", + "PHARMGKB.DISEASE", + "SNOMEDCT", + "UMLS", + "medgen", + "orphanet" ; + linkml:is_a ; linkml:slot_usage [ ] ; - linkml:slots , - , - , - , - , - , - , - , - . + linkml:slots , + , + , + , + , + , + , + , + , + . a linkml:ClassDefinition ; OIO:inSubset , @@ -20814,39 +21130,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:range ; linkml:slot_uri . - a linkml:SlotDefinition ; - skos:definition "number of things with a particular property" ; - skos:exactMatch ; - skos:inScheme ; - linkml:definition_uri ; - linkml:domain ; - linkml:domain_of ; - linkml:is_a ; - linkml:owner ; - linkml:range ; - linkml:slot_uri . - - a linkml:SlotDefinition ; - skos:inScheme ; - linkml:definition_uri ; - linkml:domain ; - linkml:domain_of ; - linkml:is_a ; - linkml:owner ; - linkml:range ; - linkml:slot_uri . - - a linkml:SlotDefinition ; - skos:definition "total number of things in a particular reference set" ; - skos:inScheme ; - linkml:definition_uri ; - linkml:domain ; - linkml:domain_of ; - linkml:is_a ; - linkml:owner ; - linkml:range ; - linkml:slot_uri . - a linkml:ClassDefinition ; OIO:inSubset ; skos:closeMatch ; @@ -20898,6 +21181,25 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , . + a linkml:ClassDefinition ; + skos:inScheme ; + linkml:class_uri ; + linkml:defining_slots ; + linkml:definition_uri ; + linkml:is_a ; + linkml:mixin true ; + linkml:mixins ; + linkml:slot_usage [ ] ; + linkml:slots , + , + , + , + , + , + , + , + . + a linkml:ClassDefinition ; skos:definition "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities" ; skos:exactMatch , @@ -21014,6 +21316,20 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , . + a linkml:ClassDefinition ; + skos:definition "mixin class for any association whose object (target node) is a disease" ; + skos:inScheme ; + linkml:class_uri ; + linkml:defining_slots ; + linkml:definition_uri ; + linkml:is_a ; + linkml:mixin true ; + linkml:slot_usage [ ] ; + linkml:slots , + , + , + . + a linkml:ClassDefinition ; skos:altLabel "molecular event", "molecular function", @@ -21132,49 +21448,24 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , , , - , - , - , - , - , - , - , - , - . - - a linkml:ClassDefinition ; - skos:definition "Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge." ; - skos:inScheme ; - linkml:class_uri ; - linkml:definition_uri ; - linkml:is_a ; - linkml:mixin true ; - linkml:slot_usage [ ] . - - a linkml:ClassDefinition ; - OIO:inSubset ; - skos:altLabel "knowledgebase" ; - skos:definition "A database or knowledgebase and its supporting ecosystem of interfaces and services that deliver content to consumers (e.g. web portals, APIs, query endpoints, streaming services, data downloads, etc.). A single Information Resource by this definition may span many different datasets or databases, and include many access endpoints and user interfaces. Information Resources include project-specific resources such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb." ; - skos:inScheme ; - linkml:class_uri ; - linkml:definition_uri ; - linkml:is_a ; - linkml:slot_usage [ ] ; - linkml:slots , - , - , - , - , - , - , - , - , - , - , - , - , - , - . + , + , + , + , + , + , + , + , + . + + a linkml:ClassDefinition ; + skos:definition "Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge." ; + skos:inScheme ; + linkml:class_uri ; + linkml:definition_uri ; + linkml:is_a ; + linkml:mixin true ; + linkml:slot_usage [ ] . a linkml:ClassDefinition ; skos:definition "" ; @@ -21289,6 +21580,18 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:range ; linkml:slot_uri . + a linkml:SlotDefinition ; + OIO:inSubset ; + skos:definition "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:is_a ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + a linkml:TypeDefinition ; skos:definition "a URI or a CURIE" ; skos:inScheme linkml:types ; @@ -21364,20 +21667,38 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t ; linkml:values_from . - a linkml:ClassDefinition ; - skos:definition "Root Biolink Model class for all things and informational relationships, real or imagined." ; + a linkml:SlotDefinition ; + skos:definition "equivalent to has quotient multiplied by 100" ; skos:inScheme ; - linkml:abstract true ; - linkml:class_uri ; - linkml:definition_uri ; - linkml:slot_usage [ ] ; - linkml:slots , - , - , - , - , - , - . + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:is_a ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + + a linkml:SlotDefinition ; + OIO:inSubset ; + skos:altLabel "alias" ; + skos:definition "Alternate human-readable names for a thing" ; + skos:inScheme ; + skos:narrowMatch , + , + , + skos:altLabel, + , + , + ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of , + ; + linkml:is_a ; + linkml:multivalued true ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . a linkml:ClassDefinition ; OIO:inSubset ; @@ -21394,63 +21715,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:slots , . - a linkml:ClassDefinition ; - skos:inScheme ; - skos:narrowMatch , - , - ; - skos:note "NCIT:R176 refers to the inverse relationship", - "for use in describing the affect that the loss of function of a gene can have on exacerbating or ameliorating a symptom/phenotype", - "if the relationship of the statement using this predicate is statistical in nature, please use `associated with likelihood` or one of its children." ; - linkml:class_uri ; - linkml:definition_uri ; - linkml:is_a ; - linkml:mixins , - ; - linkml:slot_usage [ ] ; - linkml:slots , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - . - a linkml:ClassDefinition ; skos:definition "A processual entity." ; skos:exactMatch ; @@ -21461,62 +21725,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:mixin true ; linkml:slot_usage [ ] . - a linkml:TypeDefinition ; - skos:definition "An integer" ; - skos:exactMatch schema:Integer ; - skos:inScheme linkml:types ; - linkml:base "int" ; - linkml:definition_uri linkml:Integer ; - linkml:imported_from "linkml:types" ; - linkml:uri xsd:integer . - - a linkml:SlotDefinition ; - OIO:inSubset ; - skos:definition "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; - skos:inScheme ; - linkml:definition_uri ; - linkml:domain ; - linkml:domain_of ; - linkml:is_a ; - linkml:owner ; - linkml:range ; - linkml:slot_uri . - - a linkml:SlotDefinition ; - OIO:inSubset ; - skos:definition "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; - skos:inScheme ; - linkml:definition_uri ; - linkml:domain ; - linkml:domain_of ; - linkml:is_a ; - linkml:owner ; - linkml:range ; - linkml:slot_uri . - - a linkml:SlotDefinition ; - OIO:inSubset ; - skos:altLabel "alias" ; - skos:definition "Alternate human-readable names for a thing" ; - skos:inScheme ; - skos:narrowMatch , - , - , - skos:altLabel, - , - , - ; - linkml:definition_uri ; - linkml:domain ; - linkml:domain_of , - , - ; - linkml:is_a ; - linkml:multivalued true ; - linkml:owner ; - linkml:range ; - linkml:slot_uri . - a linkml:ClassDefinition ; rdfs:seeAlso ; skos:definition "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; @@ -21613,30 +21821,135 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , . + a linkml:SlotDefinition ; + skos:definition "number of things with a particular property" ; + skos:exactMatch ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:is_a ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + + a linkml:SlotDefinition ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:is_a ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + + a linkml:SlotDefinition ; + skos:definition "total number of things in a particular reference set" ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:is_a ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + a linkml:ClassDefinition ; skos:definition "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system." ; skos:inScheme ; - linkml:class_uri ; - linkml:definition_uri ; - linkml:id_prefixes "GO", - "REACT" ; - linkml:is_a ; - linkml:mixins , - ; + linkml:class_uri ; + linkml:definition_uri ; + linkml:id_prefixes "GO", + "REACT" ; + linkml:is_a ; + linkml:mixins , + ; + linkml:slot_usage [ ] ; + linkml:slots , + , + , + , + , + , + , + , + , + , + , + , + . + + a linkml:ClassDefinition ; + skos:definition "Root Biolink Model class for all things and informational relationships, real or imagined." ; + skos:inScheme ; + linkml:abstract true ; + linkml:class_uri ; + linkml:definition_uri ; + linkml:slot_usage [ ] ; + linkml:slots , + , + , + , + , + , + . + + a linkml:ClassDefinition ; + skos:inScheme ; + skos:narrowMatch , + , + ; + skos:note "NCIT:R176 refers to the inverse relationship", + "for use in describing the affect that the loss of function of a gene can have on exacerbating or ameliorating a symptom/phenotype", + "if the relationship of the statement using this predicate is statistical in nature, please use `associated with likelihood` or one of its children." ; + linkml:class_uri ; + linkml:definition_uri ; + linkml:is_a ; + linkml:mixins , + ; linkml:slot_usage [ ] ; - linkml:slots , - , + linkml:slots , + , + , + , + , + , + , + , + , + , , - , - , + , + , + , + , + , , - , , + , , - , - , - , - . + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + . a linkml:ClassDefinition ; skos:definition "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." ; @@ -21674,24 +21987,14 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:range ; linkml:slot_uri . - a linkml:SlotDefinition ; - OIO:inSubset ; - skos:definition "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - skos:inScheme ; - linkml:definition_uri ; - linkml:domain ; - linkml:domain_of ; - linkml:is_a ; - linkml:owner ; - linkml:range ; - linkml:slot_uri . - a linkml:SlotDefinition ; skos:definition "A role is particular behaviour which a chemical entity may exhibit." ; skos:inScheme ; + skos:note "We expect primarily to use CHEBI chemical roles here; however, we are looking for a mapping between CHEBI And ATC codes to support this slot." ; linkml:definition_uri ; linkml:domain ; linkml:domain_of ; + linkml:id_prefixes "CHEBI" ; linkml:inherited true ; linkml:is_a ; linkml:multivalued true ; @@ -21699,6 +22002,15 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:range ; linkml:slot_uri . + a linkml:TypeDefinition ; + skos:definition "An integer" ; + skos:exactMatch schema:Integer ; + skos:inScheme linkml:types ; + linkml:base "int" ; + linkml:definition_uri linkml:Integer ; + linkml:imported_from "linkml:types" ; + linkml:uri xsd:integer . + a linkml:SlotDefinition ; skos:definition "" ; skos:inScheme ; @@ -21931,6 +22243,30 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , . + a linkml:SlotDefinition ; + OIO:inSubset ; + skos:definition "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:is_a ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + + a linkml:SlotDefinition ; + OIO:inSubset ; + skos:definition "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:is_a ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + a linkml:SlotDefinition ; skos:definition "connects a genomic feature to its sequence" ; skos:inScheme ; @@ -21948,6 +22284,18 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t skos:inScheme ; linkml:definition_uri . + a linkml:SlotDefinition ; + OIO:inSubset ; + skos:definition "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:domain_of ; + linkml:is_a ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + a linkml:ClassDefinition ; OIO:inSubset , ; @@ -22120,6 +22468,45 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:range ; linkml:slot_uri . + a linkml:ClassDefinition ; + skos:altLabel "information", + "information artefact", + "information entity" ; + skos:definition "a piece of information that typically describes some topic of discourse or is used as support." ; + skos:exactMatch ; + skos:inScheme ; + skos:narrowMatch , + , + , + , + , + , + , + , + , + , + , + ; + linkml:abstract true ; + linkml:class_uri ; + linkml:definition_uri ; + linkml:id_prefixes "doi" ; + linkml:is_a ; + linkml:slot_usage [ ] ; + linkml:slots , + , + , + , + , + , + , + , + , + , + , + , + . + a linkml:ClassDefinition ; skos:definition "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." ; skos:inScheme ; @@ -22210,45 +22597,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:slot_usage [ ] ; linkml:slots . - a linkml:ClassDefinition ; - skos:altLabel "information", - "information artefact", - "information entity" ; - skos:definition "a piece of information that typically describes some topic of discourse or is used as support." ; - skos:exactMatch ; - skos:inScheme ; - skos:narrowMatch , - , - , - , - , - , - , - , - , - , - , - ; - linkml:abstract true ; - linkml:class_uri ; - linkml:definition_uri ; - linkml:id_prefixes "doi" ; - linkml:is_a ; - linkml:slot_usage [ ] ; - linkml:slots , - , - , - , - , - , - , - , - , - , - , - , - . - a linkml:ClassDefinition ; skos:definition "A union of chemical entities and children, and gene or gene product. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities." ; skos:inScheme ; @@ -22369,11 +22717,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t skos:inScheme ; skos:note "This class is for modeling the specific state at a locus. A single DBSNP rs ID could correspond to more than one sequence variants (e.g CIViC:1252 and CIViC:1253, two distinct BRCA2 alleles for rs28897743)" ; linkml:alt_descriptions [ a linkml:AltDescription ; - skos:definition "A contiguous change at a Location" ; - linkml:source "VMC" ], - [ a linkml:AltDescription ; skos:definition "An entity that describes a single affected, endogenous allele. These can be of any type that matches that definition" ; - linkml:source "AGR" ] ; + linkml:source "AGR" ], + [ a linkml:AltDescription ; + skos:definition "A contiguous change at a Location" ; + linkml:source "VMC" ] ; linkml:class_uri ; linkml:definition_uri ; linkml:id_prefixes "AGRKB", @@ -22545,21 +22893,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:range ; linkml:slot_uri . - a linkml:SlotDefinition ; - skos:altLabel "edge property", - "edge qualifier", - "node qualifier", - "statement property", - "statement qualifier" ; - skos:definition "any slot that relates an association to another entity" ; - skos:inScheme ; - linkml:abstract true ; - linkml:definition_uri ; - linkml:domain ; - linkml:owner ; - linkml:range ; - linkml:slot_uri . - a linkml:SlotDefinition ; OIO:inSubset ; owl:inverseOf ; @@ -22586,6 +22919,21 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:range ; linkml:slot_uri . + a linkml:SlotDefinition ; + skos:altLabel "edge property", + "edge qualifier", + "node qualifier", + "statement property", + "statement qualifier" ; + skos:definition "any slot that relates an association to another entity" ; + skos:inScheme ; + linkml:abstract true ; + linkml:definition_uri ; + linkml:domain ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + a linkml:ClassDefinition ; skos:definition "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity, localization, processing, expression, etc.)" ; skos:inScheme ; @@ -22958,7 +23306,7 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:is_a ; linkml:multivalued true ; linkml:owner ; - linkml:range ; + linkml:range ; linkml:slot_uri . a linkml:SlotDefinition ; @@ -22970,7 +23318,7 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:domain_of ; linkml:is_a ; linkml:owner ; - linkml:range ; + linkml:range ; linkml:slot_uri . a linkml:SlotDefinition ; @@ -22995,7 +23343,7 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:domain_of ; linkml:is_a ; linkml:owner ; - linkml:range ; + linkml:range ; linkml:slot_uri . a linkml:SlotDefinition ; @@ -23048,11 +23396,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t ; linkml:is_a ; linkml:local_names [ a linkml:LocalName ; - skos:altLabel "predicate" ; - linkml:local_name_source "translator" ], - [ a linkml:LocalName ; skos:altLabel "annotation predicate" ; - linkml:local_name_source "ga4gh" ] ; + linkml:local_name_source "ga4gh" ], + [ a linkml:LocalName ; + skos:altLabel "predicate" ; + linkml:local_name_source "translator" ] ; linkml:owner ; linkml:range ; linkml:required true ; @@ -23109,7 +23457,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:domain ; linkml:domain_of , , - , , , ; @@ -23143,11 +23490,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:domain_of ; linkml:is_a ; linkml:local_names [ a linkml:LocalName ; - skos:altLabel "descriptor" ; - linkml:local_name_source "ga4gh" ], - [ a linkml:LocalName ; skos:altLabel "node with incoming relationship" ; - linkml:local_name_source "neo4j" ] ; + linkml:local_name_source "neo4j" ], + [ a linkml:LocalName ; + skos:altLabel "descriptor" ; + linkml:local_name_source "ga4gh" ] ; linkml:owner ; linkml:range ; linkml:required true ; @@ -23175,7 +23522,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:domain ; linkml:domain_of , , - , ; linkml:owner ; linkml:range ; @@ -23344,9 +23690,8 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t skos:mappingRelation dcterms:description ; skos:narrowMatch ; linkml:definition_uri ; - linkml:domain_of , - ; - linkml:owner ; + linkml:domain_of ; + linkml:owner ; linkml:range ; linkml:slot_uri dcterms:description . @@ -23373,10 +23718,9 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:definition_uri ; linkml:domain ; linkml:domain_of , - , ; linkml:identifier true ; - linkml:owner ; + linkml:owner ; linkml:range ; linkml:required true ; linkml:slot_uri . diff --git a/biolink-modeln.shex b/biolink-modeln.shex index cfef7af93a..f71d07616c 100644 --- a/biolink-modeln.shex +++ b/biolink-modeln.shex @@ -1,5 +1,5 @@ # metamodel_version: 1.7.0 -# version: 3.3.2 +# version: 3.4.0 BASE PREFIX rdf: PREFIX xsd: @@ -203,9 +203,9 @@ linkml:Nodeidentifier NONLITERAL @ * ; @ * ; @ * ; - @ ? ; - @ ? ; - @ * ; + @linkml:String ? ; + @linkml:String ? ; + @linkml:String * ; @ ? ; @linkml:String ? ; @linkml:Uriorcurie ? ; @@ -235,10 +235,9 @@ linkml:Nodeidentifier NONLITERAL @ OR @ OR @ OR @ OR @ OR @ OR @ OR @ OR - @ OR @ OR @ OR - @ OR @ OR @ OR - @ OR @ OR @ OR - @ OR @ OR @ OR + @ OR @ OR @ OR + @ OR @ OR @ OR @ + OR @ OR @ OR @ OR @ OR @ OR @ OR @ OR @ OR @ OR @@ -463,6 +462,20 @@ linkml:Nodeidentifier NONLITERAL ) } + CLOSED { + ( $ ( & ; + rdf:type [ ] ? ; + & ; + rdf:type [ ] ? ; + & ; + rdf:type [ ] ? ; + @ ; + @ + ) ; + rdf:type [ ] + ) +} + CLOSED { ( $ ( & ; rdf:type [ ] ? @@ -935,6 +948,20 @@ linkml:Nodeidentifier NONLITERAL ) } + CLOSED { + ( $ ( & ; + rdf:type [ ] ? ; + & ; + rdf:type [ ] ? ; + & ; + rdf:type [ ] ? ; + @ ; + @ + ) ; + rdf:type [ ] + ) +} + CLOSED { ( $ ( & ; rdf:type [ ] ? @@ -1169,10 +1196,7 @@ linkml:Nodeidentifier NONLITERAL rdf:type [ ] ? ; @ ; @ ; - @ * ; - @ ? ; - @ ? ; - @ ? + @ * ) ; rdf:type [ ] ) @@ -1481,10 +1505,7 @@ linkml:Nodeidentifier NONLITERAL rdf:type [ ] ? ; & ; rdf:type [ ] ? ; - @ ; - @ ? ; - @ ? ; - @ ? + @ ) ; rdf:type [ ] ) @@ -1563,39 +1584,47 @@ linkml:Nodeidentifier NONLITERAL ( CLOSED { - ( $ ( & ; - rdf:type [ ] ? + ( $ ( & ; + rdf:type [ ] ? ; + & ; + rdf:type [ ] ? ; + & ; + rdf:type [ ] ? ; + @ ; + @ ) ; rdf:type [ ] ) - } OR @ OR @ OR - @ + } OR @ OR @ OR @ OR + @ OR @ ) - CLOSED { - ( $ ( & ; - rdf:type [ ] ? ; - & ; - rdf:type [ ] ? ; - & ; - rdf:type [ ] ? ; - @ ? ; - @ ? ; - @ ; - @ ; - @ ; - @ ? ; - @ ? ; - @ ? ; - @ ? ; - @linkml:Integer ? ; - @linkml:Integer ? ; - @linkml:Double ? ; - @linkml:Double ? - ) ; - rdf:type [ ] - ) -} + ( + CLOSED { + ( $ ( & ; + rdf:type [ ] ? ; + & ; + rdf:type [ ] ? ; + & ; + rdf:type [ ] ? ; + @ ? ; + @ ? ; + @ ; + @ ; + @ ; + @ ? ; + @ ? ; + @ ? ; + @ ? ; + @linkml:Integer ? ; + @linkml:Integer ? ; + @linkml:Double ? ; + @linkml:Double ? + ) ; + rdf:type [ ] + ) + } OR @ OR @ +) { ( $ @ ; @@ -1701,8 +1730,14 @@ linkml:Nodeidentifier NONLITERAL } CLOSED { - ( $ ( & ; - rdf:type [ ] ? + ( $ ( & ; + rdf:type [ ] ? ; + & ; + rdf:type [ ] ? ; + & ; + rdf:type [ ] ? ; + @ ; + @ ) ; rdf:type [ ] ) @@ -1989,7 +2024,7 @@ linkml:Nodeidentifier NONLITERAL ( @ OR @ OR @ OR @ OR @ OR @ OR - @ OR @ OR @ OR @ OR @ OR @ + @ OR @ OR @ OR @ OR @ ) { @@ -2015,22 +2050,6 @@ linkml:Nodeidentifier NONLITERAL ) } - CLOSED { - ( $ ( & ; - rdf:type [ ] ? ; - @ ? ; - @ * - ) ; - rdf:type [ ] - ) -} - - CLOSED { - ( $ @ * ; - rdf:type [ ] ? - ) -} - CLOSED { ( $ ( & ; rdf:type [ ] ? @@ -2055,6 +2074,14 @@ linkml:Nodeidentifier NONLITERAL ) } + CLOSED { + ( $ ( & ; + rdf:type [ ] ? + ) ; + rdf:type [ ] + ) +} + CLOSED { ( $ ( & ; rdf:type [ ] ? ; @@ -2775,7 +2802,7 @@ linkml:Nodeidentifier NONLITERAL @linkml:String ? ; @linkml:String ? ; @ ? ; - @ ? ; + @linkml:String ? ; @ ? ; @ * ; @ * ; @@ -2870,7 +2897,7 @@ linkml:Nodeidentifier NONLITERAL @linkml:String * ; @linkml:Uriorcurie * ; @ ? ; - @linkml:String + @linkml:String + ) ; rdf:type [ ] ) @@ -3163,8 +3190,8 @@ linkml:Nodeidentifier NONLITERAL ) ( - @ OR @ OR @ OR - @ OR @ + @ OR @ OR @ OR + @ OR @ OR @ ) { diff --git a/biolink-modeln.shexj b/biolink-modeln.shexj index 6353464c42..f2016a10c0 100644 --- a/biolink-modeln.shexj +++ b/biolink-modeln.shexj @@ -1,5 +1,5 @@ # metamodel_version: 1.7.0 -# version: 3.3.2 +# version: 3.4.0 { "type": "Schema", "@context": [ @@ -868,21 +868,21 @@ { "type": "TripleConstraint", "predicate": "https://w3id.org/biolink/vocab/knowledge_source", - "valueExpr": "https://w3id.org/biolink/vocab/InformationResource", + "valueExpr": "https://w3id.org/linkml/String", "min": 0, "max": 1 }, { "type": "TripleConstraint", "predicate": "https://w3id.org/biolink/vocab/primary_knowledge_source", - "valueExpr": "https://w3id.org/biolink/vocab/InformationResource", + "valueExpr": "https://w3id.org/linkml/String", "min": 0, "max": 1 }, { "type": "TripleConstraint", "predicate": "https://w3id.org/biolink/vocab/aggregator_knowledge_source", - "valueExpr": "https://w3id.org/biolink/vocab/InformationResource", + "valueExpr": "https://w3id.org/linkml/String", "min": 0, "max": -1 }, @@ -1044,13 +1044,11 @@ "https://w3id.org/biolink/vocab/ExposureEventToOutcomeAssociation", "https://w3id.org/biolink/vocab/ExposureEventToPhenotypicFeatureAssociation", "https://w3id.org/biolink/vocab/FunctionalAssociation", - "https://w3id.org/biolink/vocab/GeneToDiseaseAssociation", "https://w3id.org/biolink/vocab/GeneToDiseaseOrPhenotypicFeatureAssociation", "https://w3id.org/biolink/vocab/GeneToExpressionSiteAssociation", "https://w3id.org/biolink/vocab/GeneToGeneAssociation", "https://w3id.org/biolink/vocab/GeneToGeneFamilyAssociation", "https://w3id.org/biolink/vocab/GeneToPathwayAssociation", - "https://w3id.org/biolink/vocab/GeneToPhenotypeAssociation", "https://w3id.org/biolink/vocab/GenotypeToDiseaseAssociation", "https://w3id.org/biolink/vocab/GenotypeToGeneAssociation", "https://w3id.org/biolink/vocab/GenotypeToGenotypePartAssociation", @@ -2193,6 +2191,83 @@ ] } }, + { + "type": "Shape", + "id": "https://w3id.org/biolink/vocab/CausalGeneToDiseaseAssociation", + "closed": true, + "expression": { + "type": "EachOf", + "expressions": [ + { + "type": "EachOf", + "id": "https://w3id.org/biolink/vocab/CausalGeneToDiseaseAssociation_tes", + "expressions": [ + "https://w3id.org/biolink/vocab/GeneToDiseaseAssociation_tes", + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/GeneToDiseaseAssociation" + ] + }, + "min": 0 + }, + "https://w3id.org/biolink/vocab/EntityToDiseaseAssociationMixin_tes", + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/EntityToDiseaseAssociationMixin" + ] + }, + "min": 0 + }, + "https://w3id.org/biolink/vocab/GeneToEntityAssociationMixin_tes", + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/GeneToEntityAssociationMixin" + ] + }, + "min": 0 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/subject", + "valueExpr": "https://w3id.org/biolink/vocab/GeneOrGeneProduct", + "min": 1, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/object", + "valueExpr": "https://w3id.org/biolink/vocab/Disease", + "min": 1, + "max": 1 + } + ] + }, + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/CausalGeneToDiseaseAssociation" + ] + }, + "min": 1 + } + ] + } + }, { "type": "Shape", "id": "https://w3id.org/biolink/vocab/Cell", @@ -4640,6 +4715,83 @@ ] } }, + { + "type": "Shape", + "id": "https://w3id.org/biolink/vocab/CorrelatedGeneToDiseaseAssociation", + "closed": true, + "expression": { + "type": "EachOf", + "expressions": [ + { + "type": "EachOf", + "id": "https://w3id.org/biolink/vocab/CorrelatedGeneToDiseaseAssociation_tes", + "expressions": [ + "https://w3id.org/biolink/vocab/GeneToDiseaseAssociation_tes", + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/GeneToDiseaseAssociation" + ] + }, + "min": 0 + }, + "https://w3id.org/biolink/vocab/EntityToDiseaseAssociationMixin_tes", + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/EntityToDiseaseAssociationMixin" + ] + }, + "min": 0 + }, + "https://w3id.org/biolink/vocab/GeneToEntityAssociationMixin_tes", + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/GeneToEntityAssociationMixin" + ] + }, + "min": 0 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/subject", + "valueExpr": "https://w3id.org/biolink/vocab/GeneOrGeneProduct", + "min": 1, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/object", + "valueExpr": "https://w3id.org/biolink/vocab/Disease", + "min": 1, + "max": 1 + } + ] + }, + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/CorrelatedGeneToDiseaseAssociation" + ] + }, + "min": 1 + } + ] + } + }, { "type": "Shape", "id": "https://w3id.org/biolink/vocab/Dataset", @@ -5875,27 +6027,6 @@ "valueExpr": "https://w3id.org/biolink/vocab/DruggableGeneCategoryEnum", "min": 0, "max": -1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/frequency_qualifier", - "valueExpr": "https://w3id.org/biolink/vocab/FrequencyValue", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/severity_qualifier", - "valueExpr": "https://w3id.org/biolink/vocab/SeverityValue", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/onset_qualifier", - "valueExpr": "https://w3id.org/biolink/vocab/Onset", - "min": 0, - "max": 1 } ] }, @@ -7479,27 +7610,6 @@ "valueExpr": "https://w3id.org/biolink/vocab/GeneOrGeneProduct", "min": 1, "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/frequency_qualifier", - "valueExpr": "https://w3id.org/biolink/vocab/FrequencyValue", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/severity_qualifier", - "valueExpr": "https://w3id.org/biolink/vocab/SeverityValue", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/onset_qualifier", - "valueExpr": "https://w3id.org/biolink/vocab/Onset", - "min": 0, - "max": 1 } ] }, @@ -7895,17 +8005,55 @@ "type": "EachOf", "id": "https://w3id.org/biolink/vocab/GeneToDiseaseAssociation_tes", "expressions": [ - "https://w3id.org/biolink/vocab/Association_tes", + "https://w3id.org/biolink/vocab/GeneToDiseaseOrPhenotypicFeatureAssociation_tes", { "type": "TripleConstraint", "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", "valueExpr": { "type": "NodeConstraint", "values": [ - "https://w3id.org/biolink/vocab/Association" + "https://w3id.org/biolink/vocab/GeneToDiseaseOrPhenotypicFeatureAssociation" + ] + }, + "min": 0 + }, + "https://w3id.org/biolink/vocab/EntityToDiseaseAssociationMixin_tes", + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/EntityToDiseaseAssociationMixin" ] }, "min": 0 + }, + "https://w3id.org/biolink/vocab/GeneToEntityAssociationMixin_tes", + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/GeneToEntityAssociationMixin" + ] + }, + "min": 0 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/subject", + "valueExpr": "https://w3id.org/biolink/vocab/GeneOrGeneProduct", + "min": 1, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/object", + "valueExpr": "https://w3id.org/biolink/vocab/Disease", + "min": 1, + "max": 1 } ] }, @@ -7923,164 +8071,173 @@ ] } }, + "https://w3id.org/biolink/vocab/CausalGeneToDiseaseAssociation", + "https://w3id.org/biolink/vocab/CorrelatedGeneToDiseaseAssociation", "https://w3id.org/biolink/vocab/DruggableGeneToDiseaseAssociation", "https://w3id.org/biolink/vocab/GeneAsAModelOfDiseaseAssociation", "https://w3id.org/biolink/vocab/GeneHasVariantThatContributesToDiseaseAssociation" ] }, { - "type": "Shape", + "type": "ShapeOr", "id": "https://w3id.org/biolink/vocab/GeneToDiseaseOrPhenotypicFeatureAssociation", - "closed": true, - "expression": { - "type": "EachOf", - "expressions": [ - { + "shapeExprs": [ + { + "type": "Shape", + "closed": true, + "expression": { "type": "EachOf", - "id": "https://w3id.org/biolink/vocab/GeneToDiseaseOrPhenotypicFeatureAssociation_tes", "expressions": [ - "https://w3id.org/biolink/vocab/Association_tes", - { - "type": "TripleConstraint", - "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", - "valueExpr": { - "type": "NodeConstraint", - "values": [ - "https://w3id.org/biolink/vocab/Association" - ] - }, - "min": 0 - }, - "https://w3id.org/biolink/vocab/EntityToPhenotypicFeatureAssociationMixin_tes", { - "type": "TripleConstraint", - "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", - "valueExpr": { - "type": "NodeConstraint", - "values": [ - "https://w3id.org/biolink/vocab/EntityToPhenotypicFeatureAssociationMixin" - ] - }, - "min": 0 + "type": "EachOf", + "id": "https://w3id.org/biolink/vocab/GeneToDiseaseOrPhenotypicFeatureAssociation_tes", + "expressions": [ + "https://w3id.org/biolink/vocab/Association_tes", + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/Association" + ] + }, + "min": 0 + }, + "https://w3id.org/biolink/vocab/EntityToPhenotypicFeatureAssociationMixin_tes", + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/EntityToPhenotypicFeatureAssociationMixin" + ] + }, + "min": 0 + }, + "https://w3id.org/biolink/vocab/GeneToEntityAssociationMixin_tes", + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/GeneToEntityAssociationMixin" + ] + }, + "min": 0 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/subject_aspect_qualifier", + "valueExpr": "https://w3id.org/biolink/vocab/GeneOrGeneProductOrChemicalEntityAspectEnum", + "min": 0, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/object_direction_qualifier", + "valueExpr": "https://w3id.org/biolink/vocab/DirectionQualifierEnum", + "min": 0, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/subject", + "valueExpr": "https://w3id.org/biolink/vocab/GeneOrGeneProduct", + "min": 1, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/object", + "valueExpr": "https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeature", + "min": 1, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/predicate", + "valueExpr": "https://w3id.org/biolink/vocab/PredicateType", + "min": 1, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/frequency_qualifier", + "valueExpr": "https://w3id.org/biolink/vocab/FrequencyValue", + "min": 0, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/severity_qualifier", + "valueExpr": "https://w3id.org/biolink/vocab/SeverityValue", + "min": 0, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/onset_qualifier", + "valueExpr": "https://w3id.org/biolink/vocab/Onset", + "min": 0, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/sex_qualifier", + "valueExpr": "https://w3id.org/biolink/vocab/BiologicalSex", + "min": 0, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/has_count", + "valueExpr": "https://w3id.org/linkml/Integer", + "min": 0, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/has_total", + "valueExpr": "https://w3id.org/linkml/Integer", + "min": 0, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/has_quotient", + "valueExpr": "https://w3id.org/linkml/Double", + "min": 0, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/has_percentage", + "valueExpr": "https://w3id.org/linkml/Double", + "min": 0, + "max": 1 + } + ] }, - "https://w3id.org/biolink/vocab/GeneToEntityAssociationMixin_tes", { "type": "TripleConstraint", "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", "valueExpr": { "type": "NodeConstraint", "values": [ - "https://w3id.org/biolink/vocab/GeneToEntityAssociationMixin" + "https://w3id.org/biolink/vocab/GeneToDiseaseOrPhenotypicFeatureAssociation" ] }, - "min": 0 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/subject_aspect_qualifier", - "valueExpr": "https://w3id.org/biolink/vocab/GeneOrGeneProductOrChemicalEntityAspectEnum", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/object_direction_qualifier", - "valueExpr": "https://w3id.org/biolink/vocab/DirectionQualifierEnum", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/subject", - "valueExpr": "https://w3id.org/biolink/vocab/GeneOrGeneProduct", - "min": 1, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/object", - "valueExpr": "https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeature", - "min": 1, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/predicate", - "valueExpr": "https://w3id.org/biolink/vocab/PredicateType", - "min": 1, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/frequency_qualifier", - "valueExpr": "https://w3id.org/biolink/vocab/FrequencyValue", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/severity_qualifier", - "valueExpr": "https://w3id.org/biolink/vocab/SeverityValue", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/onset_qualifier", - "valueExpr": "https://w3id.org/biolink/vocab/Onset", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/sex_qualifier", - "valueExpr": "https://w3id.org/biolink/vocab/BiologicalSex", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/has_count", - "valueExpr": "https://w3id.org/linkml/Integer", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/has_total", - "valueExpr": "https://w3id.org/linkml/Integer", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/has_quotient", - "valueExpr": "https://w3id.org/linkml/Double", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/has_percentage", - "valueExpr": "https://w3id.org/linkml/Double", - "min": 0, - "max": 1 + "min": 1 } ] - }, - { - "type": "TripleConstraint", - "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", - "valueExpr": { - "type": "NodeConstraint", - "values": [ - "https://w3id.org/biolink/vocab/GeneToDiseaseOrPhenotypicFeatureAssociation" - ] - }, - "min": 1 } - ] - } + }, + "https://w3id.org/biolink/vocab/GeneToDiseaseAssociation", + "https://w3id.org/biolink/vocab/GeneToPhenotypeAssociation" + ] }, { "type": "Shape", @@ -8642,17 +8799,55 @@ "type": "EachOf", "id": "https://w3id.org/biolink/vocab/GeneToPhenotypeAssociation_tes", "expressions": [ - "https://w3id.org/biolink/vocab/Association_tes", + "https://w3id.org/biolink/vocab/GeneToDiseaseOrPhenotypicFeatureAssociation_tes", { "type": "TripleConstraint", "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", "valueExpr": { "type": "NodeConstraint", "values": [ - "https://w3id.org/biolink/vocab/Association" + "https://w3id.org/biolink/vocab/GeneToDiseaseOrPhenotypicFeatureAssociation" ] }, "min": 0 + }, + "https://w3id.org/biolink/vocab/EntityToPhenotypicFeatureAssociationMixin_tes", + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/EntityToPhenotypicFeatureAssociationMixin" + ] + }, + "min": 0 + }, + "https://w3id.org/biolink/vocab/GeneToEntityAssociationMixin_tes", + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": { + "type": "NodeConstraint", + "values": [ + "https://w3id.org/biolink/vocab/GeneToEntityAssociationMixin" + ] + }, + "min": 0 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/subject", + "valueExpr": "https://w3id.org/biolink/vocab/GeneOrGeneProduct", + "min": 1, + "max": 1 + }, + { + "type": "TripleConstraint", + "predicate": "https://w3id.org/biolink/vocab/object", + "valueExpr": "https://w3id.org/biolink/vocab/PhenotypicFeature", + "min": 1, + "max": 1 } ] }, @@ -10179,7 +10374,6 @@ "https://w3id.org/biolink/vocab/DatasetSummary", "https://w3id.org/biolink/vocab/DatasetVersion", "https://w3id.org/biolink/vocab/EvidenceType", - "https://w3id.org/biolink/vocab/InformationResource", "https://w3id.org/biolink/vocab/Publication", "https://w3id.org/biolink/vocab/RetrievalSource", "https://w3id.org/biolink/vocab/StudyResult", @@ -10315,40 +10509,26 @@ }, { "type": "Shape", - "id": "https://w3id.org/biolink/vocab/InformationResource", + "id": "https://w3id.org/biolink/vocab/Invertebrate", "closed": true, "expression": { "type": "EachOf", "expressions": [ { "type": "EachOf", - "id": "https://w3id.org/biolink/vocab/InformationResource_tes", + "id": "https://w3id.org/biolink/vocab/Invertebrate_tes", "expressions": [ - "https://w3id.org/biolink/vocab/InformationContentEntity_tes", + "https://w3id.org/biolink/vocab/CellularOrganism_tes", { "type": "TripleConstraint", "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", "valueExpr": { "type": "NodeConstraint", "values": [ - "https://w3id.org/biolink/vocab/InformationContentEntity" + "https://w3id.org/biolink/vocab/CellularOrganism" ] }, "min": 0 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/information_resource_status", - "valueExpr": "https://w3id.org/biolink/vocab/InformationResourceStatusEnum", - "min": 0, - "max": 1 - }, - { - "type": "TripleConstraint", - "predicate": "https://w3id.org/biolink/vocab/synonym", - "valueExpr": "https://w3id.org/biolink/vocab/LabelType", - "min": 0, - "max": -1 } ] }, @@ -10358,7 +10538,7 @@ "valueExpr": { "type": "NodeConstraint", "values": [ - "https://w3id.org/biolink/vocab/InformationResource" + "https://w3id.org/biolink/vocab/Invertebrate" ] }, "min": 1 @@ -10368,52 +10548,23 @@ }, { "type": "Shape", - "id": "https://w3id.org/biolink/vocab/InformationResourceCollection", - "closed": true, - "expression": { - "type": "EachOf", - "expressions": [ - { - "type": "TripleConstraint", - "id": "https://w3id.org/biolink/vocab/InformationResourceCollection_tes", - "predicate": "https://w3id.org/biolink/vocab/information_resources", - "valueExpr": "https://w3id.org/biolink/vocab/InformationResource", - "min": 0, - "max": -1 - }, - { - "type": "TripleConstraint", - "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", - "valueExpr": { - "type": "NodeConstraint", - "values": [ - "https://w3id.org/biolink/vocab/InformationResourceCollection" - ] - }, - "min": 0 - } - ] - } - }, - { - "type": "Shape", - "id": "https://w3id.org/biolink/vocab/Invertebrate", + "id": "https://w3id.org/biolink/vocab/JournalArticle", "closed": true, "expression": { "type": "EachOf", "expressions": [ { "type": "EachOf", - "id": "https://w3id.org/biolink/vocab/Invertebrate_tes", + "id": "https://w3id.org/biolink/vocab/JournalArticle_tes", "expressions": [ - "https://w3id.org/biolink/vocab/CellularOrganism_tes", + "https://w3id.org/biolink/vocab/Article_tes", { "type": "TripleConstraint", "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", "valueExpr": { "type": "NodeConstraint", "values": [ - "https://w3id.org/biolink/vocab/CellularOrganism" + "https://w3id.org/biolink/vocab/Article" ] }, "min": 0 @@ -10426,7 +10577,7 @@ "valueExpr": { "type": "NodeConstraint", "values": [ - "https://w3id.org/biolink/vocab/Invertebrate" + "https://w3id.org/biolink/vocab/JournalArticle" ] }, "min": 1 @@ -10436,23 +10587,23 @@ }, { "type": "Shape", - "id": "https://w3id.org/biolink/vocab/JournalArticle", + "id": "https://w3id.org/biolink/vocab/LifeStage", "closed": true, "expression": { "type": "EachOf", "expressions": [ { "type": "EachOf", - "id": "https://w3id.org/biolink/vocab/JournalArticle_tes", + "id": "https://w3id.org/biolink/vocab/LifeStage_tes", "expressions": [ - "https://w3id.org/biolink/vocab/Article_tes", + "https://w3id.org/biolink/vocab/OrganismalEntity_tes", { "type": "TripleConstraint", "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", "valueExpr": { "type": "NodeConstraint", "values": [ - "https://w3id.org/biolink/vocab/Article" + "https://w3id.org/biolink/vocab/OrganismalEntity" ] }, "min": 0 @@ -10465,7 +10616,7 @@ "valueExpr": { "type": "NodeConstraint", "values": [ - "https://w3id.org/biolink/vocab/JournalArticle" + "https://w3id.org/biolink/vocab/LifeStage" ] }, "min": 1 @@ -10475,23 +10626,23 @@ }, { "type": "Shape", - "id": "https://w3id.org/biolink/vocab/LifeStage", + "id": "https://w3id.org/biolink/vocab/LogOddsAnalysisResult", "closed": true, "expression": { "type": "EachOf", "expressions": [ { "type": "EachOf", - "id": "https://w3id.org/biolink/vocab/LifeStage_tes", + "id": "https://w3id.org/biolink/vocab/LogOddsAnalysisResult_tes", "expressions": [ - "https://w3id.org/biolink/vocab/OrganismalEntity_tes", + "https://w3id.org/biolink/vocab/StudyResult_tes", { "type": "TripleConstraint", "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", "valueExpr": { "type": "NodeConstraint", "values": [ - "https://w3id.org/biolink/vocab/OrganismalEntity" + "https://w3id.org/biolink/vocab/StudyResult" ] }, "min": 0 @@ -10504,7 +10655,7 @@ "valueExpr": { "type": "NodeConstraint", "values": [ - "https://w3id.org/biolink/vocab/LifeStage" + "https://w3id.org/biolink/vocab/LogOddsAnalysisResult" ] }, "min": 1 @@ -14177,7 +14328,7 @@ { "type": "TripleConstraint", "predicate": "https://w3id.org/biolink/vocab/anatomical_context_qualifier", - "valueExpr": "https://w3id.org/biolink/vocab/AnatomicalContextQualifierEnum", + "valueExpr": "https://w3id.org/linkml/String", "min": 0, "max": 1 }, @@ -14682,7 +14833,7 @@ "predicate": "https://w3id.org/biolink/vocab/publication_type", "valueExpr": "https://w3id.org/linkml/String", "min": 1, - "max": 1 + "max": -1 } ] }, @@ -16150,6 +16301,7 @@ "shapeExprs": [ "https://w3id.org/biolink/vocab/ChiSquaredAnalysisResult", "https://w3id.org/biolink/vocab/ConceptCountAnalysisResult", + "https://w3id.org/biolink/vocab/LogOddsAnalysisResult", "https://w3id.org/biolink/vocab/ObservedExpectedFrequencyAnalysisResult", "https://w3id.org/biolink/vocab/RelativeFrequencyAnalysisResult", "https://w3id.org/biolink/vocab/TextMiningResult" diff --git a/biolink/model.py b/biolink/model.py index df02f071c6..34482ca22f 100644 --- a/biolink/model.py +++ b/biolink/model.py @@ -1,5 +1,5 @@ # Auto generated from biolink-model.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-05-04T23:02:03 +# Generation date: 2023-05-23T23:05:19 # Schema: Biolink-Model # # id: https://w3id.org/biolink/biolink-model @@ -7,7 +7,6 @@ # license: https://creativecommons.org/publicdomain/zero/1.0/ import dataclasses -import sys import re from jsonasobj2 import JsonObj, as_dict from typing import Optional, List, Union, Dict, ClassVar, Any @@ -490,6 +489,10 @@ class ChiSquaredAnalysisResultId(StudyResultId): pass +class LogOddsAnalysisResultId(StudyResultId): + pass + + class DatasetId(InformationContentEntityId): pass @@ -514,10 +517,6 @@ class EvidenceTypeId(InformationContentEntityId): pass -class InformationResourceId(InformationContentEntityId): - pass - - class PublicationId(InformationContentEntityId): pass @@ -1190,11 +1189,19 @@ class GeneToDiseaseOrPhenotypicFeatureAssociationId(AssociationId): pass -class GeneToDiseaseAssociationId(AssociationId): +class GeneToPhenotypeAssociationId(GeneToDiseaseOrPhenotypicFeatureAssociationId): pass -class GeneToPhenotypeAssociationId(AssociationId): +class GeneToDiseaseAssociationId(GeneToDiseaseOrPhenotypicFeatureAssociationId): + pass + + +class CausalGeneToDiseaseAssociationId(GeneToDiseaseAssociationId): + pass + + +class CorrelatedGeneToDiseaseAssociationId(GeneToDiseaseAssociationId): pass @@ -1413,7 +1420,7 @@ class PredicateMapping(YAMLRoot): object_derivative_qualifier: Optional[str] = None object_context_qualifier: Optional[str] = None causal_mechanism_qualifier: Optional[Union[str, "CausalMechanismQualifierEnum"]] = None - anatomical_context_qualifier: Optional[Union[str, "AnatomicalContextQualifierEnum"]] = None + anatomical_context_qualifier: Optional[str] = None species_context_qualifier: Optional[Union[str, OrganismTaxonId]] = None exact_match: Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]] = empty_list() narrow_match: Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]] = empty_list() @@ -1470,8 +1477,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.causal_mechanism_qualifier is not None and not isinstance(self.causal_mechanism_qualifier, CausalMechanismQualifierEnum): self.causal_mechanism_qualifier = CausalMechanismQualifierEnum(self.causal_mechanism_qualifier) - if self.anatomical_context_qualifier is not None and not isinstance(self.anatomical_context_qualifier, AnatomicalContextQualifierEnum): - self.anatomical_context_qualifier = AnatomicalContextQualifierEnum(self.anatomical_context_qualifier) + if self.anatomical_context_qualifier is not None and not isinstance(self.anatomical_context_qualifier, str): + self.anatomical_context_qualifier = str(self.anatomical_context_qualifier) if self.species_context_qualifier is not None and not isinstance(self.species_context_qualifier, OrganismTaxonId): self.species_context_qualifier = OrganismTaxonId(self.species_context_qualifier) @@ -2265,6 +2272,30 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) +@dataclass +class LogOddsAnalysisResult(StudyResult): + """ + A result of a log odds ratio analysis. + """ + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = BIOLINK.LogOddsAnalysisResult + class_class_curie: ClassVar[str] = "biolink:LogOddsAnalysisResult" + class_name: ClassVar[str] = "log odds analysis result" + class_model_uri: ClassVar[URIRef] = BIOLINK.LogOddsAnalysisResult + + id: Union[str, LogOddsAnalysisResultId] = None + category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self._is_empty(self.id): + self.MissingRequiredField("id") + if not isinstance(self.id, LogOddsAnalysisResultId): + self.id = LogOddsAnalysisResultId(self.id) + + super().__post_init__(**kwargs) + + @dataclass class Dataset(InformationContentEntity): """ @@ -2433,76 +2464,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass -class InformationResource(InformationContentEntity): - """ - A database or knowledgebase and its supporting ecosystem of interfaces and services that deliver content to - consumers (e.g. web portals, APIs, query endpoints, streaming services, data downloads, etc.). A single - Information Resource by this definition may span many different datasets or databases, and include many access - endpoints and user interfaces. Information Resources include project-specific resources such as a Translator - Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb. - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BIOLINK.InformationResource - class_class_curie: ClassVar[str] = "biolink:InformationResource" - class_name: ClassVar[str] = "information resource" - class_model_uri: ClassVar[URIRef] = BIOLINK.InformationResource - - id: Union[str, InformationResourceId] = None - category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None - information_resource_status: Optional[Union[str, "InformationResourceStatusEnum"]] = None - name: Optional[Union[str, LabelType]] = None - xref: Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]] = empty_list() - synonym: Optional[Union[Union[str, LabelType], List[Union[str, LabelType]]]] = empty_list() - description: Optional[Union[str, NarrativeText]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, InformationResourceId): - self.id = InformationResourceId(self.id) - - if self.information_resource_status is not None and not isinstance(self.information_resource_status, InformationResourceStatusEnum): - self.information_resource_status = InformationResourceStatusEnum(self.information_resource_status) - - if self.name is not None and not isinstance(self.name, LabelType): - self.name = LabelType(self.name) - - if not isinstance(self.xref, list): - self.xref = [self.xref] if self.xref is not None else [] - self.xref = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.xref] - - if not isinstance(self.synonym, list): - self.synonym = [self.synonym] if self.synonym is not None else [] - self.synonym = [v if isinstance(v, LabelType) else LabelType(v) for v in self.synonym] - - if self.description is not None and not isinstance(self.description, NarrativeText): - self.description = NarrativeText(self.description) - - super().__post_init__(**kwargs) - - -@dataclass -class InformationResourceCollection(YAMLRoot): - """ - A collection of information resources - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BIOLINK.InformationResourceCollection - class_class_curie: ClassVar[str] = "biolink:InformationResourceCollection" - class_name: ClassVar[str] = "InformationResourceCollection" - class_model_uri: ClassVar[URIRef] = BIOLINK.InformationResourceCollection - - information_resources: Optional[Union[Dict[Union[str, InformationResourceId], Union[dict, InformationResource]], List[Union[dict, InformationResource]]]] = empty_dict() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - self._normalize_inlined_as_list(slot_name="information_resources", slot_type=InformationResource, key_name="id", keyed=True) - - super().__post_init__(**kwargs) - - @dataclass class Publication(InformationContentEntity): """ @@ -2521,7 +2482,7 @@ class Publication(InformationContentEntity): id: Union[str, PublicationId] = None category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None - publication_type: str = None + publication_type: Union[str, List[str]] = None authors: Optional[Union[Union[str, AgentId], List[Union[str, AgentId]]]] = empty_list() pages: Optional[Union[str, List[str]]] = empty_list() summary: Optional[str] = None @@ -2538,8 +2499,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.publication_type): self.MissingRequiredField("publication_type") - if not isinstance(self.publication_type, str): - self.publication_type = str(self.publication_type) + if not isinstance(self.publication_type, list): + self.publication_type = [self.publication_type] if self.publication_type is not None else [] + self.publication_type = [v if isinstance(v, str) else str(v) for v in self.publication_type] if not isinstance(self.authors, list): self.authors = [self.authors] if self.authors is not None else [] @@ -2584,7 +2546,7 @@ class Book(Publication): id: Union[str, BookId] = None category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None - publication_type: str = None + publication_type: Union[str, List[str]] = None type: Optional[Union[str, List[str]]] = empty_list() def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -2611,7 +2573,7 @@ class BookChapter(Publication): id: Union[str, BookChapterId] = None category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None - publication_type: str = None + publication_type: Union[str, List[str]] = None published_in: Union[str, URIorCURIE] = None volume: Optional[str] = None chapter: Optional[str] = None @@ -2650,7 +2612,7 @@ class Serial(Publication): id: Union[str, SerialId] = None category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None - publication_type: str = None + publication_type: Union[str, List[str]] = None iso_abbreviation: Optional[str] = None volume: Optional[str] = None issue: Optional[str] = None @@ -2692,7 +2654,7 @@ class Article(Publication): id: Union[str, ArticleId] = None category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None - publication_type: str = None + publication_type: Union[str, List[str]] = None published_in: Union[str, URIorCURIE] = None iso_abbreviation: Optional[str] = None volume: Optional[str] = None @@ -2735,7 +2697,7 @@ class JournalArticle(Article): id: Union[str, JournalArticleId] = None category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None - publication_type: str = None + publication_type: Union[str, List[str]] = None published_in: Union[str, URIorCURIE] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -2762,7 +2724,7 @@ class Patent(Publication): id: Union[str, PatentId] = None category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None - publication_type: str = None + publication_type: Union[str, List[str]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -2788,7 +2750,7 @@ class WebPage(Publication): id: Union[str, WebPageId] = None category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None - publication_type: str = None + publication_type: Union[str, List[str]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -2814,7 +2776,7 @@ class PreprintPublication(Publication): id: Union[str, PreprintPublicationId] = None category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None - publication_type: str = None + publication_type: Union[str, List[str]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -2841,7 +2803,7 @@ class DrugLabel(Publication): id: Union[str, DrugLabelId] = None category: Union[Union[str, CategoryType], List[Union[str, CategoryType]]] = None - publication_type: str = None + publication_type: Union[str, List[str]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -6411,9 +6373,9 @@ class Association(Entity): qualifiers: Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]] = empty_list() publications: Optional[Union[Union[str, PublicationId], List[Union[str, PublicationId]]]] = empty_list() has_evidence: Optional[Union[Union[str, EvidenceTypeId], List[Union[str, EvidenceTypeId]]]] = empty_list() - knowledge_source: Optional[Union[str, InformationResourceId]] = None - primary_knowledge_source: Optional[Union[str, InformationResourceId]] = None - aggregator_knowledge_source: Optional[Union[Union[str, InformationResourceId], List[Union[str, InformationResourceId]]]] = empty_list() + knowledge_source: Optional[str] = None + primary_knowledge_source: Optional[str] = None + aggregator_knowledge_source: Optional[Union[str, List[str]]] = empty_list() timepoint: Optional[Union[str, TimeType]] = None original_subject: Optional[str] = None original_predicate: Optional[Union[str, URIorCURIE]] = None @@ -6468,15 +6430,15 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.has_evidence = [self.has_evidence] if self.has_evidence is not None else [] self.has_evidence = [v if isinstance(v, EvidenceTypeId) else EvidenceTypeId(v) for v in self.has_evidence] - if self.knowledge_source is not None and not isinstance(self.knowledge_source, InformationResourceId): - self.knowledge_source = InformationResourceId(self.knowledge_source) + if self.knowledge_source is not None and not isinstance(self.knowledge_source, str): + self.knowledge_source = str(self.knowledge_source) - if self.primary_knowledge_source is not None and not isinstance(self.primary_knowledge_source, InformationResourceId): - self.primary_knowledge_source = InformationResourceId(self.primary_knowledge_source) + if self.primary_knowledge_source is not None and not isinstance(self.primary_knowledge_source, str): + self.primary_knowledge_source = str(self.primary_knowledge_source) if not isinstance(self.aggregator_knowledge_source, list): self.aggregator_knowledge_source = [self.aggregator_knowledge_source] if self.aggregator_knowledge_source is not None else [] - self.aggregator_knowledge_source = [v if isinstance(v, InformationResourceId) else InformationResourceId(v) for v in self.aggregator_knowledge_source] + self.aggregator_knowledge_source = [v if isinstance(v, str) else str(v) for v in self.aggregator_knowledge_source] if self.timepoint is not None and not isinstance(self.timepoint, TimeType): self.timepoint = TimeType(self.timepoint) @@ -8570,7 +8532,44 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @dataclass -class GeneToDiseaseAssociation(Association): +class GeneToPhenotypeAssociation(GeneToDiseaseOrPhenotypicFeatureAssociation): + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = BIOLINK.GeneToPhenotypeAssociation + class_class_curie: ClassVar[str] = "biolink:GeneToPhenotypeAssociation" + class_name: ClassVar[str] = "gene to phenotype association" + class_model_uri: ClassVar[URIRef] = BIOLINK.GeneToPhenotypeAssociation + + id: Union[str, GeneToPhenotypeAssociationId] = None + predicate: Union[str, PredicateType] = None + subject: Union[dict, GeneOrGeneProduct] = None + object: Union[str, PhenotypicFeatureId] = None + sex_qualifier: Optional[Union[str, BiologicalSexId]] = None + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self._is_empty(self.id): + self.MissingRequiredField("id") + if not isinstance(self.id, GeneToPhenotypeAssociationId): + self.id = GeneToPhenotypeAssociationId(self.id) + + if self._is_empty(self.subject): + self.MissingRequiredField("subject") + if not isinstance(self.subject, GeneOrGeneProduct): + self.subject = GeneOrGeneProduct(**as_dict(self.subject)) + + if self._is_empty(self.object): + self.MissingRequiredField("object") + if not isinstance(self.object, PhenotypicFeatureId): + self.object = PhenotypicFeatureId(self.object) + + if self.sex_qualifier is not None and not isinstance(self.sex_qualifier, BiologicalSexId): + self.sex_qualifier = BiologicalSexId(self.sex_qualifier) + + super().__post_init__(**kwargs) + + +@dataclass +class GeneToDiseaseAssociation(GeneToDiseaseOrPhenotypicFeatureAssociation): _inherited_slots: ClassVar[List[str]] = [] class_class_uri: ClassVar[URIRef] = BIOLINK.GeneToDiseaseAssociation @@ -8579,9 +8578,9 @@ class GeneToDiseaseAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.GeneToDiseaseAssociation id: Union[str, GeneToDiseaseAssociationId] = None - subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None - object: Union[str, NamedThingId] = None + subject: Union[dict, GeneOrGeneProduct] = None + object: Union[str, DiseaseId] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8589,28 +8588,81 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if not isinstance(self.id, GeneToDiseaseAssociationId): self.id = GeneToDiseaseAssociationId(self.id) + if self._is_empty(self.subject): + self.MissingRequiredField("subject") + if not isinstance(self.subject, GeneOrGeneProduct): + self.subject = GeneOrGeneProduct(**as_dict(self.subject)) + + if self._is_empty(self.object): + self.MissingRequiredField("object") + if not isinstance(self.object, DiseaseId): + self.object = DiseaseId(self.object) + super().__post_init__(**kwargs) @dataclass -class GeneToPhenotypeAssociation(Association): +class CausalGeneToDiseaseAssociation(GeneToDiseaseAssociation): _inherited_slots: ClassVar[List[str]] = [] - class_class_uri: ClassVar[URIRef] = BIOLINK.GeneToPhenotypeAssociation - class_class_curie: ClassVar[str] = "biolink:GeneToPhenotypeAssociation" - class_name: ClassVar[str] = "gene to phenotype association" - class_model_uri: ClassVar[URIRef] = BIOLINK.GeneToPhenotypeAssociation + class_class_uri: ClassVar[URIRef] = BIOLINK.CausalGeneToDiseaseAssociation + class_class_curie: ClassVar[str] = "biolink:CausalGeneToDiseaseAssociation" + class_name: ClassVar[str] = "causal gene to disease association" + class_model_uri: ClassVar[URIRef] = BIOLINK.CausalGeneToDiseaseAssociation - id: Union[str, GeneToPhenotypeAssociationId] = None - subject: Union[str, NamedThingId] = None + id: Union[str, CausalGeneToDiseaseAssociationId] = None predicate: Union[str, PredicateType] = None - object: Union[str, NamedThingId] = None + subject: Union[dict, GeneOrGeneProduct] = None + object: Union[str, DiseaseId] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): self.MissingRequiredField("id") - if not isinstance(self.id, GeneToPhenotypeAssociationId): - self.id = GeneToPhenotypeAssociationId(self.id) + if not isinstance(self.id, CausalGeneToDiseaseAssociationId): + self.id = CausalGeneToDiseaseAssociationId(self.id) + + if self._is_empty(self.subject): + self.MissingRequiredField("subject") + if not isinstance(self.subject, GeneOrGeneProduct): + self.subject = GeneOrGeneProduct(**as_dict(self.subject)) + + if self._is_empty(self.object): + self.MissingRequiredField("object") + if not isinstance(self.object, DiseaseId): + self.object = DiseaseId(self.object) + + super().__post_init__(**kwargs) + + +@dataclass +class CorrelatedGeneToDiseaseAssociation(GeneToDiseaseAssociation): + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = BIOLINK.CorrelatedGeneToDiseaseAssociation + class_class_curie: ClassVar[str] = "biolink:CorrelatedGeneToDiseaseAssociation" + class_name: ClassVar[str] = "correlated gene to disease association" + class_model_uri: ClassVar[URIRef] = BIOLINK.CorrelatedGeneToDiseaseAssociation + + id: Union[str, CorrelatedGeneToDiseaseAssociationId] = None + predicate: Union[str, PredicateType] = None + subject: Union[dict, GeneOrGeneProduct] = None + object: Union[str, DiseaseId] = None + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self._is_empty(self.id): + self.MissingRequiredField("id") + if not isinstance(self.id, CorrelatedGeneToDiseaseAssociationId): + self.id = CorrelatedGeneToDiseaseAssociationId(self.id) + + if self._is_empty(self.subject): + self.MissingRequiredField("subject") + if not isinstance(self.subject, GeneOrGeneProduct): + self.subject = GeneOrGeneProduct(**as_dict(self.subject)) + + if self._is_empty(self.object): + self.MissingRequiredField("object") + if not isinstance(self.object, DiseaseId): + self.object = DiseaseId(self.object) super().__post_init__(**kwargs) @@ -8625,7 +8677,7 @@ class DruggableGeneToDiseaseAssociation(GeneToDiseaseAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.DruggableGeneToDiseaseAssociation id: Union[str, DruggableGeneToDiseaseAssociationId] = None - object: Union[str, NamedThingId] = None + object: Union[str, DiseaseId] = None subject: Union[dict, GeneOrGeneProduct] = None predicate: Union[str, PredicateType] = None has_evidence: Optional[Union[Union[str, "DruggableGeneCategoryEnum"], List[Union[str, "DruggableGeneCategoryEnum"]]]] = empty_list() @@ -8984,7 +9036,7 @@ class GeneAsAModelOfDiseaseAssociation(GeneToDiseaseAssociation): id: Union[str, GeneAsAModelOfDiseaseAssociationId] = None predicate: Union[str, PredicateType] = None - object: Union[str, NamedThingId] = None + object: Union[str, DiseaseId] = None subject: Union[dict, GeneOrGeneProduct] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -10194,22 +10246,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): # Enumerations -class InformationResourceStatusEnum(EnumDefinitionImpl): - - released = PermissibleValue(text="released") - deprecated = PermissibleValue(text="deprecated") - draft = PermissibleValue(text="draft") - - _defn = EnumDefinition( - name="InformationResourceStatusEnum", - ) - -class AnatomicalContextQualifierEnum(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="AnatomicalContextQualifierEnum", - ) - class DirectionQualifierEnum(EnumDefinitionImpl): increased = PermissibleValue(text="increased") @@ -10258,14 +10294,15 @@ class GeneOrGeneProductOrChemicalPartQualifierEnum(EnumDefinitionImpl): @classmethod def _addvals(cls): setattr(cls, "3_prime_utr", - PermissibleValue(text="3_prime_utr") ) + PermissibleValue(text="3_prime_utr")) setattr(cls, "5_prime_utr", - PermissibleValue(text="5_prime_utr") ) + PermissibleValue(text="5_prime_utr")) class GeneOrGeneProductOrChemicalEntityAspectEnum(EnumDefinitionImpl): - activity_or_abundance = PermissibleValue(text="activity_or_abundance", - description="Used in cases where the specificity of the relationship can not be determined to be either activity or abundance. In general, a more specific value from this enumeration should be used.") + activity_or_abundance = PermissibleValue( + text="activity_or_abundance", + description="""Used in cases where the specificity of the relationship can not be determined to be either activity or abundance. In general, a more specific value from this enumeration should be used.""") abundance = PermissibleValue(text="abundance") activity = PermissibleValue(text="activity") expression = PermissibleValue(text="expression") @@ -10320,40 +10357,55 @@ class GeneOrGeneProductOrChemicalEntityAspectEnum(EnumDefinitionImpl): @classmethod def _addvals(cls): setattr(cls, "ADP-ribosylation", - PermissibleValue(text="ADP-ribosylation") ) + PermissibleValue(text="ADP-ribosylation")) class CausalMechanismQualifierEnum(EnumDefinitionImpl): - binding = PermissibleValue(text="binding", - description="A causal mechanism mediated by the direct contact between effector and target chemical or biomolecular entity, which form a stable physical interaction.") - inhibition = PermissibleValue(text="inhibition", - description="A causal mechanism in which the effector binds to the target and negatively effects its normal function, e.g. prevention of enzymatic reaction or activation of downstream pathway.") - antibody_inhibition = PermissibleValue(text="antibody_inhibition", - description="A causal mechanism in which an antibody specifically binds to and interferes with the target.") - antagonism = PermissibleValue(text="antagonism", - description="A causal mechanism in which the effector binds to a receptor and prevents activation by an agonist through competing for the binding site.") - molecular_channel_blockage = PermissibleValue(text="molecular_channel_blockage", - description="A causal mechanism in which the effector binds to a molecular channel and prevents or reduces transport of ions through it.") - inverse_agonism = PermissibleValue(text="inverse_agonism", - description="A causal mechanism in which the effector binds to the same receptor-binding site as an agonist and antagonizes its effects, often exerting the opposite effect of the agonist by suppressing spontaneous receptor signaling.") - negative_allosteric_modulation = PermissibleValue(text="negative_allosteric_modulation", - description="A causal mechanism in which the effector reduces or prevents the action of the endogenous ligand of a receptor by binding to a site distinct from that ligand (i.e. non-competitive inhibition)") - agonism = PermissibleValue(text="agonism", - description="A causal mechanism in which the effector binds and activates a receptor to mimic the effect of an endogenous ligand.") - molecular_channel_opening = PermissibleValue(text="molecular_channel_opening", - description="A causal mechanism in which the effector binds to a molecular channel and facilitates transport of ions through it.") - positive_allosteric_modulation = PermissibleValue(text="positive_allosteric_modulation", - description="A causal mechanism in which the effector enhances the action of the endogenous ligand of a receptor by binding to a site distinct from that ligand (i.e. non-competitive inhibition)") - potentiation = PermissibleValue(text="potentiation", - description="A causal mechanism in which the effector binds to and enhances or intensifies the effect of some other chemical or drug on its target.") - activation = PermissibleValue(text="activation", - description="A causal mechanism in which the effector binds to and positively affects the normal functioning of its target.") - inducer = PermissibleValue(text="inducer", - description="A causal mechanism in which the effector binds to and increases the activity/rate of an enzyme that processes drugs in the body.") - transcriptional_regulation = PermissibleValue(text="transcriptional_regulation", - description="A causal mechanism mediated by through the control of target gene transcription") - signaling_mediated_control = PermissibleValue(text="signaling_mediated_control", - description="A causal mechanism mediated by the activation or control of signaling events that influence the some aspect of the target entity (e.g. its activity, processing, transport, etc)") + binding = PermissibleValue( + text="binding", + description="""A causal mechanism mediated by the direct contact between effector and target chemical or biomolecular entity, which form a stable physical interaction.""") + inhibition = PermissibleValue( + text="inhibition", + description="""A causal mechanism in which the effector binds to the target and negatively effects its normal function, e.g. prevention of enzymatic reaction or activation of downstream pathway.""") + antibody_inhibition = PermissibleValue( + text="antibody_inhibition", + description="A causal mechanism in which an antibody specifically binds to and interferes with the target.") + antagonism = PermissibleValue( + text="antagonism", + description="""A causal mechanism in which the effector binds to a receptor and prevents activation by an agonist through competing for the binding site.""") + molecular_channel_blockage = PermissibleValue( + text="molecular_channel_blockage", + description="""A causal mechanism in which the effector binds to a molecular channel and prevents or reduces transport of ions through it.""") + inverse_agonism = PermissibleValue( + text="inverse_agonism", + description="""A causal mechanism in which the effector binds to the same receptor-binding site as an agonist and antagonizes its effects, often exerting the opposite effect of the agonist by suppressing spontaneous receptor signaling.""") + negative_allosteric_modulation = PermissibleValue( + text="negative_allosteric_modulation", + description="""A causal mechanism in which the effector reduces or prevents the action of the endogenous ligand of a receptor by binding to a site distinct from that ligand (i.e. non-competitive inhibition)""") + agonism = PermissibleValue( + text="agonism", + description="""A causal mechanism in which the effector binds and activates a receptor to mimic the effect of an endogenous ligand.""") + molecular_channel_opening = PermissibleValue( + text="molecular_channel_opening", + description="""A causal mechanism in which the effector binds to a molecular channel and facilitates transport of ions through it.""") + positive_allosteric_modulation = PermissibleValue( + text="positive_allosteric_modulation", + description="""A causal mechanism in which the effector enhances the action of the endogenous ligand of a receptor by binding to a site distinct from that ligand (i.e. non-competitive inhibition)""") + potentiation = PermissibleValue( + text="potentiation", + description="""A causal mechanism in which the effector binds to and enhances or intensifies the effect of some other chemical or drug on its target.""") + activation = PermissibleValue( + text="activation", + description="""A causal mechanism in which the effector binds to and positively affects the normal functioning of its target.""") + inducer = PermissibleValue( + text="inducer", + description="""A causal mechanism in which the effector binds to and increases the activity/rate of an enzyme that processes drugs in the body.""") + transcriptional_regulation = PermissibleValue( + text="transcriptional_regulation", + description="A causal mechanism mediated by through the control of target gene transcription") + signaling_mediated_control = PermissibleValue( + text="signaling_mediated_control", + description="""A causal mechanism mediated by the activation or control of signaling events that influence the some aspect of the target entity (e.g. its activity, processing, transport, etc)""") stabilization = PermissibleValue(text="stabilization") stimulation = PermissibleValue(text="stimulation") releasing_activity = PermissibleValue(text="releasing_activity") @@ -10364,12 +10416,14 @@ class CausalMechanismQualifierEnum(EnumDefinitionImpl): class LogicalInterpretationEnum(EnumDefinitionImpl): - some_some = PermissibleValue(text="some_some", - description="A modifier on a triple that causes the triple to be interpreted as a some-some statement", - meaning=OS.SomeSomeInterpretation) - all_some = PermissibleValue(text="all_some", - description="A modifier on a triple that causes the triple to be interpreted as an all-some statement.", - meaning=OS.AllSomeInterpretation) + some_some = PermissibleValue( + text="some_some", + description="A modifier on a triple that causes the triple to be interpreted as a some-some statement", + meaning=OS.SomeSomeInterpretation) + all_some = PermissibleValue( + text="all_some", + description="A modifier on a triple that causes the triple to be interpreted as an all-some statement.", + meaning=OS.AllSomeInterpretation) inverse_all_some = PermissibleValue(text="inverse_all_some") _defn = EnumDefinition( @@ -10408,11 +10462,11 @@ class PhaseEnum(EnumDefinitionImpl): @classmethod def _addvals(cls): setattr(cls, "0", - PermissibleValue(text="0") ) + PermissibleValue(text="0")) setattr(cls, "1", - PermissibleValue(text="1") ) + PermissibleValue(text="1")) setattr(cls, "2", - PermissibleValue(text="2") ) + PermissibleValue(text="2")) class StrandEnum(EnumDefinitionImpl): """ @@ -10426,26 +10480,32 @@ class StrandEnum(EnumDefinitionImpl): @classmethod def _addvals(cls): setattr(cls, "+", - PermissibleValue(text="+", - description="Positive") ) + PermissibleValue( + text="+", + description="Positive")) setattr(cls, "-", - PermissibleValue(text="-", - description="Negative") ) + PermissibleValue( + text="-", + description="Negative")) setattr(cls, ".", - PermissibleValue(text=".", - description="Unstranded") ) + PermissibleValue( + text=".", + description="Unstranded")) setattr(cls, "?", - PermissibleValue(text="?", - description="Unknown") ) + PermissibleValue( + text="?", + description="Unknown")) class SequenceEnum(EnumDefinitionImpl): """ type of sequence """ - na = PermissibleValue(text="na", - description="nucleic acid") - aa = PermissibleValue(text="aa", - description="amino acid") + na = PermissibleValue( + text="na", + description="nucleic acid") + aa = PermissibleValue( + text="aa", + description="amino acid") _defn = EnumDefinition( name="SequenceEnum", @@ -10454,14 +10514,18 @@ class SequenceEnum(EnumDefinitionImpl): class DruggableGeneCategoryEnum(EnumDefinitionImpl): - tclin = PermissibleValue(text="tclin", - description="These targets have activities in DrugCentral (ie. approved drugs) with known mechanism of action.") - tbio = PermissibleValue(text="tbio", - description="These targets have activities in ChEMBL, Guide to Pharmacology or DrugCentral that satisfy the activity thresholds detailed below.") - tchem = PermissibleValue(text="tchem", - description="These targets do not have known drug or small molecule activities that satisfy the activity thresholds detailed below AND satisfy one or more of the following criteria: target is above the cutoff criteria for Tdark target is annotated with a Gene Ontology Molecular Function or Biological Process leaf term(s) with an Experimental Evidence code") - tdark = PermissibleValue(text="tdark", - description="These are targets about which virtually nothing is known. They do not have known drug or small molecule activities that satisfy the activity thresholds detailed below AND satisfy two or more of the following criteria: A PubMed text-mining score from Jensen Lab less than 5, greater than or equal TO 3 Gene RIFs, or less than or equal to 50 Antibodies available according to http://antibodypedia.com.") + tclin = PermissibleValue( + text="tclin", + description="""These targets have activities in DrugCentral (ie. approved drugs) with known mechanism of action.""") + tbio = PermissibleValue( + text="tbio", + description="""These targets have activities in ChEMBL, Guide to Pharmacology or DrugCentral that satisfy the activity thresholds detailed below.""") + tchem = PermissibleValue( + text="tchem", + description="""These targets do not have known drug or small molecule activities that satisfy the activity thresholds detailed below AND satisfy one or more of the following criteria: target is above the cutoff criteria for Tdark target is annotated with a Gene Ontology Molecular Function or Biological Process leaf term(s) with an Experimental Evidence code""") + tdark = PermissibleValue( + text="tdark", + description="""These are targets about which virtually nothing is known. They do not have known drug or small molecule activities that satisfy the activity thresholds detailed below AND satisfy two or more of the following criteria: A PubMed text-mining score from Jensen Lab less than 5, greater than or equal TO 3 Gene RIFs, or less than or equal to 50 Antibodies available according to http://antibodypedia.com.""") _defn = EnumDefinition( name="DruggableGeneCategoryEnum", @@ -10469,10 +10533,12 @@ class DruggableGeneCategoryEnum(EnumDefinitionImpl): class DrugAvailabilityEnum(EnumDefinitionImpl): - over_the_counter = PermissibleValue(text="over_the_counter", - description="chemical entity is available over the counter without a prescription.") - prescription = PermissibleValue(text="prescription", - description="chemical entity is available by prescription.") + over_the_counter = PermissibleValue( + text="over_the_counter", + description="chemical entity is available over the counter without a prescription.") + prescription = PermissibleValue( + text="prescription", + description="chemical entity is available by prescription.") _defn = EnumDefinition( name="DrugAvailabilityEnum", @@ -10501,39 +10567,53 @@ class ResourceRoleEnum(EnumDefinitionImpl): _defn = EnumDefinition( name="ResourceRoleEnum", - description="The role played by the information reource in serving as a source for an edge in a TRAPI message. Note that a given Edge should have one and only one 'primary' source, and may have any number of 'aggregator' or 'supporting data' sources. This enumeration is found in Biolink Model, but is repeated here for convenience.", + description="""The role played by the information reource in serving as a source for an edge in a TRAPI message. Note that a given Edge should have one and only one 'primary' source, and may have any number of 'aggregator' or 'supporting data' sources. This enumeration is found in Biolink Model, but is repeated here for convenience.""", ) class FDAApprovalStatusEnum(EnumDefinitionImpl): - discovery_and_development_phase = PermissibleValue(text="discovery_and_development_phase", - description="Discovery & Development Phase. Discovery involves researchers finding new possibilities for medication through testing molecular compounds, noting unexpected effects from existing treatments, or the creation of new technology that allows novel ways of targeting medical products to sites in the body. Drug development occurs after researchers identify potential compounds for experiments.") - preclinical_research_phase = PermissibleValue(text="preclinical_research_phase", - description="Preclinical Research Phase. Once researchers have examined the possibilities a new drug may contain, they must do preliminary research to determine its potential for harm (toxicity). This is categorized as preclinical research and can be one of two types: in vitro or in vivo.") - fda_clinical_research_phase = PermissibleValue(text="fda_clinical_research_phase", - description="Clinical Research Phase. Clinical research involves trials of the drug on people, and it is one of the most involved stages in the drug development and approval process. Clinical trials must answer specific questions and follow a protocol determined by the drug researcher or manufacturer.") - fda_review_phase_4 = PermissibleValue(text="fda_review_phase_4", - description="FDA Review") - fda_post_market_safety_review = PermissibleValue(text="fda_post_market_safety_review", - description="FDA Post-Market Safety Monitoring. The last phase of drug approval is an ongoing one while the drug is on the marketplace. If a developer wants to change anything about the drug formulation or approve it for a new use, they must apply with the FDA. The FDA also frequently reviews the drug’s advertising and its manufacturing facility to make sure everything involved in its creation and marketing is in compliance with regulations.") - fda_clinical_research_phase_1 = PermissibleValue(text="fda_clinical_research_phase_1", - description="In the FDA Clinical Research Phase, the Clinical Research Phase 1 involves 20 – 100 study participants and lasts several months. This phase is used to determine the safety and dosage of the drug, and about 70% of these drugs move on to the next clinical research phase.") - fda_clinical_research_phase_2 = PermissibleValue(text="fda_clinical_research_phase_2", - description="In the FDA Clinical Research Phase, the Clinical Research Phase 2 involves up to several hundred people, who must have the disease or condition the drug supposes to treat. This phase can last from a few months to two years, and its purpose is to monitor the efficacy of the drug, as well as note side effects that may occur.") - fda_clinical_research_phase_3 = PermissibleValue(text="fda_clinical_research_phase_3", - description="In the FDA Clinical Research Phase, the Clinical Research Phase 3 involves 300 – 3000 volunteers and can last up to four years. It is used to continue monitoring the efficacy of the drug, as well as exploring any longer-term adverse reactions.") - fda_clinical_research_phase_4 = PermissibleValue(text="fda_clinical_research_phase_4", - description="In the FDA Clinical Research Phase, the Clinical Research Phase 4 involves several thousands of volunteers who have the disease or condition and continues to monitor safety and efficacy. If a drug passes this phase, it goes on to FDA review.") - fda_fast_track = PermissibleValue(text="fda_fast_track", - description="Fast track is a process designed to facilitate the development, and expedite the review of drugs to treat serious conditions and fill an unmet medical need. The purpose is to get important new drugs to the patient earlier. Fast Track addresses a broad range of serious conditions. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/fast-track") - fda_breakthrough_therapy = PermissibleValue(text="fda_breakthrough_therapy", - description="Breakthrough Therapy designation is a process designed to expedite the development and review of drugs that are intended to treat a serious condition and preliminary clinical evidence indicates that the drug may demonstrate substantial improvement over available therapy on a clinically significant endpoint(s). For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/breakthrough-therapy") - fda_accelerated_approval = PermissibleValue(text="fda_accelerated_approval", - description="When studying a new drug, it can sometimes take many years to learn whether a drug actually provides a real effect on how a patient survives, feels, or functions. A positive therapeutic effect that is clinically meaningful in the context of a given disease is known as “clinical benefit”. Mindful of the fact that it may take an extended period of time to measure a drug’s intended clinical benefit, in 1992 FDA instituted the Accelerated Approval regulations. These regulations allowed drugs for serious conditions that filled an unmet medical need to be approved based on a surrogate endpoint. Using a surrogate endpoint enabled the FDA to approve these drugs faster. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/accelerated-approval") - fda_priority_review = PermissibleValue(text="fda_priority_review", - description="Prior to approval, each drug marketed in the United States must go through a detailed FDA review process. In 1992, under the Prescription Drug User Act (PDUFA), FDA agreed to specific goals for improving the drug review time and created a two-tiered system of review times – Standard Review and Priority Review. A Priority Review designation means FDA’s goal is to take action on an application within 6 months (compared to 10 months under standard review). For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/priority-review") - regular_fda_approval = PermissibleValue(text="regular_fda_approval", - description="Regular FDA Approval. The last phase of drug approval is an ongoing one while the drug is on the marketplace. If a developer wants to change anything about the drug formulation or approve it for a new use, they must apply with the FDA. The FDA also frequently reviews the drug’s advertising and its manufacturing facility to make sure everything involved in its creation and marketing is in compliance with regulations.") + discovery_and_development_phase = PermissibleValue( + text="discovery_and_development_phase", + description="""Discovery & Development Phase. Discovery involves researchers finding new possibilities for medication through testing molecular compounds, noting unexpected effects from existing treatments, or the creation of new technology that allows novel ways of targeting medical products to sites in the body. Drug development occurs after researchers identify potential compounds for experiments.""") + preclinical_research_phase = PermissibleValue( + text="preclinical_research_phase", + description="""Preclinical Research Phase. Once researchers have examined the possibilities a new drug may contain, they must do preliminary research to determine its potential for harm (toxicity). This is categorized as preclinical research and can be one of two types: in vitro or in vivo.""") + fda_clinical_research_phase = PermissibleValue( + text="fda_clinical_research_phase", + description="""Clinical Research Phase. Clinical research involves trials of the drug on people, and it is one of the most involved stages in the drug development and approval process. Clinical trials must answer specific questions and follow a protocol determined by the drug researcher or manufacturer.""") + fda_review_phase_4 = PermissibleValue( + text="fda_review_phase_4", + description="FDA Review") + fda_post_market_safety_review = PermissibleValue( + text="fda_post_market_safety_review", + description="""FDA Post-Market Safety Monitoring. The last phase of drug approval is an ongoing one while the drug is on the marketplace. If a developer wants to change anything about the drug formulation or approve it for a new use, they must apply with the FDA. The FDA also frequently reviews the drug’s advertising and its manufacturing facility to make sure everything involved in its creation and marketing is in compliance with regulations.""") + fda_clinical_research_phase_1 = PermissibleValue( + text="fda_clinical_research_phase_1", + description="""In the FDA Clinical Research Phase, the Clinical Research Phase 1 involves 20 – 100 study participants and lasts several months. This phase is used to determine the safety and dosage of the drug, and about 70% of these drugs move on to the next clinical research phase.""") + fda_clinical_research_phase_2 = PermissibleValue( + text="fda_clinical_research_phase_2", + description="""In the FDA Clinical Research Phase, the Clinical Research Phase 2 involves up to several hundred people, who must have the disease or condition the drug supposes to treat. This phase can last from a few months to two years, and its purpose is to monitor the efficacy of the drug, as well as note side effects that may occur.""") + fda_clinical_research_phase_3 = PermissibleValue( + text="fda_clinical_research_phase_3", + description="""In the FDA Clinical Research Phase, the Clinical Research Phase 3 involves 300 – 3000 volunteers and can last up to four years. It is used to continue monitoring the efficacy of the drug, as well as exploring any longer-term adverse reactions.""") + fda_clinical_research_phase_4 = PermissibleValue( + text="fda_clinical_research_phase_4", + description="""In the FDA Clinical Research Phase, the Clinical Research Phase 4 involves several thousands of volunteers who have the disease or condition and continues to monitor safety and efficacy. If a drug passes this phase, it goes on to FDA review.""") + fda_fast_track = PermissibleValue( + text="fda_fast_track", + description="""Fast track is a process designed to facilitate the development, and expedite the review of drugs to treat serious conditions and fill an unmet medical need. The purpose is to get important new drugs to the patient earlier. Fast Track addresses a broad range of serious conditions. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/fast-track""") + fda_breakthrough_therapy = PermissibleValue( + text="fda_breakthrough_therapy", + description="""Breakthrough Therapy designation is a process designed to expedite the development and review of drugs that are intended to treat a serious condition and preliminary clinical evidence indicates that the drug may demonstrate substantial improvement over available therapy on a clinically significant endpoint(s). For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/breakthrough-therapy""") + fda_accelerated_approval = PermissibleValue( + text="fda_accelerated_approval", + description="""When studying a new drug, it can sometimes take many years to learn whether a drug actually provides a real effect on how a patient survives, feels, or functions. A positive therapeutic effect that is clinically meaningful in the context of a given disease is known as “clinical benefit”. Mindful of the fact that it may take an extended period of time to measure a drug’s intended clinical benefit, in 1992 FDA instituted the Accelerated Approval regulations. These regulations allowed drugs for serious conditions that filled an unmet medical need to be approved based on a surrogate endpoint. Using a surrogate endpoint enabled the FDA to approve these drugs faster. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/accelerated-approval""") + fda_priority_review = PermissibleValue( + text="fda_priority_review", + description="""Prior to approval, each drug marketed in the United States must go through a detailed FDA review process. In 1992, under the Prescription Drug User Act (PDUFA), FDA agreed to specific goals for improving the drug review time and created a two-tiered system of review times – Standard Review and Priority Review. A Priority Review designation means FDA’s goal is to take action on an application within 6 months (compared to 10 months under standard review). For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/priority-review""") + regular_fda_approval = PermissibleValue( + text="regular_fda_approval", + description="""Regular FDA Approval. The last phase of drug approval is an ongoing one while the drug is on the marketplace. If a developer wants to change anything about the drug formulation or approve it for a new use, they must apply with the FDA. The FDA also frequently reviews the drug’s advertising and its manufacturing facility to make sure everything involved in its creation and marketing is in compliance with regulations.""") post_approval_withdrawal = PermissibleValue(text="post_approval_withdrawal") _defn = EnumDefinition( @@ -10545,18 +10625,22 @@ class FDAIDAAdverseEventEnum(EnumDefinitionImpl): please consult with the FDA guidelines as proposed in this document: https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm?fr=312.32 """ - life_threatening_adverse_event = PermissibleValue(text="life_threatening_adverse_event", - description="An adverse event or suspected adverse reaction is considered 'life-threatening' if, in the view of either the investigator or sponsor, its occurrence places the patient or subject at immediate risk of death. It does not include an adverse event or suspected adverse reaction that, had it occurred in a more severe form, might have caused death.") - serious_adverse_event = PermissibleValue(text="serious_adverse_event", - description="An adverse event or suspected adverse reaction is considered 'serious' if, in the view of either the investigator or sponsor, it results in any of the following outcomes: Death, a life-threatening adverse event, inpatient hospitalization or prolongation of existing hospitalization, a persistent or significant incapacity or substantial disruption of the ability to conduct normal life functions, or a congenital anomaly/birth defect. Important medical events that may not result in death, be life-threatening, or require hospitalization may be considered serious when, based upon appropriate medical judgment, they may jeopardize the patient or subject and may require medical or surgical intervention to prevent one of the outcomes listed in this definition. Examples of such medical events include allergic bronchospasm requiring intensive treatment in an emergency room or at home, blood dyscrasias or convulsions that do not result in inpatient hospitalization, or the development of drug dependency or drug abuse.") - suspected_adverse_reaction = PermissibleValue(text="suspected_adverse_reaction", - description="means any adverse event for which there is a reasonable possibility that the drug caused the adverse event. For the purposes of IND safety reporting, 'reasonable possibility' means there is evidence to suggest a causal relationship between the drug and the adverse event. Suspected adverse reaction implies a lesser degree of certainty about causality than adverse reaction, which means any adverse event caused by a drug.") - unexpected_adverse_event = PermissibleValue(text="unexpected_adverse_event", - description="An adverse event or suspected adverse reaction is considered 'unexpected' if it is not listed in the investigator brochure or is not listed at the specificity or severity that has been observed; or, if an investigator brochure is not required or available, is not consistent with the risk information described in the general investigational plan or elsewhere in the current application, as amended. For example, under this definition, hepatic necrosis would be unexpected (by virtue of greater severity) if the investigator brochure referred only to elevated hepatic enzymes or hepatitis. Similarly, cerebral thromboembolism and cerebral vasculitis would be unexpected (by virtue of greater specificity) if the investigator brochure listed only cerebral vascular accidents. 'Unexpected', as used in this definition, also refers to adverse events or suspected adverse reactions that are mentioned in the investigator brochure as occurring with a class of drugs or as anticipated from the pharmacological properties of the drug, but are not specifically mentioned as occurring with the particular drug under investigation.") + life_threatening_adverse_event = PermissibleValue( + text="life_threatening_adverse_event", + description="""An adverse event or suspected adverse reaction is considered 'life-threatening' if, in the view of either the investigator or sponsor, its occurrence places the patient or subject at immediate risk of death. It does not include an adverse event or suspected adverse reaction that, had it occurred in a more severe form, might have caused death.""") + serious_adverse_event = PermissibleValue( + text="serious_adverse_event", + description="""An adverse event or suspected adverse reaction is considered 'serious' if, in the view of either the investigator or sponsor, it results in any of the following outcomes: Death, a life-threatening adverse event, inpatient hospitalization or prolongation of existing hospitalization, a persistent or significant incapacity or substantial disruption of the ability to conduct normal life functions, or a congenital anomaly/birth defect. Important medical events that may not result in death, be life-threatening, or require hospitalization may be considered serious when, based upon appropriate medical judgment, they may jeopardize the patient or subject and may require medical or surgical intervention to prevent one of the outcomes listed in this definition. Examples of such medical events include allergic bronchospasm requiring intensive treatment in an emergency room or at home, blood dyscrasias or convulsions that do not result in inpatient hospitalization, or the development of drug dependency or drug abuse.""") + suspected_adverse_reaction = PermissibleValue( + text="suspected_adverse_reaction", + description="""means any adverse event for which there is a reasonable possibility that the drug caused the adverse event. For the purposes of IND safety reporting, 'reasonable possibility' means there is evidence to suggest a causal relationship between the drug and the adverse event. Suspected adverse reaction implies a lesser degree of certainty about causality than adverse reaction, which means any adverse event caused by a drug.""") + unexpected_adverse_event = PermissibleValue( + text="unexpected_adverse_event", + description="""An adverse event or suspected adverse reaction is considered 'unexpected' if it is not listed in the investigator brochure or is not listed at the specificity or severity that has been observed; or, if an investigator brochure is not required or available, is not consistent with the risk information described in the general investigational plan or elsewhere in the current application, as amended. For example, under this definition, hepatic necrosis would be unexpected (by virtue of greater severity) if the investigator brochure referred only to elevated hepatic enzymes or hepatitis. Similarly, cerebral thromboembolism and cerebral vasculitis would be unexpected (by virtue of greater specificity) if the investigator brochure listed only cerebral vascular accidents. 'Unexpected', as used in this definition, also refers to adverse events or suspected adverse reactions that are mentioned in the investigator brochure as occurring with a class of drugs or as anticipated from the pharmacological properties of the drug, but are not specifically mentioned as occurring with the particular drug under investigation.""") _defn = EnumDefinition( name="FDAIDAAdverseEventEnum", - description="please consult with the FDA guidelines as proposed in this document: https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm?fr=312.32", + description="""please consult with the FDA guidelines as proposed in this document: https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm?fr=312.32""", ) # Slots @@ -10600,7 +10684,7 @@ class slots: model_uri=BIOLINK.category, domain=Entity, range=Optional[Union[Union[str, CategoryType], List[Union[str, CategoryType]]]]) slots.publication_type = Slot(uri=DCT.type, name="publication type", curie=DCT.curie('type'), - model_uri=BIOLINK.publication_type, domain=None, range=Optional[str]) + model_uri=BIOLINK.publication_type, domain=None, range=Optional[Union[str, List[str]]]) slots.name = Slot(uri=RDFS.label, name="name", curie=RDFS.curie('label'), model_uri=BIOLINK.name, domain=Entity, range=Optional[Union[str, LabelType]]) @@ -10942,7 +11026,7 @@ class slots: model_uri=BIOLINK.causal_mechanism_qualifier, domain=Association, range=Optional[Union[str, "CausalMechanismQualifierEnum"]]) slots.anatomical_context_qualifier = Slot(uri=BIOLINK.anatomical_context_qualifier, name="anatomical context qualifier", curie=BIOLINK.curie('anatomical_context_qualifier'), - model_uri=BIOLINK.anatomical_context_qualifier, domain=Association, range=Optional[Union[str, "AnatomicalContextQualifierEnum"]]) + model_uri=BIOLINK.anatomical_context_qualifier, domain=Association, range=Optional[str]) slots.species_context_qualifier = Slot(uri=BIOLINK.species_context_qualifier, name="species context qualifier", curie=BIOLINK.curie('species_context_qualifier'), model_uri=BIOLINK.species_context_qualifier, domain=Association, range=Optional[Union[str, OrganismTaxonId]]) @@ -11739,26 +11823,35 @@ class slots: slots.has_supporting_study_result = Slot(uri=BIOLINK.has_supporting_study_result, name="has supporting study result", curie=BIOLINK.curie('has_supporting_study_result'), model_uri=BIOLINK.has_supporting_study_result, domain=Association, range=Optional[str]) +slots.log_odds_ratio = Slot(uri=BIOLINK.log_odds_ratio, name="log odds ratio", curie=BIOLINK.curie('log_odds_ratio'), + model_uri=BIOLINK.log_odds_ratio, domain=Association, range=Optional[float]) + +slots.log_odds_ration_95_ci = Slot(uri=BIOLINK.log_odds_ration_95_ci, name="log odds ration 95 ci", curie=BIOLINK.curie('log_odds_ration_95_ci'), + model_uri=BIOLINK.log_odds_ration_95_ci, domain=Association, range=Optional[float]) + +slots.total_sample_size = Slot(uri=BIOLINK.total_sample_size, name="total sample size", curie=BIOLINK.curie('total_sample_size'), + model_uri=BIOLINK.total_sample_size, domain=Association, range=Optional[int]) + slots.mechanism_of_action = Slot(uri=BIOLINK.mechanism_of_action, name="mechanism of action", curie=BIOLINK.curie('mechanism_of_action'), model_uri=BIOLINK.mechanism_of_action, domain=Association, range=Optional[Union[bool, Bool]]) slots.knowledge_source = Slot(uri=BIOLINK.knowledge_source, name="knowledge source", curie=BIOLINK.curie('knowledge_source'), - model_uri=BIOLINK.knowledge_source, domain=Association, range=Optional[Union[str, InformationResourceId]]) + model_uri=BIOLINK.knowledge_source, domain=Association, range=Optional[str]) slots.provided_by = Slot(uri=BIOLINK.provided_by, name="provided by", curie=BIOLINK.curie('provided_by'), model_uri=BIOLINK.provided_by, domain=NamedThing, range=Optional[Union[str, List[str]]]) slots.primary_knowledge_source = Slot(uri=BIOLINK.primary_knowledge_source, name="primary knowledge source", curie=BIOLINK.curie('primary_knowledge_source'), - model_uri=BIOLINK.primary_knowledge_source, domain=Association, range=Optional[Union[str, InformationResourceId]]) + model_uri=BIOLINK.primary_knowledge_source, domain=Association, range=Optional[str]) slots.aggregator_knowledge_source = Slot(uri=BIOLINK.aggregator_knowledge_source, name="aggregator knowledge source", curie=BIOLINK.curie('aggregator_knowledge_source'), - model_uri=BIOLINK.aggregator_knowledge_source, domain=Association, range=Optional[Union[Union[str, InformationResourceId], List[Union[str, InformationResourceId]]]]) + model_uri=BIOLINK.aggregator_knowledge_source, domain=Association, range=Optional[Union[str, List[str]]]) slots.supporting_data_source = Slot(uri=BIOLINK.supporting_data_source, name="supporting data source", curie=BIOLINK.curie('supporting_data_source'), - model_uri=BIOLINK.supporting_data_source, domain=Association, range=Optional[Union[Union[str, InformationResourceId], List[Union[str, InformationResourceId]]]]) + model_uri=BIOLINK.supporting_data_source, domain=Association, range=Optional[Union[str, List[str]]]) slots.supporting_data_set = Slot(uri=BIOLINK.supporting_data_set, name="supporting data set", curie=BIOLINK.curie('supporting_data_set'), - model_uri=BIOLINK.supporting_data_set, domain=Association, range=Optional[Union[Union[str, InformationResourceId], List[Union[str, InformationResourceId]]]]) + model_uri=BIOLINK.supporting_data_set, domain=Association, range=Optional[Union[str, List[str]]]) slots.chi_squared_statistic = Slot(uri=BIOLINK.chi_squared_statistic, name="chi squared statistic", curie=BIOLINK.curie('chi_squared_statistic'), model_uri=BIOLINK.chi_squared_statistic, domain=Association, range=Optional[float]) @@ -11769,6 +11862,9 @@ class slots: slots.evidence_count = Slot(uri=BIOLINK.evidence_count, name="evidence count", curie=BIOLINK.curie('evidence_count'), model_uri=BIOLINK.evidence_count, domain=Association, range=Optional[int]) +slots.dataset_count = Slot(uri=BIOLINK.dataset_count, name="dataset count", curie=BIOLINK.curie('dataset_count'), + model_uri=BIOLINK.dataset_count, domain=Association, range=Optional[int]) + slots.concept_count_subject = Slot(uri=BIOLINK.concept_count_subject, name="concept count subject", curie=BIOLINK.curie('concept_count_subject'), model_uri=BIOLINK.concept_count_subject, domain=Association, range=Optional[int]) @@ -11838,9 +11934,6 @@ class slots: slots.phenotypic_state = Slot(uri=BIOLINK.phenotypic_state, name="phenotypic state", curie=BIOLINK.curie('phenotypic_state'), model_uri=BIOLINK.phenotypic_state, domain=Association, range=Optional[Union[str, DiseaseOrPhenotypicFeatureId]]) -slots.information_resources = Slot(uri=BIOLINK.information_resources, name="information resources", curie=BIOLINK.curie('information_resources'), - model_uri=BIOLINK.information_resources, domain=None, range=Optional[Union[Dict[Union[str, InformationResourceId], Union[dict, InformationResource]], List[Union[dict, InformationResource]]]]) - slots.publications = Slot(uri=BIOLINK.publications, name="publications", curie=BIOLINK.curie('publications'), model_uri=BIOLINK.publications, domain=Association, range=Optional[Union[Union[str, PublicationId], List[Union[str, PublicationId]]]]) @@ -11877,9 +11970,6 @@ class slots: slots.FDA_approval_status = Slot(uri=BIOLINK.FDA_approval_status, name="FDA approval status", curie=BIOLINK.curie('FDA_approval_status'), model_uri=BIOLINK.FDA_approval_status, domain=Association, range=Optional[Union[str, "FDAApprovalStatusEnum"]]) -slots.information_resource_status = Slot(uri=BIOLINK.information_resource_status, name="information resource status", curie=BIOLINK.curie('information_resource_status'), - model_uri=BIOLINK.information_resource_status, domain=NamedThing, range=Optional[Union[str, "InformationResourceStatusEnum"]]) - slots.supporting_study_metadata = Slot(uri=BIOLINK.supporting_study_metadata, name="supporting study metadata", curie=BIOLINK.curie('supporting_study_metadata'), model_uri=BIOLINK.supporting_study_metadata, domain=Association, range=Optional[str]) @@ -11924,7 +12014,7 @@ class slots: model_uri=BIOLINK.publication_name, domain=Publication, range=Optional[Union[str, LabelType]]) slots.publication_publication_type = Slot(uri=DCT.type, name="publication_publication type", curie=DCT.curie('type'), - model_uri=BIOLINK.publication_publication_type, domain=Publication, range=str) + model_uri=BIOLINK.publication_publication_type, domain=Publication, range=Union[str, List[str]]) slots.publication_pages = Slot(uri=BIOLINK.pages, name="publication_pages", curie=BIOLINK.curie('pages'), model_uri=BIOLINK.publication_pages, domain=Publication, range=Optional[Union[str, List[str]]]) @@ -12364,6 +12454,30 @@ class slots: slots.gene_to_disease_or_phenotypic_feature_association_predicate = Slot(uri=RDF.predicate, name="gene to disease or phenotypic feature association_predicate", curie=RDF.curie('predicate'), model_uri=BIOLINK.gene_to_disease_or_phenotypic_feature_association_predicate, domain=GeneToDiseaseOrPhenotypicFeatureAssociation, range=Union[str, PredicateType]) +slots.gene_to_phenotype_association_subject = Slot(uri=RDF.subject, name="gene to phenotype association_subject", curie=RDF.curie('subject'), + model_uri=BIOLINK.gene_to_phenotype_association_subject, domain=GeneToPhenotypeAssociation, range=Union[dict, GeneOrGeneProduct]) + +slots.gene_to_phenotype_association_object = Slot(uri=RDF.object, name="gene to phenotype association_object", curie=RDF.curie('object'), + model_uri=BIOLINK.gene_to_phenotype_association_object, domain=GeneToPhenotypeAssociation, range=Union[str, PhenotypicFeatureId]) + +slots.gene_to_disease_association_subject = Slot(uri=RDF.subject, name="gene to disease association_subject", curie=RDF.curie('subject'), + model_uri=BIOLINK.gene_to_disease_association_subject, domain=GeneToDiseaseAssociation, range=Union[dict, GeneOrGeneProduct]) + +slots.gene_to_disease_association_object = Slot(uri=RDF.object, name="gene to disease association_object", curie=RDF.curie('object'), + model_uri=BIOLINK.gene_to_disease_association_object, domain=GeneToDiseaseAssociation, range=Union[str, DiseaseId]) + +slots.causal_gene_to_disease_association_subject = Slot(uri=RDF.subject, name="causal gene to disease association_subject", curie=RDF.curie('subject'), + model_uri=BIOLINK.causal_gene_to_disease_association_subject, domain=CausalGeneToDiseaseAssociation, range=Union[dict, GeneOrGeneProduct]) + +slots.causal_gene_to_disease_association_object = Slot(uri=RDF.object, name="causal gene to disease association_object", curie=RDF.curie('object'), + model_uri=BIOLINK.causal_gene_to_disease_association_object, domain=CausalGeneToDiseaseAssociation, range=Union[str, DiseaseId]) + +slots.correlated_gene_to_disease_association_subject = Slot(uri=RDF.subject, name="correlated gene to disease association_subject", curie=RDF.curie('subject'), + model_uri=BIOLINK.correlated_gene_to_disease_association_subject, domain=CorrelatedGeneToDiseaseAssociation, range=Union[dict, GeneOrGeneProduct]) + +slots.correlated_gene_to_disease_association_object = Slot(uri=RDF.object, name="correlated gene to disease association_object", curie=RDF.curie('object'), + model_uri=BIOLINK.correlated_gene_to_disease_association_object, domain=CorrelatedGeneToDiseaseAssociation, range=Union[str, DiseaseId]) + slots.druggable_gene_to_disease_association_subject = Slot(uri=RDF.subject, name="druggable gene to disease association_subject", curie=RDF.curie('subject'), model_uri=BIOLINK.druggable_gene_to_disease_association_subject, domain=DruggableGeneToDiseaseAssociation, range=Union[dict, GeneOrGeneProduct]) diff --git a/context.jsonld b/context.jsonld index 600a97eaaf..d85bc98cc2 100644 --- a/context.jsonld +++ b/context.jsonld @@ -1,7 +1,7 @@ { "comments": { "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-05-04T23:01:18", + "generation_date": "2023-05-23T23:04:19", "source": "biolink-model.yaml" }, "@context": { @@ -629,9 +629,6 @@ "@type": "@id" }, "id": "@id", - "aggregator_knowledge_source": { - "@type": "@id" - }, "ameliorates": { "@type": "@id" }, @@ -641,14 +638,6 @@ "amount_or_activity_increased_by": { "@type": "@id" }, - "anatomical_context_qualifier": { - "@context": { - "@vocab": "@null", - "text": "skos:notation", - "description": "skos:prefLabel", - "meaning": "@id" - } - }, "animal_model_available_from": { "@type": "@id" }, @@ -797,6 +786,9 @@ "creation_date": { "@type": "xsd:date" }, + "dataset_count": { + "@type": "xsd:integer" + }, "dataset_download_url": { "@id": "dcat:downloadURL" }, @@ -1198,17 +1190,6 @@ "indirectly_physically_interacts_with": { "@type": "@id" }, - "information_resource_status": { - "@context": { - "@vocab": "@null", - "text": "skos:notation", - "description": "skos:prefLabel", - "meaning": "@id" - } - }, - "information_resources": { - "@type": "@id" - }, "ingest_date": { "@id": "pav:version" }, @@ -1293,9 +1274,6 @@ "is_toxic": { "@type": "xsd:boolean" }, - "knowledge_source": { - "@type": "@id" - }, "lacks_part": { "@type": "@id" }, @@ -1320,6 +1298,12 @@ "location_of_disease": { "@type": "@id" }, + "log_odds_ratio": { + "@type": "xsd:float" + }, + "log_odds_ration_95_ci": { + "@type": "xsd:float" + }, "logical_interpretation": { "@context": { "@vocab": "@null", @@ -1487,9 +1471,6 @@ "primarily_composed_of": { "@type": "@id" }, - "primary_knowledge_source": { - "@type": "@id" - }, "produced_by": { "@type": "@id" }, @@ -1671,12 +1652,6 @@ "superclass_of": { "@type": "@id" }, - "supporting_data_set": { - "@type": "@id" - }, - "supporting_data_source": { - "@type": "@id" - }, "supporting_document_year": { "@type": "xsd:integer" }, @@ -1713,6 +1688,9 @@ "timepoint": { "@type": "xsd:time" }, + "total_sample_size": { + "@type": "xsd:integer" + }, "trade_name": { "@type": "@id" }, diff --git a/contextn.jsonld b/contextn.jsonld index ac7557c90a..36def9d573 100644 --- a/contextn.jsonld +++ b/contextn.jsonld @@ -1,7 +1,7 @@ { "comments": { "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-05-04T23:01:22", + "generation_date": "2023-05-23T23:04:25", "source": "biolink-model.yaml" }, "@context": { @@ -629,9 +629,6 @@ "@type": "@id" }, "id": "@id", - "aggregator_knowledge_source": { - "@type": "@id" - }, "ameliorates": { "@type": "@id" }, @@ -641,14 +638,6 @@ "amount_or_activity_increased_by": { "@type": "@id" }, - "anatomical_context_qualifier": { - "@context": { - "@vocab": "@null", - "text": "skos:notation", - "description": "skos:prefLabel", - "meaning": "@id" - } - }, "animal_model_available_from": { "@type": "@id" }, @@ -797,6 +786,9 @@ "creation_date": { "@type": "xsd:date" }, + "dataset_count": { + "@type": "xsd:integer" + }, "decreased_amount_in": { "@type": "@id" }, @@ -1184,17 +1176,6 @@ "indirectly_physically_interacts_with": { "@type": "@id" }, - "information_resource_status": { - "@context": { - "@vocab": "@null", - "text": "skos:notation", - "description": "skos:prefLabel", - "meaning": "@id" - } - }, - "information_resources": { - "@type": "@id" - }, "interacting_molecules_category": { "@type": "@id" }, @@ -1276,9 +1257,6 @@ "is_toxic": { "@type": "xsd:boolean" }, - "knowledge_source": { - "@type": "@id" - }, "lacks_part": { "@type": "@id" }, @@ -1303,6 +1281,12 @@ "location_of_disease": { "@type": "@id" }, + "log_odds_ratio": { + "@type": "xsd:float" + }, + "log_odds_ration_95_ci": { + "@type": "xsd:float" + }, "logical_interpretation": { "@context": { "@vocab": "@null", @@ -1465,9 +1449,6 @@ "primarily_composed_of": { "@type": "@id" }, - "primary_knowledge_source": { - "@type": "@id" - }, "produced_by": { "@type": "@id" }, @@ -1642,12 +1623,6 @@ "superclass_of": { "@type": "@id" }, - "supporting_data_set": { - "@type": "@id" - }, - "supporting_data_source": { - "@type": "@id" - }, "supporting_document_year": { "@type": "xsd:integer" }, @@ -1681,6 +1656,9 @@ "timepoint": { "@type": "xsd:time" }, + "total_sample_size": { + "@type": "xsd:integer" + }, "trade_name": { "@type": "@id" }, diff --git a/golr-views/RNA_product_config.yaml b/golr-views/RNA_product_config.yaml index 2fe6e9802e..caad323001 100644 --- a/golr-views/RNA_product_config.yaml +++ b/golr-views/RNA_product_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: RNA_product +# metamodel_version: 1.7.0# version: 3.4.0id: RNA_product schema_generating: true display_name: RNA product document_category: RNA product diff --git a/golr-views/RNA_product_isoform_config.yaml b/golr-views/RNA_product_isoform_config.yaml index a492366e2e..3197e675c9 100644 --- a/golr-views/RNA_product_isoform_config.yaml +++ b/golr-views/RNA_product_isoform_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: RNA_product_isoform +# metamodel_version: 1.7.0# version: 3.4.0id: RNA_product_isoform schema_generating: true description: Represents a protein that is a specific isoform of the canonical or reference RNA diff --git a/golr-views/accessible_dna_region_config.yaml b/golr-views/accessible_dna_region_config.yaml index 7fb4f04ab9..4794112780 100644 --- a/golr-views/accessible_dna_region_config.yaml +++ b/golr-views/accessible_dna_region_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: accessible_dna_region +# metamodel_version: 1.7.0# version: 3.4.0id: accessible_dna_region schema_generating: true description: A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose diff --git a/golr-views/activity_config.yaml b/golr-views/activity_config.yaml index 7d45377556..28a8ae6c95 100644 --- a/golr-views/activity_config.yaml +++ b/golr-views/activity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: activity +# metamodel_version: 1.7.0# version: 3.4.0id: activity schema_generating: true description: An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, diff --git a/golr-views/agent_config.yaml b/golr-views/agent_config.yaml index 5dd43aa9d0..04094cc288 100644 --- a/golr-views/agent_config.yaml +++ b/golr-views/agent_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: agent +# metamodel_version: 1.7.0# version: 3.4.0id: agent schema_generating: true description: person, group, organization or project that provides a piece of information (i.e. a knowledge association) diff --git a/golr-views/anatomical_entity_config.yaml b/golr-views/anatomical_entity_config.yaml index 810387d93a..0ab55b519d 100644 --- a/golr-views/anatomical_entity_config.yaml +++ b/golr-views/anatomical_entity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: anatomical_entity +# metamodel_version: 1.7.0# version: 3.4.0id: anatomical_entity schema_generating: true description: A subcellular location, cell type or gross anatomical part display_name: anatomical entity diff --git a/golr-views/anatomical_entity_to_anatomical_entity_ontogenic_association_config.yaml b/golr-views/anatomical_entity_to_anatomical_entity_ontogenic_association_config.yaml index c560eaa046..c92331fe24 100644 --- a/golr-views/anatomical_entity_to_anatomical_entity_ontogenic_association_config.yaml +++ b/golr-views/anatomical_entity_to_anatomical_entity_ontogenic_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: anatomical_entity_to_anatomical_entity_ontogenic_association +# metamodel_version: 1.7.0# version: 3.4.0id: anatomical_entity_to_anatomical_entity_ontogenic_association schema_generating: true description: A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different diff --git a/golr-views/anatomical_entity_to_anatomical_entity_part_of_association_config.yaml b/golr-views/anatomical_entity_to_anatomical_entity_part_of_association_config.yaml index a46d4e36e3..ce9c011450 100644 --- a/golr-views/anatomical_entity_to_anatomical_entity_part_of_association_config.yaml +++ b/golr-views/anatomical_entity_to_anatomical_entity_part_of_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: anatomical_entity_to_anatomical_entity_part_of_association +# metamodel_version: 1.7.0# version: 3.4.0id: anatomical_entity_to_anatomical_entity_part_of_association schema_generating: true description: A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships diff --git a/golr-views/article_config.yaml b/golr-views/article_config.yaml index 4fe812b33e..ecc3018424 100644 --- a/golr-views/article_config.yaml +++ b/golr-views/article_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: article +# metamodel_version: 1.7.0# version: 3.4.0id: article schema_generating: true description: "a piece of writing on a particular topic presented as a stand-alone\ \ section of a larger publication\t " @@ -111,6 +111,7 @@ fields: knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass. display_name: publication_publication type + cardinality: multi - id: published_in description: The enclosing parent serial containing the article should have industry-standard identifier from ISSN. diff --git a/golr-views/association_config.yaml b/golr-views/association_config.yaml index 4d131a0e96..15250d72ef 100644 --- a/golr-views/association_config.yaml +++ b/golr-views/association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: association +# metamodel_version: 1.7.0# version: 3.4.0id: association schema_generating: true description: A typed association between two entities, supported by evidence display_name: association diff --git a/golr-views/attribute_config.yaml b/golr-views/attribute_config.yaml index 7ce6efed47..ce00dcae4a 100644 --- a/golr-views/attribute_config.yaml +++ b/golr-views/attribute_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: attribute +# metamodel_version: 1.7.0# version: 3.4.0id: attribute schema_generating: true description: A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may diff --git a/golr-views/bacterium_config.yaml b/golr-views/bacterium_config.yaml index c6df3b10cd..c8b81b188b 100644 --- a/golr-views/bacterium_config.yaml +++ b/golr-views/bacterium_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: bacterium +# metamodel_version: 1.7.0# version: 3.4.0id: bacterium schema_generating: true description: A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and are often motile. diff --git a/golr-views/behavior_config.yaml b/golr-views/behavior_config.yaml index 67beb42ec6..8ddcb15066 100644 --- a/golr-views/behavior_config.yaml +++ b/golr-views/behavior_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: behavior +# metamodel_version: 1.7.0# version: 3.4.0id: behavior schema_generating: true display_name: behavior document_category: behavior diff --git a/golr-views/behavior_to_behavioral_feature_association_config.yaml b/golr-views/behavior_to_behavioral_feature_association_config.yaml index aba625dd6e..fd3f08bf2c 100644 --- a/golr-views/behavior_to_behavioral_feature_association_config.yaml +++ b/golr-views/behavior_to_behavioral_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: behavior_to_behavioral_feature_association +# metamodel_version: 1.7.0# version: 3.4.0id: behavior_to_behavioral_feature_association schema_generating: true description: An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior. diff --git a/golr-views/behavioral_exposure_config.yaml b/golr-views/behavioral_exposure_config.yaml index 8d9428fb9e..2c1f2d57fe 100644 --- a/golr-views/behavioral_exposure_config.yaml +++ b/golr-views/behavioral_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: behavioral_exposure +# metamodel_version: 1.7.0# version: 3.4.0id: behavioral_exposure schema_generating: true description: A behavioral exposure is a factor relating to behavior impacting an individual. display_name: behavioral exposure diff --git a/golr-views/behavioral_feature_config.yaml b/golr-views/behavioral_feature_config.yaml index 625f79a23d..b988886149 100644 --- a/golr-views/behavioral_feature_config.yaml +++ b/golr-views/behavioral_feature_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: behavioral_feature +# metamodel_version: 1.7.0# version: 3.4.0id: behavioral_feature schema_generating: true description: A phenotypic feature which is behavioral in nature. display_name: behavioral feature diff --git a/golr-views/biological_process_config.yaml b/golr-views/biological_process_config.yaml index 6cc21dfb05..3d4a5e92e9 100644 --- a/golr-views/biological_process_config.yaml +++ b/golr-views/biological_process_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: biological_process +# metamodel_version: 1.7.0# version: 3.4.0id: biological_process schema_generating: true description: One or more causally connected executions of molecular functions display_name: biological process diff --git a/golr-views/biological_process_or_activity_config.yaml b/golr-views/biological_process_or_activity_config.yaml index 334268ee12..fb3dddcada 100644 --- a/golr-views/biological_process_or_activity_config.yaml +++ b/golr-views/biological_process_or_activity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: biological_process_or_activity +# metamodel_version: 1.7.0# version: 3.4.0id: biological_process_or_activity schema_generating: true description: Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system. diff --git a/golr-views/biological_sex_config.yaml b/golr-views/biological_sex_config.yaml index 7bd6c96fab..e63d46fe42 100644 --- a/golr-views/biological_sex_config.yaml +++ b/golr-views/biological_sex_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: biological_sex +# metamodel_version: 1.7.0# version: 3.4.0id: biological_sex schema_generating: true display_name: biological sex document_category: biological sex diff --git a/golr-views/biotic_exposure_config.yaml b/golr-views/biotic_exposure_config.yaml index 6ce84aae67..a25bef6165 100644 --- a/golr-views/biotic_exposure_config.yaml +++ b/golr-views/biotic_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: biotic_exposure +# metamodel_version: 1.7.0# version: 3.4.0id: biotic_exposure schema_generating: true description: An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses). diff --git a/golr-views/book_chapter_config.yaml b/golr-views/book_chapter_config.yaml index 4f53b1de9a..bfe70bb41d 100644 --- a/golr-views/book_chapter_config.yaml +++ b/golr-views/book_chapter_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: book_chapter +# metamodel_version: 1.7.0# version: 3.4.0id: book_chapter schema_generating: true display_name: book chapter document_category: book chapter @@ -109,6 +109,7 @@ fields: knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass. display_name: publication_publication type + cardinality: multi - id: published_in description: The enclosing parent book containing the chapter should have industry-standard identifier from ISBN. diff --git a/golr-views/book_config.yaml b/golr-views/book_config.yaml index 54c60b0b36..b86c5ff0d5 100644 --- a/golr-views/book_config.yaml +++ b/golr-views/book_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: book +# metamodel_version: 1.7.0# version: 3.4.0id: book schema_generating: true description: This class may rarely be instantiated except if use cases of a given knowledge graph support its utility. @@ -100,6 +100,7 @@ fields: knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass. display_name: publication_publication type + cardinality: multi - id: id description: Books should have industry-standard identifier such as from ISBN. display_name: book_id diff --git a/golr-views/case_config.yaml b/golr-views/case_config.yaml index a95545fcec..109df1e6ef 100644 --- a/golr-views/case_config.yaml +++ b/golr-views/case_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: case +# metamodel_version: 1.7.0# version: 3.4.0id: case schema_generating: true description: An individual (human) organism that has a patient role in some clinical context. diff --git a/golr-views/case_to_phenotypic_feature_association_config.yaml b/golr-views/case_to_phenotypic_feature_association_config.yaml index 8753be1b23..5f55a36b76 100644 --- a/golr-views/case_to_phenotypic_feature_association_config.yaml +++ b/golr-views/case_to_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: case_to_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 3.4.0id: case_to_phenotypic_feature_association schema_generating: true description: An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype. diff --git a/golr-views/causal_gene_to_disease_association_config.yaml b/golr-views/causal_gene_to_disease_association_config.yaml new file mode 100644 index 0000000000..d09082dffe --- /dev/null +++ b/golr-views/causal_gene_to_disease_association_config.yaml @@ -0,0 +1,197 @@ +# metamodel_version: 1.7.0# version: 3.4.0id: causal_gene_to_disease_association +schema_generating: true +display_name: causal gene to disease association +document_category: causal gene to disease association +weight: 20 +fields: +- id: id + description: A unique identifier for an entity. Must be either a CURIE shorthand + for a URI or a complete URI + display_name: id +- id: iri + description: An IRI for an entity. This is determined by the id using expansion + rules. + display_name: iri +- id: name + description: A human-readable name for an attribute or entity. + display_name: name +- id: description + description: a human-readable description of an entity + display_name: description +- id: has_attribute + description: connects any entity to an attribute + display_name: has attribute + cardinality: multi +- id: negated + description: if set to true, then the association is negated i.e. is not true + display_name: negated +- id: qualifiers + description: connects an association to qualifiers that modify or qualify the meaning + of that association + display_name: qualifiers + cardinality: multi +- id: publications + description: One or more publications that report the statement expressed in an Association, + or provide information used as evidence supporting this statement. + display_name: publications + cardinality: multi +- id: has_evidence + description: connects an association to an instance of supporting evidence + display_name: has evidence + cardinality: multi +- id: knowledge_source + description: An Information Resource from which the knowledge expressed in an Association + was retrieved, directly or indirectly. This can be any resource through which + the knowledge passed on its way to its currently serialized form. In practice, + implementers should use one of the more specific subtypes of this generic property. + display_name: knowledge source +- id: primary_knowledge_source + description: The most upstream source of the knowledge expressed in an Association + that an implementer can identify. Performing a rigorous analysis of upstream + data providers is expected; every effort is made to catalog the most upstream + source of data in this property. Only one data source should be declared primary + in any association. "aggregator knowledge source" can be used to capture non-primary + sources. + display_name: primary knowledge source +- id: aggregator_knowledge_source + description: An intermediate aggregator resource from which knowledge expressed + in an Association was retrieved downstream of the original source, on its path + to its current serialized form. + display_name: aggregator knowledge source + cardinality: multi +- id: timepoint + description: a point in time + display_name: timepoint +- id: original_subject + description: used to hold the original subject of a relation (or predicate) that + an external knowledge source uses before transformation to match the biolink-model + specification. + display_name: original subject +- id: original_predicate + description: used to hold the original relation/predicate that an external knowledge + source uses before transformation to match the biolink-model specification. + display_name: original predicate +- id: original_object + description: used to hold the original object of a relation (or predicate) that + an external knowledge source uses before transformation to match the biolink-model + specification. + display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi +- id: type + description: rdf:type of biolink:Association should be fixed at rdf:Statement + display_name: association_type + cardinality: multi +- id: category + description: "Name of the high level ontology class in which this entity is categorized.\ + \ Corresponds to the label for the biolink entity type class.\n * In a neo4j database\ + \ this MAY correspond to the neo4j label tag.\n * In an RDF database it should\ + \ be a biolink model class URI.\nThis field is multi-valued. It should include\ + \ values for ancestors of the biolink class; for example, a protein such as Shh\ + \ would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`,\ + \ ...\nIn an RDF database, nodes will typically have an rdf:type triples. This\ + \ can be to the most specific biolink class, or potentially to a class more specific\ + \ than something in biolink. For example, a sequence feature `f` may have a rdf:type\ + \ assertion to a SO class such as TF_binding_site, which is more specific than\ + \ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,\ + \ biolink:NamedThing}" + display_name: association_category + cardinality: multi +- id: subject_aspect_qualifier + display_name: gene to disease or phenotypic feature association_subject aspect qualifier +- id: object_direction_qualifier + display_name: gene to disease or phenotypic feature association_object direction + qualifier +- id: predicate + description: A high-level grouping for the relationship type. AKA minimal predicate. + This is analogous to category for nodes. + display_name: gene to disease or phenotypic feature association_predicate +- id: frequency_qualifier + description: a qualifier used in a phenotypic association to state how frequent + the phenotype is observed in the subject + display_name: frequency qualifier +- id: severity_qualifier + description: a qualifier used in a phenotypic association to state how severe the + phenotype is in the subject + display_name: severity qualifier +- id: onset_qualifier + description: a qualifier used in a phenotypic association to state when the phenotype + appears is in the subject + display_name: onset qualifier +- id: sex_qualifier + description: a qualifier used in a phenotypic association to state whether the association + is specific to a particular sex. + display_name: sex qualifier +- id: has_count + description: number of things with a particular property + display_name: has count +- id: has_total + description: total number of things in a particular reference set + display_name: has total +- id: has_quotient + display_name: has quotient +- id: has_percentage + description: equivalent to has quotient multiplied by 100 + display_name: has percentage +- id: subject + description: gene in which variation is shown to cause the disease. + display_name: causal gene to disease association_subject +- id: object + description: connects an association to the object of the association. For example, + in a gene-to-phenotype association, the gene is subject and phenotype is object. + display_name: causal gene to disease association_object diff --git a/golr-views/cell_config.yaml b/golr-views/cell_config.yaml index 481f484dbf..2646eef6f7 100644 --- a/golr-views/cell_config.yaml +++ b/golr-views/cell_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: cell +# metamodel_version: 1.7.0# version: 3.4.0id: cell schema_generating: true display_name: cell document_category: cell diff --git a/golr-views/cell_line_as_a_model_of_disease_association_config.yaml b/golr-views/cell_line_as_a_model_of_disease_association_config.yaml index ba0a824764..6832d25ece 100644 --- a/golr-views/cell_line_as_a_model_of_disease_association_config.yaml +++ b/golr-views/cell_line_as_a_model_of_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: cell_line_as_a_model_of_disease_association +# metamodel_version: 1.7.0# version: 3.4.0id: cell_line_as_a_model_of_disease_association schema_generating: true display_name: cell line as a model of disease association document_category: cell line as a model of disease association diff --git a/golr-views/cell_line_config.yaml b/golr-views/cell_line_config.yaml index eab08c0087..6f3aa860cf 100644 --- a/golr-views/cell_line_config.yaml +++ b/golr-views/cell_line_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: cell_line +# metamodel_version: 1.7.0# version: 3.4.0id: cell_line schema_generating: true display_name: cell line document_category: cell line diff --git a/golr-views/cell_line_to_disease_or_phenotypic_feature_association_config.yaml b/golr-views/cell_line_to_disease_or_phenotypic_feature_association_config.yaml index b1ead63f15..70b43d87a2 100644 --- a/golr-views/cell_line_to_disease_or_phenotypic_feature_association_config.yaml +++ b/golr-views/cell_line_to_disease_or_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: cell_line_to_disease_or_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 3.4.0id: cell_line_to_disease_or_phenotypic_feature_association schema_generating: true description: An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype. diff --git a/golr-views/cellular_component_config.yaml b/golr-views/cellular_component_config.yaml index b12f5345ec..c2dd0f3d6b 100644 --- a/golr-views/cellular_component_config.yaml +++ b/golr-views/cellular_component_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: cellular_component +# metamodel_version: 1.7.0# version: 3.4.0id: cellular_component schema_generating: true description: A location in or around a cell display_name: cellular component diff --git a/golr-views/cellular_organism_config.yaml b/golr-views/cellular_organism_config.yaml index efe4776a85..a334263e6f 100644 --- a/golr-views/cellular_organism_config.yaml +++ b/golr-views/cellular_organism_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: cellular_organism +# metamodel_version: 1.7.0# version: 3.4.0id: cellular_organism schema_generating: true description: '' display_name: cellular organism diff --git a/golr-views/chemical_affects_gene_association_config.yaml b/golr-views/chemical_affects_gene_association_config.yaml index 90210d1f16..7f00da586f 100644 --- a/golr-views/chemical_affects_gene_association_config.yaml +++ b/golr-views/chemical_affects_gene_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: chemical_affects_gene_association +# metamodel_version: 1.7.0# version: 3.4.0id: chemical_affects_gene_association schema_generating: true description: Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity, localization, processing, expression, etc.) diff --git a/golr-views/chemical_entity_assesses_named_thing_association_config.yaml b/golr-views/chemical_entity_assesses_named_thing_association_config.yaml index fc0652214c..f46fa46fa1 100644 --- a/golr-views/chemical_entity_assesses_named_thing_association_config.yaml +++ b/golr-views/chemical_entity_assesses_named_thing_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: chemical_entity_assesses_named_thing_association +# metamodel_version: 1.7.0# version: 3.4.0id: chemical_entity_assesses_named_thing_association schema_generating: true display_name: chemical entity assesses named thing association document_category: chemical entity assesses named thing association diff --git a/golr-views/chemical_entity_config.yaml b/golr-views/chemical_entity_config.yaml index 18197d05c4..17f43d13fc 100644 --- a/golr-views/chemical_entity_config.yaml +++ b/golr-views/chemical_entity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: chemical_entity +# metamodel_version: 1.7.0# version: 3.4.0id: chemical_entity schema_generating: true description: A chemical entity is a physical entity that pertains to chemistry or biochemistry. diff --git a/golr-views/chemical_entity_or_gene_or_gene_product_regulates_gene_association_config.yaml b/golr-views/chemical_entity_or_gene_or_gene_product_regulates_gene_association_config.yaml index 1e15ee1c79..268a084523 100644 --- a/golr-views/chemical_entity_or_gene_or_gene_product_regulates_gene_association_config.yaml +++ b/golr-views/chemical_entity_or_gene_or_gene_product_regulates_gene_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: chemical_entity_or_gene_or_gene_product_regulates_gene_association +# metamodel_version: 1.7.0# version: 3.4.0id: chemical_entity_or_gene_or_gene_product_regulates_gene_association schema_generating: true description: A regulatory relationship between two genes display_name: chemical entity or gene or gene product regulates gene association diff --git a/golr-views/chemical_exposure_config.yaml b/golr-views/chemical_exposure_config.yaml index 7a846d531e..f962ba95c2 100644 --- a/golr-views/chemical_exposure_config.yaml +++ b/golr-views/chemical_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: chemical_exposure +# metamodel_version: 1.7.0# version: 3.4.0id: chemical_exposure schema_generating: true description: A chemical exposure is an intake of a particular chemical entity. display_name: chemical exposure diff --git a/golr-views/chemical_gene_interaction_association_config.yaml b/golr-views/chemical_gene_interaction_association_config.yaml index 7078f32a39..36774264b9 100644 --- a/golr-views/chemical_gene_interaction_association_config.yaml +++ b/golr-views/chemical_gene_interaction_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: chemical_gene_interaction_association +# metamodel_version: 1.7.0# version: 3.4.0id: chemical_gene_interaction_association schema_generating: true description: describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction diff --git a/golr-views/chemical_mixture_config.yaml b/golr-views/chemical_mixture_config.yaml index fb3cf5b3e9..0dc226af2a 100644 --- a/golr-views/chemical_mixture_config.yaml +++ b/golr-views/chemical_mixture_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: chemical_mixture +# metamodel_version: 1.7.0# version: 3.4.0id: chemical_mixture schema_generating: true description: A chemical mixture is a chemical entity composed of two or more molecular entities. diff --git a/golr-views/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association_config.yaml b/golr-views/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association_config.yaml index 44602f607c..b6c730d9f4 100644 --- a/golr-views/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association_config.yaml +++ b/golr-views/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 3.4.0id: chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association schema_generating: true description: This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic diff --git a/golr-views/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association_config.yaml b/golr-views/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association_config.yaml index 4b90545faa..96cca27a37 100644 --- a/golr-views/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association_config.yaml +++ b/golr-views/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 3.4.0id: chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association schema_generating: true description: This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic diff --git a/golr-views/chemical_role_config.yaml b/golr-views/chemical_role_config.yaml index 025c751f5e..2d3cd9cff7 100644 --- a/golr-views/chemical_role_config.yaml +++ b/golr-views/chemical_role_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: chemical_role +# metamodel_version: 1.7.0# version: 3.4.0id: chemical_role schema_generating: true description: "\tA role played by the molecular entity or part thereof within a chemical\ \ context." diff --git a/golr-views/chemical_to_chemical_association_config.yaml b/golr-views/chemical_to_chemical_association_config.yaml index e0497edc27..887b4073e4 100644 --- a/golr-views/chemical_to_chemical_association_config.yaml +++ b/golr-views/chemical_to_chemical_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: chemical_to_chemical_association +# metamodel_version: 1.7.0# version: 3.4.0id: chemical_to_chemical_association schema_generating: true description: A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another. diff --git a/golr-views/chemical_to_chemical_derivation_association_config.yaml b/golr-views/chemical_to_chemical_derivation_association_config.yaml index 01cb93402e..24a2401e43 100644 --- a/golr-views/chemical_to_chemical_derivation_association_config.yaml +++ b/golr-views/chemical_to_chemical_derivation_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: chemical_to_chemical_derivation_association +# metamodel_version: 1.7.0# version: 3.4.0id: chemical_to_chemical_derivation_association schema_generating: true description: "A causal relationship between two chemical entities, where the subject\ \ represents the upstream entity and the object represents the downstream. For any\ diff --git a/golr-views/chemical_to_disease_or_phenotypic_feature_association_config.yaml b/golr-views/chemical_to_disease_or_phenotypic_feature_association_config.yaml index 6024a69a55..12f9adf398 100644 --- a/golr-views/chemical_to_disease_or_phenotypic_feature_association_config.yaml +++ b/golr-views/chemical_to_disease_or_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: chemical_to_disease_or_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 3.4.0id: chemical_to_disease_or_phenotypic_feature_association schema_generating: true description: An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype. diff --git a/golr-views/chemical_to_pathway_association_config.yaml b/golr-views/chemical_to_pathway_association_config.yaml index 04fd728298..518c607f7b 100644 --- a/golr-views/chemical_to_pathway_association_config.yaml +++ b/golr-views/chemical_to_pathway_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: chemical_to_pathway_association +# metamodel_version: 1.7.0# version: 3.4.0id: chemical_to_pathway_association schema_generating: true description: An interaction between a chemical entity and a biological process or pathway. diff --git a/golr-views/chi_squared_analysis_result_config.yaml b/golr-views/chi_squared_analysis_result_config.yaml index 23b32e8874..23a5b2ea1a 100644 --- a/golr-views/chi_squared_analysis_result_config.yaml +++ b/golr-views/chi_squared_analysis_result_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: chi_squared_analysis_result +# metamodel_version: 1.7.0# version: 3.4.0id: chi_squared_analysis_result schema_generating: true description: A result of a chi squared analysis. display_name: chi squared analysis result diff --git a/golr-views/clinical_attribute_config.yaml b/golr-views/clinical_attribute_config.yaml index 554b017bee..c36f1cf9a0 100644 --- a/golr-views/clinical_attribute_config.yaml +++ b/golr-views/clinical_attribute_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: clinical_attribute +# metamodel_version: 1.7.0# version: 3.4.0id: clinical_attribute schema_generating: true description: Attributes relating to a clinical manifestation display_name: clinical attribute diff --git a/golr-views/clinical_course_config.yaml b/golr-views/clinical_course_config.yaml index 6e015e7739..933228ccbc 100644 --- a/golr-views/clinical_course_config.yaml +++ b/golr-views/clinical_course_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: clinical_course +# metamodel_version: 1.7.0# version: 3.4.0id: clinical_course schema_generating: true description: The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual diff --git a/golr-views/clinical_entity_config.yaml b/golr-views/clinical_entity_config.yaml index bc0d5e76db..e083639548 100644 --- a/golr-views/clinical_entity_config.yaml +++ b/golr-views/clinical_entity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: clinical_entity +# metamodel_version: 1.7.0# version: 3.4.0id: clinical_entity schema_generating: true description: Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities diff --git a/golr-views/clinical_finding_config.yaml b/golr-views/clinical_finding_config.yaml index 90b8004d40..6e6ba20810 100644 --- a/golr-views/clinical_finding_config.yaml +++ b/golr-views/clinical_finding_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: clinical_finding +# metamodel_version: 1.7.0# version: 3.4.0id: clinical_finding schema_generating: true description: this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some diff --git a/golr-views/clinical_intervention_config.yaml b/golr-views/clinical_intervention_config.yaml index be9407fc4e..efe9263e2c 100644 --- a/golr-views/clinical_intervention_config.yaml +++ b/golr-views/clinical_intervention_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: clinical_intervention +# metamodel_version: 1.7.0# version: 3.4.0id: clinical_intervention schema_generating: true display_name: clinical intervention document_category: clinical intervention diff --git a/golr-views/clinical_measurement_config.yaml b/golr-views/clinical_measurement_config.yaml index 4cb2481e7c..58cf108046 100644 --- a/golr-views/clinical_measurement_config.yaml +++ b/golr-views/clinical_measurement_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: clinical_measurement +# metamodel_version: 1.7.0# version: 3.4.0id: clinical_measurement schema_generating: true description: A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be diff --git a/golr-views/clinical_modifier_config.yaml b/golr-views/clinical_modifier_config.yaml index 2ac47e4623..cc0fadaa50 100644 --- a/golr-views/clinical_modifier_config.yaml +++ b/golr-views/clinical_modifier_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: clinical_modifier +# metamodel_version: 1.7.0# version: 3.4.0id: clinical_modifier schema_generating: true description: Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, diff --git a/golr-views/clinical_trial_config.yaml b/golr-views/clinical_trial_config.yaml index 0c5df12ec4..88082bce4b 100644 --- a/golr-views/clinical_trial_config.yaml +++ b/golr-views/clinical_trial_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: clinical_trial +# metamodel_version: 1.7.0# version: 3.4.0id: clinical_trial schema_generating: true display_name: clinical trial document_category: clinical trial diff --git a/golr-views/coding_sequence_config.yaml b/golr-views/coding_sequence_config.yaml index 29e2b6cddb..28f5adaf92 100644 --- a/golr-views/coding_sequence_config.yaml +++ b/golr-views/coding_sequence_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: coding_sequence +# metamodel_version: 1.7.0# version: 3.4.0id: coding_sequence schema_generating: true display_name: coding sequence document_category: coding sequence diff --git a/golr-views/cohort_config.yaml b/golr-views/cohort_config.yaml index f6645578a4..1dbc7251ae 100644 --- a/golr-views/cohort_config.yaml +++ b/golr-views/cohort_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: cohort +# metamodel_version: 1.7.0# version: 3.4.0id: cohort schema_generating: true description: A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that diff --git a/golr-views/common_data_element_config.yaml b/golr-views/common_data_element_config.yaml index b8fd024cf9..1098edc42b 100644 --- a/golr-views/common_data_element_config.yaml +++ b/golr-views/common_data_element_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: common_data_element +# metamodel_version: 1.7.0# version: 3.4.0id: common_data_element schema_generating: true description: A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different diff --git a/golr-views/complex_chemical_exposure_config.yaml b/golr-views/complex_chemical_exposure_config.yaml index fd450805ce..7927e47a27 100644 --- a/golr-views/complex_chemical_exposure_config.yaml +++ b/golr-views/complex_chemical_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: complex_chemical_exposure +# metamodel_version: 1.7.0# version: 3.4.0id: complex_chemical_exposure schema_generating: true description: A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug. diff --git a/golr-views/complex_molecular_mixture_config.yaml b/golr-views/complex_molecular_mixture_config.yaml index dadcadb2a4..7fc39d9fe1 100644 --- a/golr-views/complex_molecular_mixture_config.yaml +++ b/golr-views/complex_molecular_mixture_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: complex_molecular_mixture +# metamodel_version: 1.7.0# version: 3.4.0id: complex_molecular_mixture schema_generating: true description: A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry. diff --git a/golr-views/concept_count_analysis_result_config.yaml b/golr-views/concept_count_analysis_result_config.yaml index 0e91262f0b..a44ee065c3 100644 --- a/golr-views/concept_count_analysis_result_config.yaml +++ b/golr-views/concept_count_analysis_result_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: concept_count_analysis_result +# metamodel_version: 1.7.0# version: 3.4.0id: concept_count_analysis_result schema_generating: true description: A result of a concept count analysis. display_name: concept count analysis result diff --git a/golr-views/confidence_level_config.yaml b/golr-views/confidence_level_config.yaml index f7fd64fc00..c28aa31adc 100644 --- a/golr-views/confidence_level_config.yaml +++ b/golr-views/confidence_level_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: confidence_level +# metamodel_version: 1.7.0# version: 3.4.0id: confidence_level schema_generating: true description: Level of confidence in a statement display_name: confidence level diff --git a/golr-views/contributor_association_config.yaml b/golr-views/contributor_association_config.yaml index 50bdb8920b..9780c7fff1 100644 --- a/golr-views/contributor_association_config.yaml +++ b/golr-views/contributor_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: contributor_association +# metamodel_version: 1.7.0# version: 3.4.0id: contributor_association schema_generating: true description: Any association between an entity (such as a publication) and various agents that contribute to its realisation diff --git a/golr-views/correlated_gene_to_disease_association_config.yaml b/golr-views/correlated_gene_to_disease_association_config.yaml new file mode 100644 index 0000000000..d9d3bbab91 --- /dev/null +++ b/golr-views/correlated_gene_to_disease_association_config.yaml @@ -0,0 +1,197 @@ +# metamodel_version: 1.7.0# version: 3.4.0id: correlated_gene_to_disease_association +schema_generating: true +display_name: correlated gene to disease association +document_category: correlated gene to disease association +weight: 20 +fields: +- id: id + description: A unique identifier for an entity. Must be either a CURIE shorthand + for a URI or a complete URI + display_name: id +- id: iri + description: An IRI for an entity. This is determined by the id using expansion + rules. + display_name: iri +- id: name + description: A human-readable name for an attribute or entity. + display_name: name +- id: description + description: a human-readable description of an entity + display_name: description +- id: has_attribute + description: connects any entity to an attribute + display_name: has attribute + cardinality: multi +- id: negated + description: if set to true, then the association is negated i.e. is not true + display_name: negated +- id: qualifiers + description: connects an association to qualifiers that modify or qualify the meaning + of that association + display_name: qualifiers + cardinality: multi +- id: publications + description: One or more publications that report the statement expressed in an Association, + or provide information used as evidence supporting this statement. + display_name: publications + cardinality: multi +- id: has_evidence + description: connects an association to an instance of supporting evidence + display_name: has evidence + cardinality: multi +- id: knowledge_source + description: An Information Resource from which the knowledge expressed in an Association + was retrieved, directly or indirectly. This can be any resource through which + the knowledge passed on its way to its currently serialized form. In practice, + implementers should use one of the more specific subtypes of this generic property. + display_name: knowledge source +- id: primary_knowledge_source + description: The most upstream source of the knowledge expressed in an Association + that an implementer can identify. Performing a rigorous analysis of upstream + data providers is expected; every effort is made to catalog the most upstream + source of data in this property. Only one data source should be declared primary + in any association. "aggregator knowledge source" can be used to capture non-primary + sources. + display_name: primary knowledge source +- id: aggregator_knowledge_source + description: An intermediate aggregator resource from which knowledge expressed + in an Association was retrieved downstream of the original source, on its path + to its current serialized form. + display_name: aggregator knowledge source + cardinality: multi +- id: timepoint + description: a point in time + display_name: timepoint +- id: original_subject + description: used to hold the original subject of a relation (or predicate) that + an external knowledge source uses before transformation to match the biolink-model + specification. + display_name: original subject +- id: original_predicate + description: used to hold the original relation/predicate that an external knowledge + source uses before transformation to match the biolink-model specification. + display_name: original predicate +- id: original_object + description: used to hold the original object of a relation (or predicate) that + an external knowledge source uses before transformation to match the biolink-model + specification. + display_name: original object +- id: subject_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category +- id: object_category + description: Used to hold the biolink class/category of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category +- id: subject_closure + description: Used to hold the subject closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject closure + cardinality: multi +- id: object_closure + description: Used to hold the object closure of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object closure + cardinality: multi +- id: subject_category_closure + description: Used to hold the subject category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject category closure + cardinality: multi +- id: object_category_closure + description: Used to hold the object category closure of an association. This is + a denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object category closure + cardinality: multi +- id: subject_namespace + description: Used to hold the subject namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: subject namespace +- id: object_namespace + description: Used to hold the object namespace of an association. This is a denormalized field + used primarily in the SQL serialization of a knowledge graph via KGX. + display_name: object namespace +- id: subject_label_closure + description: Used to hold the subject label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: subject label closure + cardinality: multi +- id: object_label_closure + description: Used to hold the object label closure of an association. This is a + denormalized field used primarily in the SQL serialization of a knowledge graph + via KGX. + display_name: object label closure + cardinality: multi +- id: retrieval_source_ids + description: A list of retrieval sources that served as a source of knowledge expressed + in an Edge, or a source of data used to generate this knowledge. + display_name: retrieval source ids + cardinality: multi +- id: type + description: rdf:type of biolink:Association should be fixed at rdf:Statement + display_name: association_type + cardinality: multi +- id: category + description: "Name of the high level ontology class in which this entity is categorized.\ + \ Corresponds to the label for the biolink entity type class.\n * In a neo4j database\ + \ this MAY correspond to the neo4j label tag.\n * In an RDF database it should\ + \ be a biolink model class URI.\nThis field is multi-valued. It should include\ + \ values for ancestors of the biolink class; for example, a protein such as Shh\ + \ would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`,\ + \ ...\nIn an RDF database, nodes will typically have an rdf:type triples. This\ + \ can be to the most specific biolink class, or potentially to a class more specific\ + \ than something in biolink. For example, a sequence feature `f` may have a rdf:type\ + \ assertion to a SO class such as TF_binding_site, which is more specific than\ + \ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,\ + \ biolink:NamedThing}" + display_name: association_category + cardinality: multi +- id: subject_aspect_qualifier + display_name: gene to disease or phenotypic feature association_subject aspect qualifier +- id: object_direction_qualifier + display_name: gene to disease or phenotypic feature association_object direction + qualifier +- id: predicate + description: A high-level grouping for the relationship type. AKA minimal predicate. + This is analogous to category for nodes. + display_name: gene to disease or phenotypic feature association_predicate +- id: frequency_qualifier + description: a qualifier used in a phenotypic association to state how frequent + the phenotype is observed in the subject + display_name: frequency qualifier +- id: severity_qualifier + description: a qualifier used in a phenotypic association to state how severe the + phenotype is in the subject + display_name: severity qualifier +- id: onset_qualifier + description: a qualifier used in a phenotypic association to state when the phenotype + appears is in the subject + display_name: onset qualifier +- id: sex_qualifier + description: a qualifier used in a phenotypic association to state whether the association + is specific to a particular sex. + display_name: sex qualifier +- id: has_count + description: number of things with a particular property + display_name: has count +- id: has_total + description: total number of things in a particular reference set + display_name: has total +- id: has_quotient + display_name: has quotient +- id: has_percentage + description: equivalent to has quotient multiplied by 100 + display_name: has percentage +- id: subject + description: gene in which variation is shown to correlate with the disease. + display_name: correlated gene to disease association_subject +- id: object + description: connects an association to the object of the association. For example, + in a gene-to-phenotype association, the gene is subject and phenotype is object. + display_name: correlated gene to disease association_object diff --git a/golr-views/dataset_config.yaml b/golr-views/dataset_config.yaml index 5ca0a2740d..c4a8e1eb03 100644 --- a/golr-views/dataset_config.yaml +++ b/golr-views/dataset_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: dataset +# metamodel_version: 1.7.0# version: 3.4.0id: dataset schema_generating: true description: an item that refers to a collection of data from a data source. display_name: dataset diff --git a/golr-views/dataset_distribution_config.yaml b/golr-views/dataset_distribution_config.yaml index c8401955ef..ac814fca5d 100644 --- a/golr-views/dataset_distribution_config.yaml +++ b/golr-views/dataset_distribution_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: dataset_distribution +# metamodel_version: 1.7.0# version: 3.4.0id: dataset_distribution schema_generating: true description: an item that holds distribution level information about a dataset. display_name: dataset distribution diff --git a/golr-views/dataset_summary_config.yaml b/golr-views/dataset_summary_config.yaml index 3f099a18bd..67f6baf07e 100644 --- a/golr-views/dataset_summary_config.yaml +++ b/golr-views/dataset_summary_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: dataset_summary +# metamodel_version: 1.7.0# version: 3.4.0id: dataset_summary schema_generating: true description: an item that holds summary level information about a dataset. display_name: dataset summary diff --git a/golr-views/dataset_version_config.yaml b/golr-views/dataset_version_config.yaml index 36f7ed7918..22293b37ea 100644 --- a/golr-views/dataset_version_config.yaml +++ b/golr-views/dataset_version_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: dataset_version +# metamodel_version: 1.7.0# version: 3.4.0id: dataset_version schema_generating: true description: an item that holds version level information about a dataset. display_name: dataset version diff --git a/golr-views/device_config.yaml b/golr-views/device_config.yaml index 9cc8b2a894..85af4fab83 100644 --- a/golr-views/device_config.yaml +++ b/golr-views/device_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: device +# metamodel_version: 1.7.0# version: 3.4.0id: device schema_generating: true description: A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment diff --git a/golr-views/diagnostic_aid_config.yaml b/golr-views/diagnostic_aid_config.yaml index b924c84a61..7222011ed0 100644 --- a/golr-views/diagnostic_aid_config.yaml +++ b/golr-views/diagnostic_aid_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: diagnostic_aid +# metamodel_version: 1.7.0# version: 3.4.0id: diagnostic_aid schema_generating: true description: A device or substance used to help diagnose disease or injury display_name: diagnostic aid diff --git a/golr-views/disease_config.yaml b/golr-views/disease_config.yaml index 9e2340137b..f013e59b86 100644 --- a/golr-views/disease_config.yaml +++ b/golr-views/disease_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: disease +# metamodel_version: 1.7.0# version: 3.4.0id: disease schema_generating: true description: A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct diff --git a/golr-views/disease_or_phenotypic_feature_config.yaml b/golr-views/disease_or_phenotypic_feature_config.yaml index 02568ed9b0..62868e9b77 100644 --- a/golr-views/disease_or_phenotypic_feature_config.yaml +++ b/golr-views/disease_or_phenotypic_feature_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: disease_or_phenotypic_feature +# metamodel_version: 1.7.0# version: 3.4.0id: disease_or_phenotypic_feature schema_generating: true description: Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please diff --git a/golr-views/disease_or_phenotypic_feature_exposure_config.yaml b/golr-views/disease_or_phenotypic_feature_exposure_config.yaml index 67c8b05993..0c777e9f33 100644 --- a/golr-views/disease_or_phenotypic_feature_exposure_config.yaml +++ b/golr-views/disease_or_phenotypic_feature_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: disease_or_phenotypic_feature_exposure +# metamodel_version: 1.7.0# version: 3.4.0id: disease_or_phenotypic_feature_exposure schema_generating: true description: A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an diff --git a/golr-views/disease_or_phenotypic_feature_to_genetic_inheritance_association_config.yaml b/golr-views/disease_or_phenotypic_feature_to_genetic_inheritance_association_config.yaml index 2cb4d1d08d..424336cfe7 100644 --- a/golr-views/disease_or_phenotypic_feature_to_genetic_inheritance_association_config.yaml +++ b/golr-views/disease_or_phenotypic_feature_to_genetic_inheritance_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: disease_or_phenotypic_feature_to_genetic_inheritance_association +# metamodel_version: 1.7.0# version: 3.4.0id: disease_or_phenotypic_feature_to_genetic_inheritance_association schema_generating: true description: An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance. diff --git a/golr-views/disease_or_phenotypic_feature_to_location_association_config.yaml b/golr-views/disease_or_phenotypic_feature_to_location_association_config.yaml index b5e9f45578..c9124d2a88 100644 --- a/golr-views/disease_or_phenotypic_feature_to_location_association_config.yaml +++ b/golr-views/disease_or_phenotypic_feature_to_location_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: disease_or_phenotypic_feature_to_location_association +# metamodel_version: 1.7.0# version: 3.4.0id: disease_or_phenotypic_feature_to_location_association schema_generating: true description: An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site. diff --git a/golr-views/disease_to_exposure_event_association_config.yaml b/golr-views/disease_to_exposure_event_association_config.yaml index c2693b4a35..c9e3343ef6 100644 --- a/golr-views/disease_to_exposure_event_association_config.yaml +++ b/golr-views/disease_to_exposure_event_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: disease_to_exposure_event_association +# metamodel_version: 1.7.0# version: 3.4.0id: disease_to_exposure_event_association schema_generating: true description: An association between an exposure event and a disease. display_name: disease to exposure event association diff --git a/golr-views/disease_to_phenotypic_feature_association_config.yaml b/golr-views/disease_to_phenotypic_feature_association_config.yaml index 4b485d0121..cd5a04fbc5 100644 --- a/golr-views/disease_to_phenotypic_feature_association_config.yaml +++ b/golr-views/disease_to_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: disease_to_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 3.4.0id: disease_to_phenotypic_feature_association schema_generating: true description: An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way. diff --git a/golr-views/drug_config.yaml b/golr-views/drug_config.yaml index eda66ba160..8500891d43 100644 --- a/golr-views/drug_config.yaml +++ b/golr-views/drug_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: drug +# metamodel_version: 1.7.0# version: 3.4.0id: drug schema_generating: true description: A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease diff --git a/golr-views/drug_exposure_config.yaml b/golr-views/drug_exposure_config.yaml index 7b7ad0c999..e59cd464a5 100644 --- a/golr-views/drug_exposure_config.yaml +++ b/golr-views/drug_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: drug_exposure +# metamodel_version: 1.7.0# version: 3.4.0id: drug_exposure schema_generating: true description: A drug exposure is an intake of a particular drug. display_name: drug exposure diff --git a/golr-views/drug_label_config.yaml b/golr-views/drug_label_config.yaml index 07ebc0e52d..d59005f506 100644 --- a/golr-views/drug_label_config.yaml +++ b/golr-views/drug_label_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: drug_label +# metamodel_version: 1.7.0# version: 3.4.0id: drug_label schema_generating: true description: 'a document accompanying a drug or its container that provides written, printed or graphic information about the drug, including drug contents, specific @@ -113,3 +113,4 @@ fields: knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass. display_name: publication_publication type + cardinality: multi diff --git a/golr-views/drug_to_gene_association_config.yaml b/golr-views/drug_to_gene_association_config.yaml index dd1623fd2f..6bd9db4436 100644 --- a/golr-views/drug_to_gene_association_config.yaml +++ b/golr-views/drug_to_gene_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: drug_to_gene_association +# metamodel_version: 1.7.0# version: 3.4.0id: drug_to_gene_association schema_generating: true description: An interaction between a drug and a gene or gene product. display_name: drug to gene association diff --git a/golr-views/drug_to_gene_interaction_exposure_config.yaml b/golr-views/drug_to_gene_interaction_exposure_config.yaml index 4a0f0e448b..99ab6c2295 100644 --- a/golr-views/drug_to_gene_interaction_exposure_config.yaml +++ b/golr-views/drug_to_gene_interaction_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: drug_to_gene_interaction_exposure +# metamodel_version: 1.7.0# version: 3.4.0id: drug_to_gene_interaction_exposure schema_generating: true description: drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, diff --git a/golr-views/druggable_gene_to_disease_association_config.yaml b/golr-views/druggable_gene_to_disease_association_config.yaml index 6cd997a26e..9c13fb1045 100644 --- a/golr-views/druggable_gene_to_disease_association_config.yaml +++ b/golr-views/druggable_gene_to_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: druggable_gene_to_disease_association +# metamodel_version: 1.7.0# version: 3.4.0id: druggable_gene_to_disease_association schema_generating: true display_name: druggable gene to disease association document_category: druggable gene to disease association @@ -22,10 +22,6 @@ fields: description: connects any entity to an attribute display_name: has attribute cardinality: multi -- id: object - description: connects an association to the object of the association. For example, - in a gene-to-phenotype association, the gene is subject and phenotype is object. - display_name: object - id: negated description: if set to true, then the association is negated i.e. is not true display_name: negated @@ -152,6 +148,42 @@ fields: \ biolink:NamedThing}" display_name: association_category cardinality: multi +- id: subject_aspect_qualifier + display_name: gene to disease or phenotypic feature association_subject aspect qualifier +- id: object_direction_qualifier + display_name: gene to disease or phenotypic feature association_object direction + qualifier +- id: frequency_qualifier + description: a qualifier used in a phenotypic association to state how frequent + the phenotype is observed in the subject + display_name: frequency qualifier +- id: severity_qualifier + description: a qualifier used in a phenotypic association to state how severe the + phenotype is in the subject + display_name: severity qualifier +- id: onset_qualifier + description: a qualifier used in a phenotypic association to state when the phenotype + appears is in the subject + display_name: onset qualifier +- id: sex_qualifier + description: a qualifier used in a phenotypic association to state whether the association + is specific to a particular sex. + display_name: sex qualifier +- id: has_count + description: number of things with a particular property + display_name: has count +- id: has_total + description: total number of things in a particular reference set + display_name: has total +- id: has_quotient + display_name: has quotient +- id: has_percentage + description: equivalent to has quotient multiplied by 100 + display_name: has percentage +- id: object + description: connects an association to the object of the association. For example, + in a gene-to-phenotype association, the gene is subject and phenotype is object. + display_name: gene to disease association_object - id: subject description: gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule @@ -165,15 +197,3 @@ fields: description: connects an association to an instance of supporting evidence display_name: druggable gene to disease association_has evidence cardinality: multi -- id: frequency_qualifier - description: a qualifier used in a phenotypic association to state how frequent - the phenotype is observed in the subject - display_name: frequency qualifier -- id: severity_qualifier - description: a qualifier used in a phenotypic association to state how severe the - phenotype is in the subject - display_name: severity qualifier -- id: onset_qualifier - description: a qualifier used in a phenotypic association to state when the phenotype - appears is in the subject - display_name: onset qualifier diff --git a/golr-views/entity_to_disease_association_config.yaml b/golr-views/entity_to_disease_association_config.yaml index 0aa973e60a..1204cda3f9 100644 --- a/golr-views/entity_to_disease_association_config.yaml +++ b/golr-views/entity_to_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: entity_to_disease_association +# metamodel_version: 1.7.0# version: 3.4.0id: entity_to_disease_association schema_generating: true display_name: entity to disease association document_category: entity to disease association diff --git a/golr-views/entity_to_phenotypic_feature_association_config.yaml b/golr-views/entity_to_phenotypic_feature_association_config.yaml index 9a5fb2e186..88de199605 100644 --- a/golr-views/entity_to_phenotypic_feature_association_config.yaml +++ b/golr-views/entity_to_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: entity_to_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 3.4.0id: entity_to_phenotypic_feature_association schema_generating: true display_name: entity to phenotypic feature association document_category: entity to phenotypic feature association diff --git a/golr-views/environmental_exposure_config.yaml b/golr-views/environmental_exposure_config.yaml index 367290acad..f6bffca235 100644 --- a/golr-views/environmental_exposure_config.yaml +++ b/golr-views/environmental_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: environmental_exposure +# metamodel_version: 1.7.0# version: 3.4.0id: environmental_exposure schema_generating: true description: A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) diff --git a/golr-views/environmental_feature_config.yaml b/golr-views/environmental_feature_config.yaml index c3e5a1516c..ce1e4d2d54 100644 --- a/golr-views/environmental_feature_config.yaml +++ b/golr-views/environmental_feature_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: environmental_feature +# metamodel_version: 1.7.0# version: 3.4.0id: environmental_feature schema_generating: true display_name: environmental feature document_category: environmental feature diff --git a/golr-views/environmental_food_contaminant_config.yaml b/golr-views/environmental_food_contaminant_config.yaml index ba44d8c05a..1627862828 100644 --- a/golr-views/environmental_food_contaminant_config.yaml +++ b/golr-views/environmental_food_contaminant_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: environmental_food_contaminant +# metamodel_version: 1.7.0# version: 3.4.0id: environmental_food_contaminant schema_generating: true display_name: environmental food contaminant document_category: environmental food contaminant diff --git a/golr-views/environmental_process_config.yaml b/golr-views/environmental_process_config.yaml index f9388d7839..cf4e10c383 100644 --- a/golr-views/environmental_process_config.yaml +++ b/golr-views/environmental_process_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: environmental_process +# metamodel_version: 1.7.0# version: 3.4.0id: environmental_process schema_generating: true display_name: environmental process document_category: environmental process diff --git a/golr-views/event_config.yaml b/golr-views/event_config.yaml index d6a53a73eb..e7a110ff8c 100644 --- a/golr-views/event_config.yaml +++ b/golr-views/event_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: event +# metamodel_version: 1.7.0# version: 3.4.0id: event schema_generating: true description: Something that happens at a given place and time. display_name: event diff --git a/golr-views/evidence_type_config.yaml b/golr-views/evidence_type_config.yaml index d2c519ba55..7731e211ba 100644 --- a/golr-views/evidence_type_config.yaml +++ b/golr-views/evidence_type_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: evidence_type +# metamodel_version: 1.7.0# version: 3.4.0id: evidence_type schema_generating: true description: Class of evidence that supports an association display_name: evidence type diff --git a/golr-views/exon_config.yaml b/golr-views/exon_config.yaml index 5814d0450d..84995d160a 100644 --- a/golr-views/exon_config.yaml +++ b/golr-views/exon_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: exon +# metamodel_version: 1.7.0# version: 3.4.0id: exon schema_generating: true description: A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing. diff --git a/golr-views/exon_to_transcript_relationship_config.yaml b/golr-views/exon_to_transcript_relationship_config.yaml index d6a6f2e45a..a6ee439d5b 100644 --- a/golr-views/exon_to_transcript_relationship_config.yaml +++ b/golr-views/exon_to_transcript_relationship_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: exon_to_transcript_relationship +# metamodel_version: 1.7.0# version: 3.4.0id: exon_to_transcript_relationship schema_generating: true description: A transcript is formed from multiple exons display_name: exon to transcript relationship diff --git a/golr-views/exposure_event_to_outcome_association_config.yaml b/golr-views/exposure_event_to_outcome_association_config.yaml index 9e62434bc7..2cc7bca9c1 100644 --- a/golr-views/exposure_event_to_outcome_association_config.yaml +++ b/golr-views/exposure_event_to_outcome_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: exposure_event_to_outcome_association +# metamodel_version: 1.7.0# version: 3.4.0id: exposure_event_to_outcome_association schema_generating: true description: An association between an exposure event and an outcome. display_name: exposure event to outcome association diff --git a/golr-views/exposure_event_to_phenotypic_feature_association_config.yaml b/golr-views/exposure_event_to_phenotypic_feature_association_config.yaml index 2bf88a0594..2955b25fdd 100644 --- a/golr-views/exposure_event_to_phenotypic_feature_association_config.yaml +++ b/golr-views/exposure_event_to_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: exposure_event_to_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 3.4.0id: exposure_event_to_phenotypic_feature_association schema_generating: true description: Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype. diff --git a/golr-views/food_additive_config.yaml b/golr-views/food_additive_config.yaml index 2f3e1ff25b..24cdb5e05d 100644 --- a/golr-views/food_additive_config.yaml +++ b/golr-views/food_additive_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: food_additive +# metamodel_version: 1.7.0# version: 3.4.0id: food_additive schema_generating: true display_name: food additive document_category: food additive diff --git a/golr-views/food_config.yaml b/golr-views/food_config.yaml index 8063e23457..1ea86a7119 100644 --- a/golr-views/food_config.yaml +++ b/golr-views/food_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: food +# metamodel_version: 1.7.0# version: 3.4.0id: food schema_generating: true description: A substance consumed by a living organism as a source of nutrition display_name: food diff --git a/golr-views/functional_association_config.yaml b/golr-views/functional_association_config.yaml index b940f6ea60..1982a72943 100644 --- a/golr-views/functional_association_config.yaml +++ b/golr-views/functional_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: functional_association +# metamodel_version: 1.7.0# version: 3.4.0id: functional_association schema_generating: true description: An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process diff --git a/golr-views/fungus_config.yaml b/golr-views/fungus_config.yaml index 8181b5b1a9..e9054d3521 100644 --- a/golr-views/fungus_config.yaml +++ b/golr-views/fungus_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: fungus +# metamodel_version: 1.7.0# version: 3.4.0id: fungus schema_generating: true description: A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, smuts, molds, etc. They reproduce either diff --git a/golr-views/gene_as_a_model_of_disease_association_config.yaml b/golr-views/gene_as_a_model_of_disease_association_config.yaml index af119452db..e7cf938967 100644 --- a/golr-views/gene_as_a_model_of_disease_association_config.yaml +++ b/golr-views/gene_as_a_model_of_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: gene_as_a_model_of_disease_association +# metamodel_version: 1.7.0# version: 3.4.0id: gene_as_a_model_of_disease_association schema_generating: true display_name: gene as a model of disease association document_category: gene as a model of disease association @@ -22,14 +22,6 @@ fields: description: connects any entity to an attribute display_name: has attribute cardinality: multi -- id: predicate - description: A high-level grouping for the relationship type. AKA minimal predicate. - This is analogous to category for nodes. - display_name: predicate -- id: object - description: connects an association to the object of the association. For example, - in a gene-to-phenotype association, the gene is subject and phenotype is object. - display_name: object - id: negated description: if set to true, then the association is negated i.e. is not true display_name: negated @@ -160,11 +152,15 @@ fields: \ biolink:NamedThing}" display_name: association_category cardinality: multi -- id: subject - description: A gene that has a role in modeling the disease. This may be a model - organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate - core features of the disease. - display_name: gene as a model of disease association_subject +- id: subject_aspect_qualifier + display_name: gene to disease or phenotypic feature association_subject aspect qualifier +- id: object_direction_qualifier + display_name: gene to disease or phenotypic feature association_object direction + qualifier +- id: predicate + description: A high-level grouping for the relationship type. AKA minimal predicate. + This is analogous to category for nodes. + display_name: gene to disease or phenotypic feature association_predicate - id: frequency_qualifier description: a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject @@ -177,3 +173,27 @@ fields: description: a qualifier used in a phenotypic association to state when the phenotype appears is in the subject display_name: onset qualifier +- id: sex_qualifier + description: a qualifier used in a phenotypic association to state whether the association + is specific to a particular sex. + display_name: sex qualifier +- id: has_count + description: number of things with a particular property + display_name: has count +- id: has_total + description: total number of things in a particular reference set + display_name: has total +- id: has_quotient + display_name: has quotient +- id: has_percentage + description: equivalent to has quotient multiplied by 100 + display_name: has percentage +- id: object + description: connects an association to the object of the association. For example, + in a gene-to-phenotype association, the gene is subject and phenotype is object. + display_name: gene to disease association_object +- id: subject + description: A gene that has a role in modeling the disease. This may be a model + organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate + core features of the disease. + display_name: gene as a model of disease association_subject diff --git a/golr-views/gene_config.yaml b/golr-views/gene_config.yaml index 4801265aa5..c81f64f0e4 100644 --- a/golr-views/gene_config.yaml +++ b/golr-views/gene_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: gene +# metamodel_version: 1.7.0# version: 3.4.0id: gene schema_generating: true description: A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, diff --git a/golr-views/gene_family_config.yaml b/golr-views/gene_family_config.yaml index b73fae7ae1..364ede66f7 100644 --- a/golr-views/gene_family_config.yaml +++ b/golr-views/gene_family_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: gene_family +# metamodel_version: 1.7.0# version: 3.4.0id: gene_family schema_generating: true description: any grouping of multiple genes or gene products related by common descent display_name: gene family diff --git a/golr-views/gene_has_variant_that_contributes_to_disease_association_config.yaml b/golr-views/gene_has_variant_that_contributes_to_disease_association_config.yaml index 9f38bca80e..87364b49c9 100644 --- a/golr-views/gene_has_variant_that_contributes_to_disease_association_config.yaml +++ b/golr-views/gene_has_variant_that_contributes_to_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: gene_has_variant_that_contributes_to_disease_association +# metamodel_version: 1.7.0# version: 3.4.0id: gene_has_variant_that_contributes_to_disease_association schema_generating: true display_name: gene has variant that contributes to disease association document_category: gene has variant that contributes to disease association @@ -152,6 +152,38 @@ fields: \ biolink:NamedThing}" display_name: association_category cardinality: multi +- id: subject_aspect_qualifier + display_name: gene to disease or phenotypic feature association_subject aspect qualifier +- id: object_direction_qualifier + display_name: gene to disease or phenotypic feature association_object direction + qualifier +- id: frequency_qualifier + description: a qualifier used in a phenotypic association to state how frequent + the phenotype is observed in the subject + display_name: frequency qualifier +- id: severity_qualifier + description: a qualifier used in a phenotypic association to state how severe the + phenotype is in the subject + display_name: severity qualifier +- id: onset_qualifier + description: a qualifier used in a phenotypic association to state when the phenotype + appears is in the subject + display_name: onset qualifier +- id: sex_qualifier + description: a qualifier used in a phenotypic association to state whether the association + is specific to a particular sex. + display_name: sex qualifier +- id: has_count + description: number of things with a particular property + display_name: has count +- id: has_total + description: total number of things in a particular reference set + display_name: has total +- id: has_quotient + display_name: has quotient +- id: has_percentage + description: equivalent to has quotient multiplied by 100 + display_name: has percentage - id: subject_form_or_variant_qualifier display_name: subject form or variant qualifier - id: subject diff --git a/golr-views/gene_to_disease_association_config.yaml b/golr-views/gene_to_disease_association_config.yaml index 893862bed8..bbbc942827 100644 --- a/golr-views/gene_to_disease_association_config.yaml +++ b/golr-views/gene_to_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: gene_to_disease_association +# metamodel_version: 1.7.0# version: 3.4.0id: gene_to_disease_association schema_generating: true display_name: gene to disease association document_category: gene to disease association @@ -22,18 +22,6 @@ fields: description: connects any entity to an attribute display_name: has attribute cardinality: multi -- id: subject - description: connects an association to the subject of the association. For example, - in a gene-to-phenotype association, the gene is subject and phenotype is object. - display_name: subject -- id: predicate - description: A high-level grouping for the relationship type. AKA minimal predicate. - This is analogous to category for nodes. - display_name: predicate -- id: object - description: connects an association to the object of the association. For example, - in a gene-to-phenotype association, the gene is subject and phenotype is object. - display_name: object - id: negated description: if set to true, then the association is negated i.e. is not true display_name: negated @@ -164,3 +152,47 @@ fields: \ biolink:NamedThing}" display_name: association_category cardinality: multi +- id: subject_aspect_qualifier + display_name: gene to disease or phenotypic feature association_subject aspect qualifier +- id: object_direction_qualifier + display_name: gene to disease or phenotypic feature association_object direction + qualifier +- id: predicate + description: A high-level grouping for the relationship type. AKA minimal predicate. + This is analogous to category for nodes. + display_name: gene to disease or phenotypic feature association_predicate +- id: frequency_qualifier + description: a qualifier used in a phenotypic association to state how frequent + the phenotype is observed in the subject + display_name: frequency qualifier +- id: severity_qualifier + description: a qualifier used in a phenotypic association to state how severe the + phenotype is in the subject + display_name: severity qualifier +- id: onset_qualifier + description: a qualifier used in a phenotypic association to state when the phenotype + appears is in the subject + display_name: onset qualifier +- id: sex_qualifier + description: a qualifier used in a phenotypic association to state whether the association + is specific to a particular sex. + display_name: sex qualifier +- id: has_count + description: number of things with a particular property + display_name: has count +- id: has_total + description: total number of things in a particular reference set + display_name: has total +- id: has_quotient + display_name: has quotient +- id: has_percentage + description: equivalent to has quotient multiplied by 100 + display_name: has percentage +- id: subject + description: gene in which variation is correlated with the disease, may be protective + or causative or associative, or as a model + display_name: gene to disease association_subject +- id: object + description: connects an association to the object of the association. For example, + in a gene-to-phenotype association, the gene is subject and phenotype is object. + display_name: gene to disease association_object diff --git a/golr-views/gene_to_disease_or_phenotypic_feature_association_config.yaml b/golr-views/gene_to_disease_or_phenotypic_feature_association_config.yaml index 75f30b8623..ad9ee40410 100644 --- a/golr-views/gene_to_disease_or_phenotypic_feature_association_config.yaml +++ b/golr-views/gene_to_disease_or_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: gene_to_disease_or_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 3.4.0id: gene_to_disease_or_phenotypic_feature_association schema_generating: true display_name: gene to disease or phenotypic feature association document_category: gene to disease or phenotypic feature association diff --git a/golr-views/gene_to_expression_site_association_config.yaml b/golr-views/gene_to_expression_site_association_config.yaml index 2d74f428a3..4c25dfca44 100644 --- a/golr-views/gene_to_expression_site_association_config.yaml +++ b/golr-views/gene_to_expression_site_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: gene_to_expression_site_association +# metamodel_version: 1.7.0# version: 3.4.0id: gene_to_expression_site_association schema_generating: true description: An association between a gene and a gene expression site, possibly qualified by stage/timing info. diff --git a/golr-views/gene_to_gene_coexpression_association_config.yaml b/golr-views/gene_to_gene_coexpression_association_config.yaml index 2ae2cceb1f..81ed15c802 100644 --- a/golr-views/gene_to_gene_coexpression_association_config.yaml +++ b/golr-views/gene_to_gene_coexpression_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: gene_to_gene_coexpression_association +# metamodel_version: 1.7.0# version: 3.4.0id: gene_to_gene_coexpression_association schema_generating: true description: Indicates that two genes are co-expressed, generally under the same conditions. display_name: gene to gene coexpression association diff --git a/golr-views/gene_to_gene_family_association_config.yaml b/golr-views/gene_to_gene_family_association_config.yaml index e34a11c61c..68646c3d79 100644 --- a/golr-views/gene_to_gene_family_association_config.yaml +++ b/golr-views/gene_to_gene_family_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: gene_to_gene_family_association +# metamodel_version: 1.7.0# version: 3.4.0id: gene_to_gene_family_association schema_generating: true description: Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally diff --git a/golr-views/gene_to_gene_homology_association_config.yaml b/golr-views/gene_to_gene_homology_association_config.yaml index 224c0cd5f6..c1511f9667 100644 --- a/golr-views/gene_to_gene_homology_association_config.yaml +++ b/golr-views/gene_to_gene_homology_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: gene_to_gene_homology_association +# metamodel_version: 1.7.0# version: 3.4.0id: gene_to_gene_homology_association schema_generating: true description: A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case diff --git a/golr-views/gene_to_gene_product_relationship_config.yaml b/golr-views/gene_to_gene_product_relationship_config.yaml index 081fc1286e..68251587c5 100644 --- a/golr-views/gene_to_gene_product_relationship_config.yaml +++ b/golr-views/gene_to_gene_product_relationship_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: gene_to_gene_product_relationship +# metamodel_version: 1.7.0# version: 3.4.0id: gene_to_gene_product_relationship schema_generating: true description: A gene is transcribed and potentially translated to a gene product display_name: gene to gene product relationship diff --git a/golr-views/gene_to_go_term_association_config.yaml b/golr-views/gene_to_go_term_association_config.yaml index d0cc896657..210ccbcf9b 100644 --- a/golr-views/gene_to_go_term_association_config.yaml +++ b/golr-views/gene_to_go_term_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: gene_to_go_term_association +# metamodel_version: 1.7.0# version: 3.4.0id: gene_to_go_term_association schema_generating: true display_name: gene to go term association document_category: gene to go term association diff --git a/golr-views/gene_to_pathway_association_config.yaml b/golr-views/gene_to_pathway_association_config.yaml index 04d51d2268..f04cf262c9 100644 --- a/golr-views/gene_to_pathway_association_config.yaml +++ b/golr-views/gene_to_pathway_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: gene_to_pathway_association +# metamodel_version: 1.7.0# version: 3.4.0id: gene_to_pathway_association schema_generating: true description: An interaction between a gene or gene product and a biological process or pathway. diff --git a/golr-views/gene_to_phenotype_association_config.yaml b/golr-views/gene_to_phenotype_association_config.yaml index a0ba49d2ec..ca526993b0 100644 --- a/golr-views/gene_to_phenotype_association_config.yaml +++ b/golr-views/gene_to_phenotype_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: gene_to_phenotype_association +# metamodel_version: 1.7.0# version: 3.4.0id: gene_to_phenotype_association schema_generating: true display_name: gene to phenotype association document_category: gene to phenotype association @@ -22,18 +22,6 @@ fields: description: connects any entity to an attribute display_name: has attribute cardinality: multi -- id: subject - description: connects an association to the subject of the association. For example, - in a gene-to-phenotype association, the gene is subject and phenotype is object. - display_name: subject -- id: predicate - description: A high-level grouping for the relationship type. AKA minimal predicate. - This is analogous to category for nodes. - display_name: predicate -- id: object - description: connects an association to the object of the association. For example, - in a gene-to-phenotype association, the gene is subject and phenotype is object. - display_name: object - id: negated description: if set to true, then the association is negated i.e. is not true display_name: negated @@ -164,3 +152,46 @@ fields: \ biolink:NamedThing}" display_name: association_category cardinality: multi +- id: subject_aspect_qualifier + display_name: gene to disease or phenotypic feature association_subject aspect qualifier +- id: object_direction_qualifier + display_name: gene to disease or phenotypic feature association_object direction + qualifier +- id: predicate + description: A high-level grouping for the relationship type. AKA minimal predicate. + This is analogous to category for nodes. + display_name: gene to disease or phenotypic feature association_predicate +- id: frequency_qualifier + description: a qualifier used in a phenotypic association to state how frequent + the phenotype is observed in the subject + display_name: frequency qualifier +- id: severity_qualifier + description: a qualifier used in a phenotypic association to state how severe the + phenotype is in the subject + display_name: severity qualifier +- id: onset_qualifier + description: a qualifier used in a phenotypic association to state when the phenotype + appears is in the subject + display_name: onset qualifier +- id: sex_qualifier + description: a qualifier used in a phenotypic association to state whether the association + is specific to a particular sex. + display_name: sex qualifier +- id: has_count + description: number of things with a particular property + display_name: has count +- id: has_total + description: total number of things in a particular reference set + display_name: has total +- id: has_quotient + display_name: has quotient +- id: has_percentage + description: equivalent to has quotient multiplied by 100 + display_name: has percentage +- id: subject + description: gene in which variation is correlated with the phenotypic feature + display_name: gene to phenotype association_subject +- id: object + description: connects an association to the object of the association. For example, + in a gene-to-phenotype association, the gene is subject and phenotype is object. + display_name: gene to phenotype association_object diff --git a/golr-views/genetic_inheritance_config.yaml b/golr-views/genetic_inheritance_config.yaml index 9a715e6041..be80a9cfce 100644 --- a/golr-views/genetic_inheritance_config.yaml +++ b/golr-views/genetic_inheritance_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: genetic_inheritance +# metamodel_version: 1.7.0# version: 3.4.0id: genetic_inheritance schema_generating: true description: The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, diff --git a/golr-views/genome_config.yaml b/golr-views/genome_config.yaml index 65e72450b7..5cc520be17 100644 --- a/golr-views/genome_config.yaml +++ b/golr-views/genome_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: genome +# metamodel_version: 1.7.0# version: 3.4.0id: genome schema_generating: true description: A genome is the sum of genetic material within a cell or virion. display_name: genome diff --git a/golr-views/genomic_background_exposure_config.yaml b/golr-views/genomic_background_exposure_config.yaml index 415a00b0d8..152f54b5d3 100644 --- a/golr-views/genomic_background_exposure_config.yaml +++ b/golr-views/genomic_background_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: genomic_background_exposure +# metamodel_version: 1.7.0# version: 3.4.0id: genomic_background_exposure schema_generating: true description: A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions diff --git a/golr-views/genomic_sequence_localization_config.yaml b/golr-views/genomic_sequence_localization_config.yaml index e551fa0274..983dbd8db1 100644 --- a/golr-views/genomic_sequence_localization_config.yaml +++ b/golr-views/genomic_sequence_localization_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: genomic_sequence_localization +# metamodel_version: 1.7.0# version: 3.4.0id: genomic_sequence_localization schema_generating: true description: A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or diff --git a/golr-views/genotype_as_a_model_of_disease_association_config.yaml b/golr-views/genotype_as_a_model_of_disease_association_config.yaml index fea5f3b0bd..980b708311 100644 --- a/golr-views/genotype_as_a_model_of_disease_association_config.yaml +++ b/golr-views/genotype_as_a_model_of_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: genotype_as_a_model_of_disease_association +# metamodel_version: 1.7.0# version: 3.4.0id: genotype_as_a_model_of_disease_association schema_generating: true display_name: genotype as a model of disease association document_category: genotype as a model of disease association diff --git a/golr-views/genotype_config.yaml b/golr-views/genotype_config.yaml index 3a16fd436e..bbd192b8c1 100644 --- a/golr-views/genotype_config.yaml +++ b/golr-views/genotype_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: genotype +# metamodel_version: 1.7.0# version: 3.4.0id: genotype schema_generating: true description: An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established diff --git a/golr-views/genotype_to_disease_association_config.yaml b/golr-views/genotype_to_disease_association_config.yaml index 42df6ab6cb..6ae8f67129 100644 --- a/golr-views/genotype_to_disease_association_config.yaml +++ b/golr-views/genotype_to_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: genotype_to_disease_association +# metamodel_version: 1.7.0# version: 3.4.0id: genotype_to_disease_association schema_generating: true display_name: genotype to disease association document_category: genotype to disease association diff --git a/golr-views/genotype_to_gene_association_config.yaml b/golr-views/genotype_to_gene_association_config.yaml index 55374d1d7e..c8315fb5ce 100644 --- a/golr-views/genotype_to_gene_association_config.yaml +++ b/golr-views/genotype_to_gene_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: genotype_to_gene_association +# metamodel_version: 1.7.0# version: 3.4.0id: genotype_to_gene_association schema_generating: true description: Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality diff --git a/golr-views/genotype_to_genotype_part_association_config.yaml b/golr-views/genotype_to_genotype_part_association_config.yaml index 04b148a196..5d622cd02d 100644 --- a/golr-views/genotype_to_genotype_part_association_config.yaml +++ b/golr-views/genotype_to_genotype_part_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: genotype_to_genotype_part_association +# metamodel_version: 1.7.0# version: 3.4.0id: genotype_to_genotype_part_association schema_generating: true description: Any association between one genotype and a genotypic entity that is a sub-component of it diff --git a/golr-views/genotype_to_phenotypic_feature_association_config.yaml b/golr-views/genotype_to_phenotypic_feature_association_config.yaml index 1cc5d0430a..66470c018b 100644 --- a/golr-views/genotype_to_phenotypic_feature_association_config.yaml +++ b/golr-views/genotype_to_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: genotype_to_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 3.4.0id: genotype_to_phenotypic_feature_association schema_generating: true description: Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment diff --git a/golr-views/genotype_to_variant_association_config.yaml b/golr-views/genotype_to_variant_association_config.yaml index b733847f2f..40ce79f0f4 100644 --- a/golr-views/genotype_to_variant_association_config.yaml +++ b/golr-views/genotype_to_variant_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: genotype_to_variant_association +# metamodel_version: 1.7.0# version: 3.4.0id: genotype_to_variant_association schema_generating: true description: Any association between a genotype and a sequence variant. display_name: genotype to variant association diff --git a/golr-views/genotypic_sex_config.yaml b/golr-views/genotypic_sex_config.yaml index bb813cb639..f8bed32779 100644 --- a/golr-views/genotypic_sex_config.yaml +++ b/golr-views/genotypic_sex_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: genotypic_sex +# metamodel_version: 1.7.0# version: 3.4.0id: genotypic_sex schema_generating: true description: An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes. diff --git a/golr-views/geographic_exposure_config.yaml b/golr-views/geographic_exposure_config.yaml index d004745c1f..b10a07eef3 100644 --- a/golr-views/geographic_exposure_config.yaml +++ b/golr-views/geographic_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: geographic_exposure +# metamodel_version: 1.7.0# version: 3.4.0id: geographic_exposure schema_generating: true description: A geographic exposure is a factor relating to geographic proximity to some impactful entity. diff --git a/golr-views/geographic_location_at_time_config.yaml b/golr-views/geographic_location_at_time_config.yaml index 8fbdf180b7..02f48614a1 100644 --- a/golr-views/geographic_location_at_time_config.yaml +++ b/golr-views/geographic_location_at_time_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: geographic_location_at_time +# metamodel_version: 1.7.0# version: 3.4.0id: geographic_location_at_time schema_generating: true description: a location that can be described in lat/long coordinates, for a particular time diff --git a/golr-views/geographic_location_config.yaml b/golr-views/geographic_location_config.yaml index 051826535b..807c0082b1 100644 --- a/golr-views/geographic_location_config.yaml +++ b/golr-views/geographic_location_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: geographic_location +# metamodel_version: 1.7.0# version: 3.4.0id: geographic_location schema_generating: true description: a location that can be described in lat/long coordinates display_name: geographic location diff --git a/golr-views/gross_anatomical_structure_config.yaml b/golr-views/gross_anatomical_structure_config.yaml index 44baf23f5a..06a289d922 100644 --- a/golr-views/gross_anatomical_structure_config.yaml +++ b/golr-views/gross_anatomical_structure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: gross_anatomical_structure +# metamodel_version: 1.7.0# version: 3.4.0id: gross_anatomical_structure schema_generating: true display_name: gross anatomical structure document_category: gross anatomical structure diff --git a/golr-views/haplotype_config.yaml b/golr-views/haplotype_config.yaml index 9550b869f7..28ee446a15 100644 --- a/golr-views/haplotype_config.yaml +++ b/golr-views/haplotype_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: haplotype +# metamodel_version: 1.7.0# version: 3.4.0id: haplotype schema_generating: true description: A set of zero or more Alleles on a single instance of a Sequence[VMC] display_name: haplotype diff --git a/golr-views/hospitalization_config.yaml b/golr-views/hospitalization_config.yaml index 81a08dd94d..d9bd327cdd 100644 --- a/golr-views/hospitalization_config.yaml +++ b/golr-views/hospitalization_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: hospitalization +# metamodel_version: 1.7.0# version: 3.4.0id: hospitalization schema_generating: true display_name: hospitalization document_category: hospitalization diff --git a/golr-views/human_config.yaml b/golr-views/human_config.yaml index e3b78a5b39..283ad116b1 100644 --- a/golr-views/human_config.yaml +++ b/golr-views/human_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: human +# metamodel_version: 1.7.0# version: 3.4.0id: human schema_generating: true description: A member of the the species Homo sapiens. display_name: human diff --git a/golr-views/individual_organism_config.yaml b/golr-views/individual_organism_config.yaml index 5ff44ce824..fe608d6cf3 100644 --- a/golr-views/individual_organism_config.yaml +++ b/golr-views/individual_organism_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: individual_organism +# metamodel_version: 1.7.0# version: 3.4.0id: individual_organism schema_generating: true description: 'An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576' diff --git a/golr-views/information_content_entity_to_named_thing_association_config.yaml b/golr-views/information_content_entity_to_named_thing_association_config.yaml index 089ccfbdc4..394b1a5527 100644 --- a/golr-views/information_content_entity_to_named_thing_association_config.yaml +++ b/golr-views/information_content_entity_to_named_thing_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: information_content_entity_to_named_thing_association +# metamodel_version: 1.7.0# version: 3.4.0id: information_content_entity_to_named_thing_association schema_generating: true description: association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication diff --git a/golr-views/invertebrate_config.yaml b/golr-views/invertebrate_config.yaml index 6379d55276..b426e61eb7 100644 --- a/golr-views/invertebrate_config.yaml +++ b/golr-views/invertebrate_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: invertebrate +# metamodel_version: 1.7.0# version: 3.4.0id: invertebrate schema_generating: true description: An animal lacking a vertebral column. This group consists of 98% of all animal species. diff --git a/golr-views/journal_article_config.yaml b/golr-views/journal_article_config.yaml index 27b0952817..7477a438d8 100644 --- a/golr-views/journal_article_config.yaml +++ b/golr-views/journal_article_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: journal_article +# metamodel_version: 1.7.0# version: 3.4.0id: journal_article schema_generating: true description: an article, typically presenting results of research, that is published in an issue of a scientific journal. @@ -111,6 +111,7 @@ fields: knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass. display_name: publication_publication type + cardinality: multi - id: published_in description: The enclosing parent serial containing the article should have industry-standard identifier from ISSN. diff --git a/golr-views/life_stage_config.yaml b/golr-views/life_stage_config.yaml index 98c55d71d3..f0c2189937 100644 --- a/golr-views/life_stage_config.yaml +++ b/golr-views/life_stage_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: life_stage +# metamodel_version: 1.7.0# version: 3.4.0id: life_stage schema_generating: true description: A stage of development or growth of an organism, including post-natal adult stages diff --git a/golr-views/log_odds_analysis_result_config.yaml b/golr-views/log_odds_analysis_result_config.yaml new file mode 100644 index 0000000000..c8e5068eca --- /dev/null +++ b/golr-views/log_odds_analysis_result_config.yaml @@ -0,0 +1,67 @@ +# metamodel_version: 1.7.0# version: 3.4.0id: log_odds_analysis_result +schema_generating: true +description: A result of a log odds ratio analysis. +display_name: log odds analysis result +document_category: log odds analysis result +weight: 20 +fields: +- id: id + description: A unique identifier for an entity. Must be either a CURIE shorthand + for a URI or a complete URI + display_name: id +- id: iri + description: An IRI for an entity. This is determined by the id using expansion + rules. + display_name: iri +- id: type + display_name: type + cardinality: multi +- id: name + description: A human-readable name for an attribute or entity. + display_name: name +- id: description + description: a human-readable description of an entity + display_name: description +- id: has_attribute + description: connects any entity to an attribute + display_name: has attribute + cardinality: multi +- id: provided_by + description: The value in this node property represents the knowledge provider that + created or assembled the node and all of its attributes. Used internally to represent + how a particular node made its way into a knowledge provider or graph. + display_name: provided by + cardinality: multi +- id: xref + description: A database cross reference or alternative identifier for a NamedThing + or edge between two NamedThings. This property should point to a database record + or webpage that supports the existence of the edge, or gives more detail about + the edge. This property can be used on a node or edge to provide multiple URIs + or CURIE cross references. + display_name: xref + cardinality: multi +- id: category + description: "Name of the high level ontology class in which this entity is categorized.\ + \ Corresponds to the label for the biolink entity type class.\n * In a neo4j database\ + \ this MAY correspond to the neo4j label tag.\n * In an RDF database it should\ + \ be a biolink model class URI.\nThis field is multi-valued. It should include\ + \ values for ancestors of the biolink class; for example, a protein such as Shh\ + \ would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`,\ + \ ...\nIn an RDF database, nodes will typically have an rdf:type triples. This\ + \ can be to the most specific biolink class, or potentially to a class more specific\ + \ than something in biolink. For example, a sequence feature `f` may have a rdf:type\ + \ assertion to a SO class such as TF_binding_site, which is more specific than\ + \ anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,\ + \ biolink:NamedThing}" + display_name: named thing_category + cardinality: multi +- id: license + display_name: license +- id: rights + display_name: rights +- id: format + display_name: format +- id: creation_date + description: date on which an entity was created. This can be applied to nodes or + edges + display_name: creation date diff --git a/golr-views/macromolecular_complex_config.yaml b/golr-views/macromolecular_complex_config.yaml index 4ef601b300..423732b2b7 100644 --- a/golr-views/macromolecular_complex_config.yaml +++ b/golr-views/macromolecular_complex_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: macromolecular_complex +# metamodel_version: 1.7.0# version: 3.4.0id: macromolecular_complex schema_generating: true description: A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and diff --git a/golr-views/macromolecular_machine_to_biological_process_association_config.yaml b/golr-views/macromolecular_machine_to_biological_process_association_config.yaml index 5c8cf1db51..bd510b9aac 100644 --- a/golr-views/macromolecular_machine_to_biological_process_association_config.yaml +++ b/golr-views/macromolecular_machine_to_biological_process_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: macromolecular_machine_to_biological_process_association +# metamodel_version: 1.7.0# version: 3.4.0id: macromolecular_machine_to_biological_process_association schema_generating: true description: A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO diff --git a/golr-views/macromolecular_machine_to_cellular_component_association_config.yaml b/golr-views/macromolecular_machine_to_cellular_component_association_config.yaml index 1d0315a77e..8af99cc3ae 100644 --- a/golr-views/macromolecular_machine_to_cellular_component_association_config.yaml +++ b/golr-views/macromolecular_machine_to_cellular_component_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: macromolecular_machine_to_cellular_component_association +# metamodel_version: 1.7.0# version: 3.4.0id: macromolecular_machine_to_cellular_component_association schema_generating: true description: A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular diff --git a/golr-views/macromolecular_machine_to_molecular_activity_association_config.yaml b/golr-views/macromolecular_machine_to_molecular_activity_association_config.yaml index 463644fe4a..41ff4ede5e 100644 --- a/golr-views/macromolecular_machine_to_molecular_activity_association_config.yaml +++ b/golr-views/macromolecular_machine_to_molecular_activity_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: macromolecular_machine_to_molecular_activity_association +# metamodel_version: 1.7.0# version: 3.4.0id: macromolecular_machine_to_molecular_activity_association schema_generating: true description: A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular diff --git a/golr-views/mammal_config.yaml b/golr-views/mammal_config.yaml index 8a8ec88ad6..d049a43386 100644 --- a/golr-views/mammal_config.yaml +++ b/golr-views/mammal_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: mammal +# metamodel_version: 1.7.0# version: 3.4.0id: mammal schema_generating: true description: A member of the class Mammalia, a clade of endothermic amniotes distinguished from reptiles and birds by the possession of hair, three middle ear bones, mammary diff --git a/golr-views/material_sample_config.yaml b/golr-views/material_sample_config.yaml index a6810c4ce3..dc21a35ea9 100644 --- a/golr-views/material_sample_config.yaml +++ b/golr-views/material_sample_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: material_sample +# metamodel_version: 1.7.0# version: 3.4.0id: material_sample schema_generating: true description: A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, diff --git a/golr-views/material_sample_derivation_association_config.yaml b/golr-views/material_sample_derivation_association_config.yaml index d2780a8e38..31b7fbbd69 100644 --- a/golr-views/material_sample_derivation_association_config.yaml +++ b/golr-views/material_sample_derivation_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: material_sample_derivation_association +# metamodel_version: 1.7.0# version: 3.4.0id: material_sample_derivation_association schema_generating: true description: An association between a material sample and the material entity from which it is derived. diff --git a/golr-views/material_sample_to_disease_or_phenotypic_feature_association_config.yaml b/golr-views/material_sample_to_disease_or_phenotypic_feature_association_config.yaml index d461326792..1fe166e858 100644 --- a/golr-views/material_sample_to_disease_or_phenotypic_feature_association_config.yaml +++ b/golr-views/material_sample_to_disease_or_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: material_sample_to_disease_or_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 3.4.0id: material_sample_to_disease_or_phenotypic_feature_association schema_generating: true description: An association between a material sample and a disease or phenotype. display_name: material sample to disease or phenotypic feature association diff --git a/golr-views/microRNA_config.yaml b/golr-views/microRNA_config.yaml index 620586696a..6b276aaaed 100644 --- a/golr-views/microRNA_config.yaml +++ b/golr-views/microRNA_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: microRNA +# metamodel_version: 1.7.0# version: 3.4.0id: microRNA schema_generating: true display_name: microRNA document_category: microRNA diff --git a/golr-views/molecular_activity_config.yaml b/golr-views/molecular_activity_config.yaml index c1ecd04754..d5cb9cf554 100644 --- a/golr-views/molecular_activity_config.yaml +++ b/golr-views/molecular_activity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: molecular_activity +# metamodel_version: 1.7.0# version: 3.4.0id: molecular_activity schema_generating: true description: An execution of a molecular function carried out by a gene product or macromolecular complex. diff --git a/golr-views/molecular_activity_to_chemical_entity_association_config.yaml b/golr-views/molecular_activity_to_chemical_entity_association_config.yaml index ebd8c62fa5..69d3ed6efd 100644 --- a/golr-views/molecular_activity_to_chemical_entity_association_config.yaml +++ b/golr-views/molecular_activity_to_chemical_entity_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: molecular_activity_to_chemical_entity_association +# metamodel_version: 1.7.0# version: 3.4.0id: molecular_activity_to_chemical_entity_association schema_generating: true description: Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool diff --git a/golr-views/molecular_activity_to_molecular_activity_association_config.yaml b/golr-views/molecular_activity_to_molecular_activity_association_config.yaml index 2f986d3abb..85ccb75819 100644 --- a/golr-views/molecular_activity_to_molecular_activity_association_config.yaml +++ b/golr-views/molecular_activity_to_molecular_activity_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: molecular_activity_to_molecular_activity_association +# metamodel_version: 1.7.0# version: 3.4.0id: molecular_activity_to_molecular_activity_association schema_generating: true description: Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool diff --git a/golr-views/molecular_activity_to_pathway_association_config.yaml b/golr-views/molecular_activity_to_pathway_association_config.yaml index cb899df733..6b15416a9c 100644 --- a/golr-views/molecular_activity_to_pathway_association_config.yaml +++ b/golr-views/molecular_activity_to_pathway_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: molecular_activity_to_pathway_association +# metamodel_version: 1.7.0# version: 3.4.0id: molecular_activity_to_pathway_association schema_generating: true description: Association that holds the relationship between a reaction and the pathway it participates in. diff --git a/golr-views/molecular_entity_config.yaml b/golr-views/molecular_entity_config.yaml index 939577591d..5f9d44df32 100644 --- a/golr-views/molecular_entity_config.yaml +++ b/golr-views/molecular_entity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: molecular_entity +# metamodel_version: 1.7.0# version: 3.4.0id: molecular_entity schema_generating: true description: A molecular entity is a chemical entity composed of individual or covalently bonded atoms. diff --git a/golr-views/molecular_mixture_config.yaml b/golr-views/molecular_mixture_config.yaml index ffc3519052..96aefd4c09 100644 --- a/golr-views/molecular_mixture_config.yaml +++ b/golr-views/molecular_mixture_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: molecular_mixture +# metamodel_version: 1.7.0# version: 3.4.0id: molecular_mixture schema_generating: true description: A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry. diff --git a/golr-views/named_thing_associated_with_likelihood_of_named_thing_association_config.yaml b/golr-views/named_thing_associated_with_likelihood_of_named_thing_association_config.yaml index e47d8724e4..dbd55c263b 100644 --- a/golr-views/named_thing_associated_with_likelihood_of_named_thing_association_config.yaml +++ b/golr-views/named_thing_associated_with_likelihood_of_named_thing_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: named_thing_associated_with_likelihood_of_named_thing_association +# metamodel_version: 1.7.0# version: 3.4.0id: named_thing_associated_with_likelihood_of_named_thing_association schema_generating: true description: '' display_name: named thing associated with likelihood of named thing association diff --git a/golr-views/named_thing_config.yaml b/golr-views/named_thing_config.yaml index 6b8c00146e..7e819ad4bf 100644 --- a/golr-views/named_thing_config.yaml +++ b/golr-views/named_thing_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: named_thing +# metamodel_version: 1.7.0# version: 3.4.0id: named_thing schema_generating: true description: a databased entity or concept/class display_name: named thing diff --git a/golr-views/noncoding_RNA_product_config.yaml b/golr-views/noncoding_RNA_product_config.yaml index 085e347536..c88000326c 100644 --- a/golr-views/noncoding_RNA_product_config.yaml +++ b/golr-views/noncoding_RNA_product_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: noncoding_RNA_product +# metamodel_version: 1.7.0# version: 3.4.0id: noncoding_RNA_product schema_generating: true display_name: noncoding RNA product document_category: noncoding RNA product diff --git a/golr-views/nucleic_acid_entity_config.yaml b/golr-views/nucleic_acid_entity_config.yaml index 7db006bfaf..9c17e900c7 100644 --- a/golr-views/nucleic_acid_entity_config.yaml +++ b/golr-views/nucleic_acid_entity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: nucleic_acid_entity +# metamodel_version: 1.7.0# version: 3.4.0id: nucleic_acid_entity schema_generating: true description: A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; diff --git a/golr-views/nucleic_acid_sequence_motif_config.yaml b/golr-views/nucleic_acid_sequence_motif_config.yaml index 3771916e3e..e8c410167b 100644 --- a/golr-views/nucleic_acid_sequence_motif_config.yaml +++ b/golr-views/nucleic_acid_sequence_motif_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: nucleic_acid_sequence_motif +# metamodel_version: 1.7.0# version: 3.4.0id: nucleic_acid_sequence_motif schema_generating: true description: A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, diff --git a/golr-views/nucleosome_modification_config.yaml b/golr-views/nucleosome_modification_config.yaml index 7036164f92..838ab63dfe 100644 --- a/golr-views/nucleosome_modification_config.yaml +++ b/golr-views/nucleosome_modification_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: nucleosome_modification +# metamodel_version: 1.7.0# version: 3.4.0id: nucleosome_modification schema_generating: true description: A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine diff --git a/golr-views/observed_expected_frequency_analysis_result_config.yaml b/golr-views/observed_expected_frequency_analysis_result_config.yaml index a1b4b3d48e..6727a6fc8d 100644 --- a/golr-views/observed_expected_frequency_analysis_result_config.yaml +++ b/golr-views/observed_expected_frequency_analysis_result_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: observed_expected_frequency_analysis_result +# metamodel_version: 1.7.0# version: 3.4.0id: observed_expected_frequency_analysis_result schema_generating: true description: A result of a observed expected frequency analysis. display_name: observed expected frequency analysis result diff --git a/golr-views/onset_config.yaml b/golr-views/onset_config.yaml index 4b8f9352ba..57388a6de2 100644 --- a/golr-views/onset_config.yaml +++ b/golr-views/onset_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: onset +# metamodel_version: 1.7.0# version: 3.4.0id: onset schema_generating: true description: The age group in which (disease) symptom manifestations appear display_name: onset diff --git a/golr-views/organism_attribute_config.yaml b/golr-views/organism_attribute_config.yaml index e59a28749d..29a632d603 100644 --- a/golr-views/organism_attribute_config.yaml +++ b/golr-views/organism_attribute_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: organism_attribute +# metamodel_version: 1.7.0# version: 3.4.0id: organism_attribute schema_generating: true description: describes a characteristic of an organismal entity. display_name: organism attribute diff --git a/golr-views/organism_taxon_config.yaml b/golr-views/organism_taxon_config.yaml index 0ed9622dfd..1c7fb81de5 100644 --- a/golr-views/organism_taxon_config.yaml +++ b/golr-views/organism_taxon_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: organism_taxon +# metamodel_version: 1.7.0# version: 3.4.0id: organism_taxon schema_generating: true description: 'A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or diff --git a/golr-views/organism_taxon_to_organism_taxon_interaction_config.yaml b/golr-views/organism_taxon_to_organism_taxon_interaction_config.yaml index 4ff1ca34e5..40c30bba1b 100644 --- a/golr-views/organism_taxon_to_organism_taxon_interaction_config.yaml +++ b/golr-views/organism_taxon_to_organism_taxon_interaction_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: organism_taxon_to_organism_taxon_interaction +# metamodel_version: 1.7.0# version: 3.4.0id: organism_taxon_to_organism_taxon_interaction schema_generating: true description: 'An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. diff --git a/golr-views/organism_taxon_to_organism_taxon_specialization_config.yaml b/golr-views/organism_taxon_to_organism_taxon_specialization_config.yaml index 367ccb5d5e..6b7aaea0d6 100644 --- a/golr-views/organism_taxon_to_organism_taxon_specialization_config.yaml +++ b/golr-views/organism_taxon_to_organism_taxon_specialization_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: organism_taxon_to_organism_taxon_specialization +# metamodel_version: 1.7.0# version: 3.4.0id: organism_taxon_to_organism_taxon_specialization schema_generating: true description: 'A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo' diff --git a/golr-views/organism_to_organism_association_config.yaml b/golr-views/organism_to_organism_association_config.yaml index 0db44e401d..d39d7c259d 100644 --- a/golr-views/organism_to_organism_association_config.yaml +++ b/golr-views/organism_to_organism_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: organism_to_organism_association +# metamodel_version: 1.7.0# version: 3.4.0id: organism_to_organism_association schema_generating: true display_name: organism to organism association document_category: organism to organism association diff --git a/golr-views/organismal_entity_as_a_model_of_disease_association_config.yaml b/golr-views/organismal_entity_as_a_model_of_disease_association_config.yaml index c454fbaf96..f67b23ef2f 100644 --- a/golr-views/organismal_entity_as_a_model_of_disease_association_config.yaml +++ b/golr-views/organismal_entity_as_a_model_of_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: organismal_entity_as_a_model_of_disease_association +# metamodel_version: 1.7.0# version: 3.4.0id: organismal_entity_as_a_model_of_disease_association schema_generating: true display_name: organismal entity as a model of disease association document_category: organismal entity as a model of disease association diff --git a/golr-views/pairwise_gene_to_gene_interaction_config.yaml b/golr-views/pairwise_gene_to_gene_interaction_config.yaml index fb2f199a05..a570486347 100644 --- a/golr-views/pairwise_gene_to_gene_interaction_config.yaml +++ b/golr-views/pairwise_gene_to_gene_interaction_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: pairwise_gene_to_gene_interaction +# metamodel_version: 1.7.0# version: 3.4.0id: pairwise_gene_to_gene_interaction schema_generating: true description: An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein diff --git a/golr-views/pairwise_molecular_interaction_config.yaml b/golr-views/pairwise_molecular_interaction_config.yaml index 65cbcb0427..95dafcdd56 100644 --- a/golr-views/pairwise_molecular_interaction_config.yaml +++ b/golr-views/pairwise_molecular_interaction_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: pairwise_molecular_interaction +# metamodel_version: 1.7.0# version: 3.4.0id: pairwise_molecular_interaction schema_generating: true description: An interaction at the molecular level between two physical entities display_name: pairwise molecular interaction diff --git a/golr-views/patent_config.yaml b/golr-views/patent_config.yaml index 30f72d743c..47682f3dc9 100644 --- a/golr-views/patent_config.yaml +++ b/golr-views/patent_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: patent +# metamodel_version: 1.7.0# version: 3.4.0id: patent schema_generating: true description: 'a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period @@ -112,3 +112,4 @@ fields: knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass. display_name: publication_publication type + cardinality: multi diff --git a/golr-views/pathological_anatomical_exposure_config.yaml b/golr-views/pathological_anatomical_exposure_config.yaml index 13897c2008..5a918c55ba 100644 --- a/golr-views/pathological_anatomical_exposure_config.yaml +++ b/golr-views/pathological_anatomical_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: pathological_anatomical_exposure +# metamodel_version: 1.7.0# version: 3.4.0id: pathological_anatomical_exposure schema_generating: true description: An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to diff --git a/golr-views/pathological_anatomical_structure_config.yaml b/golr-views/pathological_anatomical_structure_config.yaml index 24cd592994..9552e53c18 100644 --- a/golr-views/pathological_anatomical_structure_config.yaml +++ b/golr-views/pathological_anatomical_structure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: pathological_anatomical_structure +# metamodel_version: 1.7.0# version: 3.4.0id: pathological_anatomical_structure schema_generating: true description: An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level. diff --git a/golr-views/pathological_process_config.yaml b/golr-views/pathological_process_config.yaml index b7cfcb2f8a..7bbccd1366 100644 --- a/golr-views/pathological_process_config.yaml +++ b/golr-views/pathological_process_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: pathological_process +# metamodel_version: 1.7.0# version: 3.4.0id: pathological_process schema_generating: true description: A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level. diff --git a/golr-views/pathological_process_exposure_config.yaml b/golr-views/pathological_process_exposure_config.yaml index d2cfc1f30a..804b407245 100644 --- a/golr-views/pathological_process_exposure_config.yaml +++ b/golr-views/pathological_process_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: pathological_process_exposure +# metamodel_version: 1.7.0# version: 3.4.0id: pathological_process_exposure schema_generating: true description: A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease. diff --git a/golr-views/pathway_config.yaml b/golr-views/pathway_config.yaml index a79bbdcb02..77ba85058b 100644 --- a/golr-views/pathway_config.yaml +++ b/golr-views/pathway_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: pathway +# metamodel_version: 1.7.0# version: 3.4.0id: pathway schema_generating: true display_name: pathway document_category: pathway diff --git a/golr-views/phenomenon_config.yaml b/golr-views/phenomenon_config.yaml index 13428a1019..59f9a891f0 100644 --- a/golr-views/phenomenon_config.yaml +++ b/golr-views/phenomenon_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: phenomenon +# metamodel_version: 1.7.0# version: 3.4.0id: phenomenon schema_generating: true description: a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question diff --git a/golr-views/phenotypic_feature_config.yaml b/golr-views/phenotypic_feature_config.yaml index a033e44d76..c8f9ad33d3 100644 --- a/golr-views/phenotypic_feature_config.yaml +++ b/golr-views/phenotypic_feature_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: phenotypic_feature +# metamodel_version: 1.7.0# version: 3.4.0id: phenotypic_feature schema_generating: true description: A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of diff --git a/golr-views/phenotypic_quality_config.yaml b/golr-views/phenotypic_quality_config.yaml index c0c4fd4de9..99466dc243 100644 --- a/golr-views/phenotypic_quality_config.yaml +++ b/golr-views/phenotypic_quality_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: phenotypic_quality +# metamodel_version: 1.7.0# version: 3.4.0id: phenotypic_quality schema_generating: true description: A property of a phenotype display_name: phenotypic quality diff --git a/golr-views/phenotypic_sex_config.yaml b/golr-views/phenotypic_sex_config.yaml index f242b2ee5e..7c2f123048 100644 --- a/golr-views/phenotypic_sex_config.yaml +++ b/golr-views/phenotypic_sex_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: phenotypic_sex +# metamodel_version: 1.7.0# version: 3.4.0id: phenotypic_sex schema_generating: true description: An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present. diff --git a/golr-views/physical_entity_config.yaml b/golr-views/physical_entity_config.yaml index d77cb221cc..1c1aec9514 100644 --- a/golr-views/physical_entity_config.yaml +++ b/golr-views/physical_entity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: physical_entity +# metamodel_version: 1.7.0# version: 3.4.0id: physical_entity schema_generating: true description: An entity that has material reality (a.k.a. physical essence). display_name: physical entity diff --git a/golr-views/physiological_process_config.yaml b/golr-views/physiological_process_config.yaml index 5c9737da41..6604e3e192 100644 --- a/golr-views/physiological_process_config.yaml +++ b/golr-views/physiological_process_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: physiological_process +# metamodel_version: 1.7.0# version: 3.4.0id: physiological_process schema_generating: true display_name: physiological process document_category: physiological process diff --git a/golr-views/planetary_entity_config.yaml b/golr-views/planetary_entity_config.yaml index a5ba3a805e..051e85025d 100644 --- a/golr-views/planetary_entity_config.yaml +++ b/golr-views/planetary_entity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: planetary_entity +# metamodel_version: 1.7.0# version: 3.4.0id: planetary_entity schema_generating: true description: Any entity or process that exists at the level of the whole planet display_name: planetary entity diff --git a/golr-views/plant_config.yaml b/golr-views/plant_config.yaml index 8a197bc258..1669682000 100644 --- a/golr-views/plant_config.yaml +++ b/golr-views/plant_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: plant +# metamodel_version: 1.7.0# version: 3.4.0id: plant schema_generating: true description: '' display_name: plant diff --git a/golr-views/polypeptide_config.yaml b/golr-views/polypeptide_config.yaml index be90b392ab..34e01367d4 100644 --- a/golr-views/polypeptide_config.yaml +++ b/golr-views/polypeptide_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: polypeptide +# metamodel_version: 1.7.0# version: 3.4.0id: polypeptide schema_generating: true description: A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary diff --git a/golr-views/population_of_individual_organisms_config.yaml b/golr-views/population_of_individual_organisms_config.yaml index 1ec9d829ce..e5a49ea6ea 100644 --- a/golr-views/population_of_individual_organisms_config.yaml +++ b/golr-views/population_of_individual_organisms_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: population_of_individual_organisms +# metamodel_version: 1.7.0# version: 3.4.0id: population_of_individual_organisms schema_generating: true description: A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited diff --git a/golr-views/population_to_population_association_config.yaml b/golr-views/population_to_population_association_config.yaml index a12983ed80..baa401e7b7 100644 --- a/golr-views/population_to_population_association_config.yaml +++ b/golr-views/population_to_population_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: population_to_population_association +# metamodel_version: 1.7.0# version: 3.4.0id: population_to_population_association schema_generating: true description: An association between a two populations display_name: population to population association diff --git a/golr-views/posttranslational_modification_config.yaml b/golr-views/posttranslational_modification_config.yaml index 0cde240823..77e2d8bf7c 100644 --- a/golr-views/posttranslational_modification_config.yaml +++ b/golr-views/posttranslational_modification_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: posttranslational_modification +# metamodel_version: 1.7.0# version: 3.4.0id: posttranslational_modification schema_generating: true description: A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or diff --git a/golr-views/predicate_mapping_config.yaml b/golr-views/predicate_mapping_config.yaml index d7bd0952e9..bb348b7624 100644 --- a/golr-views/predicate_mapping_config.yaml +++ b/golr-views/predicate_mapping_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: predicate_mapping +# metamodel_version: 1.7.0# version: 3.4.0id: predicate_mapping schema_generating: true description: A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement diff --git a/golr-views/preprint_publication_config.yaml b/golr-views/preprint_publication_config.yaml index 62e002eb8d..55188e95c0 100644 --- a/golr-views/preprint_publication_config.yaml +++ b/golr-views/preprint_publication_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: preprint_publication +# metamodel_version: 1.7.0# version: 3.4.0id: preprint_publication schema_generating: true description: a document reresenting an early version of an author's original scholarly work, such as a research paper or a review, prior to formal peer review and publication in @@ -112,3 +112,4 @@ fields: knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass. display_name: publication_publication type + cardinality: multi diff --git a/golr-views/procedure_config.yaml b/golr-views/procedure_config.yaml index 57277341b4..be03a06906 100644 --- a/golr-views/procedure_config.yaml +++ b/golr-views/procedure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: procedure +# metamodel_version: 1.7.0# version: 3.4.0id: procedure schema_generating: true description: A series of actions conducted in a certain order or manner display_name: procedure diff --git a/golr-views/processed_material_config.yaml b/golr-views/processed_material_config.yaml index b97d7082b7..1253692052 100644 --- a/golr-views/processed_material_config.yaml +++ b/golr-views/processed_material_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: processed_material +# metamodel_version: 1.7.0# version: 3.4.0id: processed_material schema_generating: true description: A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during diff --git a/golr-views/protein_config.yaml b/golr-views/protein_config.yaml index 941fc0f80f..d1d86ebb2c 100644 --- a/golr-views/protein_config.yaml +++ b/golr-views/protein_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: protein +# metamodel_version: 1.7.0# version: 3.4.0id: protein schema_generating: true description: A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA diff --git a/golr-views/protein_domain_config.yaml b/golr-views/protein_domain_config.yaml index fb1f12d25f..3c9a7109a9 100644 --- a/golr-views/protein_domain_config.yaml +++ b/golr-views/protein_domain_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: protein_domain +# metamodel_version: 1.7.0# version: 3.4.0id: protein_domain schema_generating: true description: A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein diff --git a/golr-views/protein_family_config.yaml b/golr-views/protein_family_config.yaml index 6257ec0ab0..433b999c1a 100644 --- a/golr-views/protein_family_config.yaml +++ b/golr-views/protein_family_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: protein_family +# metamodel_version: 1.7.0# version: 3.4.0id: protein_family schema_generating: true display_name: protein family document_category: protein family diff --git a/golr-views/protein_isoform_config.yaml b/golr-views/protein_isoform_config.yaml index cef10e1db7..33d1691855 100644 --- a/golr-views/protein_isoform_config.yaml +++ b/golr-views/protein_isoform_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: protein_isoform +# metamodel_version: 1.7.0# version: 3.4.0id: protein_isoform schema_generating: true description: Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/ diff --git a/golr-views/publication_config.yaml b/golr-views/publication_config.yaml index 78e09ab2d6..508a1992c8 100644 --- a/golr-views/publication_config.yaml +++ b/golr-views/publication_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: publication +# metamodel_version: 1.7.0# version: 3.4.0id: publication schema_generating: true description: "Any \u2018published\u2019 piece of information. Publications are considered\ \ broadly to include any document or document part made available in print or on\ @@ -115,3 +115,4 @@ fields: knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass. display_name: publication_publication type + cardinality: multi diff --git a/golr-views/quantity_value_config.yaml b/golr-views/quantity_value_config.yaml index 9b7d152e82..45e373d631 100644 --- a/golr-views/quantity_value_config.yaml +++ b/golr-views/quantity_value_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: quantity_value +# metamodel_version: 1.7.0# version: 3.4.0id: quantity_value schema_generating: true description: A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value diff --git a/golr-views/reaction_to_catalyst_association_config.yaml b/golr-views/reaction_to_catalyst_association_config.yaml index d36a1a2113..45c09c98e9 100644 --- a/golr-views/reaction_to_catalyst_association_config.yaml +++ b/golr-views/reaction_to_catalyst_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: reaction_to_catalyst_association +# metamodel_version: 1.7.0# version: 3.4.0id: reaction_to_catalyst_association schema_generating: true display_name: reaction to catalyst association document_category: reaction to catalyst association diff --git a/golr-views/reaction_to_participant_association_config.yaml b/golr-views/reaction_to_participant_association_config.yaml index cfc61b9004..8563b9f5a4 100644 --- a/golr-views/reaction_to_participant_association_config.yaml +++ b/golr-views/reaction_to_participant_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: reaction_to_participant_association +# metamodel_version: 1.7.0# version: 3.4.0id: reaction_to_participant_association schema_generating: true display_name: reaction to participant association document_category: reaction to participant association diff --git a/golr-views/reagent_targeted_gene_config.yaml b/golr-views/reagent_targeted_gene_config.yaml index 9516977ad3..3024b60133 100644 --- a/golr-views/reagent_targeted_gene_config.yaml +++ b/golr-views/reagent_targeted_gene_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: reagent_targeted_gene +# metamodel_version: 1.7.0# version: 3.4.0id: reagent_targeted_gene schema_generating: true description: A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino diff --git a/golr-views/regulatory_region_config.yaml b/golr-views/regulatory_region_config.yaml index ed1ef5964b..bc7f5640c7 100644 --- a/golr-views/regulatory_region_config.yaml +++ b/golr-views/regulatory_region_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: regulatory_region +# metamodel_version: 1.7.0# version: 3.4.0id: regulatory_region schema_generating: true description: A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene diff --git a/golr-views/relative_frequency_analysis_result_config.yaml b/golr-views/relative_frequency_analysis_result_config.yaml index 7484f9997d..b99612138f 100644 --- a/golr-views/relative_frequency_analysis_result_config.yaml +++ b/golr-views/relative_frequency_analysis_result_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: relative_frequency_analysis_result +# metamodel_version: 1.7.0# version: 3.4.0id: relative_frequency_analysis_result schema_generating: true description: A result of a relative frequency analysis. display_name: relative frequency analysis result diff --git a/golr-views/retrieval_source_config.yaml b/golr-views/retrieval_source_config.yaml index 5c9565ef1b..29ddf09ec3 100644 --- a/golr-views/retrieval_source_config.yaml +++ b/golr-views/retrieval_source_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: retrieval_source +# metamodel_version: 1.7.0# version: 3.4.0id: retrieval_source schema_generating: true description: Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate diff --git a/golr-views/sequence_association_config.yaml b/golr-views/sequence_association_config.yaml index 7a554ae6f2..4361d75faa 100644 --- a/golr-views/sequence_association_config.yaml +++ b/golr-views/sequence_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: sequence_association +# metamodel_version: 1.7.0# version: 3.4.0id: sequence_association schema_generating: true description: An association between a sequence feature and a nucleic acid entity it is localized to. diff --git a/golr-views/sequence_feature_relationship_config.yaml b/golr-views/sequence_feature_relationship_config.yaml index 592a4a3f57..0a9f1b79ce 100644 --- a/golr-views/sequence_feature_relationship_config.yaml +++ b/golr-views/sequence_feature_relationship_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: sequence_feature_relationship +# metamodel_version: 1.7.0# version: 3.4.0id: sequence_feature_relationship schema_generating: true description: For example, a particular exon is part of a particular transcript or gene diff --git a/golr-views/sequence_variant_config.yaml b/golr-views/sequence_variant_config.yaml index 1732c968d9..eea8108ef9 100644 --- a/golr-views/sequence_variant_config.yaml +++ b/golr-views/sequence_variant_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: sequence_variant +# metamodel_version: 1.7.0# version: 3.4.0id: sequence_variant schema_generating: true description: A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. diff --git a/golr-views/serial_config.yaml b/golr-views/serial_config.yaml index 523d2c739a..2ba39da630 100644 --- a/golr-views/serial_config.yaml +++ b/golr-views/serial_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: serial +# metamodel_version: 1.7.0# version: 3.4.0id: serial schema_generating: true description: This class may rarely be instantiated except if use cases of a given knowledge graph support its utility. @@ -100,6 +100,7 @@ fields: knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass. display_name: publication_publication type + cardinality: multi - id: iso_abbreviation description: Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. diff --git a/golr-views/severity_value_config.yaml b/golr-views/severity_value_config.yaml index 64b49d4f59..c71cca9467 100644 --- a/golr-views/severity_value_config.yaml +++ b/golr-views/severity_value_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: severity_value +# metamodel_version: 1.7.0# version: 3.4.0id: severity_value schema_generating: true description: describes the severity of a phenotypic feature or disease display_name: severity value diff --git a/golr-views/siRNA_config.yaml b/golr-views/siRNA_config.yaml index 3ef98d9735..88e56690d2 100644 --- a/golr-views/siRNA_config.yaml +++ b/golr-views/siRNA_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: siRNA +# metamodel_version: 1.7.0# version: 3.4.0id: siRNA schema_generating: true description: A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via diff --git a/golr-views/small_molecule_config.yaml b/golr-views/small_molecule_config.yaml index c1e91aef6f..4de8bf93b5 100644 --- a/golr-views/small_molecule_config.yaml +++ b/golr-views/small_molecule_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: small_molecule +# metamodel_version: 1.7.0# version: 3.4.0id: small_molecule schema_generating: true description: A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation diff --git a/golr-views/snv_config.yaml b/golr-views/snv_config.yaml index 99b2ecf626..3f907c554a 100644 --- a/golr-views/snv_config.yaml +++ b/golr-views/snv_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: snv +# metamodel_version: 1.7.0# version: 3.4.0id: snv schema_generating: true description: SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist diff --git a/golr-views/socioeconomic_attribute_config.yaml b/golr-views/socioeconomic_attribute_config.yaml index 790398d4a6..bf00aa7875 100644 --- a/golr-views/socioeconomic_attribute_config.yaml +++ b/golr-views/socioeconomic_attribute_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: socioeconomic_attribute +# metamodel_version: 1.7.0# version: 3.4.0id: socioeconomic_attribute schema_generating: true description: Attributes relating to a socioeconomic manifestation display_name: socioeconomic attribute diff --git a/golr-views/socioeconomic_exposure_config.yaml b/golr-views/socioeconomic_exposure_config.yaml index 70e45ab45a..b08d2d6e8e 100644 --- a/golr-views/socioeconomic_exposure_config.yaml +++ b/golr-views/socioeconomic_exposure_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: socioeconomic_exposure +# metamodel_version: 1.7.0# version: 3.4.0id: socioeconomic_exposure schema_generating: true description: A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty). diff --git a/golr-views/study_config.yaml b/golr-views/study_config.yaml index ef36577388..0555d07ba8 100644 --- a/golr-views/study_config.yaml +++ b/golr-views/study_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: study +# metamodel_version: 1.7.0# version: 3.4.0id: study schema_generating: true description: a detailed investigation and/or analysis display_name: study diff --git a/golr-views/study_population_config.yaml b/golr-views/study_population_config.yaml index 4a12b40c02..d86cecaad8 100644 --- a/golr-views/study_population_config.yaml +++ b/golr-views/study_population_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: study_population +# metamodel_version: 1.7.0# version: 3.4.0id: study_population schema_generating: true description: A group of people banded together or treated as a group as participants in a research study. diff --git a/golr-views/study_variable_config.yaml b/golr-views/study_variable_config.yaml index 8912843c7b..15be5791dc 100644 --- a/golr-views/study_variable_config.yaml +++ b/golr-views/study_variable_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: study_variable +# metamodel_version: 1.7.0# version: 3.4.0id: study_variable schema_generating: true description: a variable that is used as a measure in the investigation of a study display_name: study variable diff --git a/golr-views/taxon_to_taxon_association_config.yaml b/golr-views/taxon_to_taxon_association_config.yaml index ea0c54c3c9..b603166b48 100644 --- a/golr-views/taxon_to_taxon_association_config.yaml +++ b/golr-views/taxon_to_taxon_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: taxon_to_taxon_association +# metamodel_version: 1.7.0# version: 3.4.0id: taxon_to_taxon_association schema_generating: true display_name: taxon to taxon association document_category: taxon to taxon association diff --git a/golr-views/text_mining_result_config.yaml b/golr-views/text_mining_result_config.yaml index f3b433eeed..56f270c053 100644 --- a/golr-views/text_mining_result_config.yaml +++ b/golr-views/text_mining_result_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: text_mining_result +# metamodel_version: 1.7.0# version: 3.4.0id: text_mining_result schema_generating: true description: A result of text mining. display_name: text mining result diff --git a/golr-views/transcript_config.yaml b/golr-views/transcript_config.yaml index dde70bff01..8eba97b68b 100644 --- a/golr-views/transcript_config.yaml +++ b/golr-views/transcript_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: transcript +# metamodel_version: 1.7.0# version: 3.4.0id: transcript schema_generating: true description: An RNA synthesized on a DNA or RNA template by an RNA polymerase. display_name: transcript diff --git a/golr-views/transcript_to_gene_relationship_config.yaml b/golr-views/transcript_to_gene_relationship_config.yaml index 4560de40eb..e1299b4adc 100644 --- a/golr-views/transcript_to_gene_relationship_config.yaml +++ b/golr-views/transcript_to_gene_relationship_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: transcript_to_gene_relationship +# metamodel_version: 1.7.0# version: 3.4.0id: transcript_to_gene_relationship schema_generating: true description: A gene is a collection of transcripts display_name: transcript to gene relationship diff --git a/golr-views/transcription_factor_binding_site_config.yaml b/golr-views/transcription_factor_binding_site_config.yaml index b0bc9356c4..c02b8f88d2 100644 --- a/golr-views/transcription_factor_binding_site_config.yaml +++ b/golr-views/transcription_factor_binding_site_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: transcription_factor_binding_site +# metamodel_version: 1.7.0# version: 3.4.0id: transcription_factor_binding_site schema_generating: true description: A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription diff --git a/golr-views/treatment_config.yaml b/golr-views/treatment_config.yaml index e680303b33..76dcf61da6 100644 --- a/golr-views/treatment_config.yaml +++ b/golr-views/treatment_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: treatment +# metamodel_version: 1.7.0# version: 3.4.0id: treatment schema_generating: true description: A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures diff --git a/golr-views/variant_as_a_model_of_disease_association_config.yaml b/golr-views/variant_as_a_model_of_disease_association_config.yaml index 53bc4ed016..b3069e9ade 100644 --- a/golr-views/variant_as_a_model_of_disease_association_config.yaml +++ b/golr-views/variant_as_a_model_of_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: variant_as_a_model_of_disease_association +# metamodel_version: 1.7.0# version: 3.4.0id: variant_as_a_model_of_disease_association schema_generating: true display_name: variant as a model of disease association document_category: variant as a model of disease association diff --git a/golr-views/variant_to_disease_association_config.yaml b/golr-views/variant_to_disease_association_config.yaml index 89391f0e83..b7aa0323f0 100644 --- a/golr-views/variant_to_disease_association_config.yaml +++ b/golr-views/variant_to_disease_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: variant_to_disease_association +# metamodel_version: 1.7.0# version: 3.4.0id: variant_to_disease_association schema_generating: true display_name: variant to disease association document_category: variant to disease association diff --git a/golr-views/variant_to_gene_association_config.yaml b/golr-views/variant_to_gene_association_config.yaml index ff7be806a0..fa4aa9b0e3 100644 --- a/golr-views/variant_to_gene_association_config.yaml +++ b/golr-views/variant_to_gene_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: variant_to_gene_association +# metamodel_version: 1.7.0# version: 3.4.0id: variant_to_gene_association schema_generating: true description: An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium) diff --git a/golr-views/variant_to_gene_expression_association_config.yaml b/golr-views/variant_to_gene_expression_association_config.yaml index 36036e7e77..009856551e 100644 --- a/golr-views/variant_to_gene_expression_association_config.yaml +++ b/golr-views/variant_to_gene_expression_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: variant_to_gene_expression_association +# metamodel_version: 1.7.0# version: 3.4.0id: variant_to_gene_expression_association schema_generating: true description: An association between a variant and expression of a gene (i.e. e-QTL) display_name: variant to gene expression association diff --git a/golr-views/variant_to_phenotypic_feature_association_config.yaml b/golr-views/variant_to_phenotypic_feature_association_config.yaml index 127af42d2e..9c9587ad41 100644 --- a/golr-views/variant_to_phenotypic_feature_association_config.yaml +++ b/golr-views/variant_to_phenotypic_feature_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: variant_to_phenotypic_feature_association +# metamodel_version: 1.7.0# version: 3.4.0id: variant_to_phenotypic_feature_association schema_generating: true display_name: variant to phenotypic feature association document_category: variant to phenotypic feature association diff --git a/golr-views/variant_to_population_association_config.yaml b/golr-views/variant_to_population_association_config.yaml index b1aad09d0a..95db2f4272 100644 --- a/golr-views/variant_to_population_association_config.yaml +++ b/golr-views/variant_to_population_association_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: variant_to_population_association +# metamodel_version: 1.7.0# version: 3.4.0id: variant_to_population_association schema_generating: true description: An association between a variant and a population, where the variant has particular frequency in the population diff --git a/golr-views/vertebrate_config.yaml b/golr-views/vertebrate_config.yaml index fa653ea8a1..69f27163e2 100644 --- a/golr-views/vertebrate_config.yaml +++ b/golr-views/vertebrate_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: vertebrate +# metamodel_version: 1.7.0# version: 3.4.0id: vertebrate schema_generating: true description: A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column. diff --git a/golr-views/virus_config.yaml b/golr-views/virus_config.yaml index 1f2578b236..95a71a111e 100644 --- a/golr-views/virus_config.yaml +++ b/golr-views/virus_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: virus +# metamodel_version: 1.7.0# version: 3.4.0id: virus schema_generating: true description: A virus is a microorganism that replicates itself as a microRNA and infects the host cell. diff --git a/golr-views/web_page_config.yaml b/golr-views/web_page_config.yaml index 760eb11c11..7fef720317 100644 --- a/golr-views/web_page_config.yaml +++ b/golr-views/web_page_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: web_page +# metamodel_version: 1.7.0# version: 3.4.0id: web_page schema_generating: true description: a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, and/or other features. @@ -111,3 +111,4 @@ fields: knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass. display_name: publication_publication type + cardinality: multi diff --git a/golr-views/zygosity_config.yaml b/golr-views/zygosity_config.yaml index 3a079fdc8b..36e6318ff8 100644 --- a/golr-views/zygosity_config.yaml +++ b/golr-views/zygosity_config.yaml @@ -1,4 +1,4 @@ -# metamodel_version: 1.7.0# version: 3.3.2id: zygosity +# metamodel_version: 1.7.0# version: 3.4.0id: zygosity schema_generating: true display_name: zygosity document_category: zygosity diff --git a/graphviz/anatomical_entity_to_anatomical_entity_association.gv b/graphviz/anatomical_entity_to_anatomical_entity_association.gv index c5c65e9abd..601068c418 100644 --- a/graphviz/anatomical_entity_to_anatomical_entity_association.gv +++ b/graphviz/anatomical_entity_to_anatomical_entity_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4788.4,283"]; + graph [bb="0,0,4570.4,283"]; node [label="\N"]; "anatomical entity to anatomical entity association" [height=0.5, label="anatomical entity to anatomical entity association", - pos="2492.4,265", + pos="2274.4,265", width=6.7341]; association [height=0.5, pos="62.394,178", width=1.7332]; "anatomical entity to anatomical entity association" -> association [label=is_a, - lp="281.39,221.5", - pos="e,103.12,191.79 2251.1,263.25 1715.5,261.14 459.47,253.62 267.39,229 213.85,222.14 154.03,206.61 112.9,194.67"]; + lp="280.39,221.5", + pos="e,102.91,191.77 2033.6,262.81 1538.2,259.93 437.01,251.11 266.39,229 213.11,222.09 153.58,206.57 112.65,194.64"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "anatomical entity to anatomical entity association" -> id [color=blue, label=id, - lp="398.39,221.5", - pos="e,210.38,190 2252.2,262.49 1739.8,258.91 571.7,248.7 391.39,229 318.35,221.02 300.2,215.65 229.39,196 226.29,195.14 223.09,194.17 \ -219.89,193.16", + lp="396.39,221.5", + pos="e,210.38,189.98 2035,262.03 1563.9,257.79 548.38,246.72 389.39,229 317.23,220.96 299.34,215.5 229.39,196 226.29,195.13 223.09,194.17 \ +219.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "anatomical entity to anatomical entity association" -> iri [color=blue, label=iri, - lp="515.39,221.5", - pos="e,315.29,190.23 2253,262.09 1762.8,257.84 676.4,246.57 507.39,229 429.97,220.95 410.81,215.26 335.39,196 332.02,195.14 328.54,194.18 \ -325.05,193.17", + lp="509.39,221.5", + pos="e,315.3,190.2 2031.8,264.51 1617.5,264.48 790.35,260.33 501.39,229 426.61,220.89 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ +325.06,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "anatomical entity to anatomical entity association" -> name [color=blue, label=name, - lp="627.39,221.5", - pos="e,440.01,191.15 2252.5,262.4 1781.1,258.83 766.07,248.94 607.39,229 552.58,222.11 491.21,206.11 449.83,194.05", + lp="617.39,221.5", + pos="e,439.19,191.41 2035,262.02 1605.4,258.02 735.55,247.73 597.39,229 545.74,222 488.1,206.31 448.78,194.36", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "anatomical entity to anatomical entity association" -> description [color=blue, label=description, - lp="755.89,221.5", - pos="e,588.8,193.65 2251.4,262.95 1800.8,260.44 862.67,252.44 715.39,229 675.03,222.58 630.79,208.66 598.44,197.14", + lp="739.89,221.5", + pos="e,586.19,194.12 2033.8,262.66 1625,259.79 826.72,251.38 699.39,229 663.52,222.69 624.55,209.24 595.6,197.88", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "anatomical entity to anatomical entity association" -> "has attribute" [color=blue, label="has attribute", - lp="913.39,221.5", - pos="e,729.98,191.75 2252.4,262.33 1833.1,258.9 999.15,249.58 866.39,229 822.26,222.16 773.51,207 739.58,195.15", + lp="887.39,221.5", + pos="e,726.83,192.67 2034.6,262.19 1656.9,258.73 954.11,249.61 840.39,229 804.17,222.43 764.8,208.24 736.39,196.65", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "anatomical entity to anatomical entity association" -> predicate [color=blue, label=predicate, - lp="1074.4,221.5", - pos="e,887.81,193.09 2249.7,264.77 1898.7,264.75 1266.5,260.15 1040.4,229 991.17,222.22 936.47,207.65 897.4,195.99", + lp="1031.4,221.5", + pos="e,880.43,194.06 2037.4,261.19 1696.2,256.58 1096.5,246.18 997.39,229 960.25,222.56 919.77,209.02 889.78,197.66", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "anatomical entity to anatomical entity association" -> negated [color=blue, label=negated, - lp="1220.4,221.5", - pos="e,1022.3,190.23 2251.2,263.02 1932.7,260.76 1389.3,253.35 1191.4,229 1135.6,222.13 1072.9,205.38 1032,193.16", + lp="1151.4,221.5", + pos="e,1015.6,192.51 2038.1,260.9 1727.1,256.2 1209.3,245.95 1122.4,229 1088.3,222.36 1051.5,208.2 1024.9,196.64", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "anatomical entity to anatomical entity association" -> qualifiers [color=blue, label=qualifiers, - lp="1356.9,221.5", - pos="e,1171.6,193.02 2251.4,263.05 1962.5,260.81 1495.9,253.39 1323.4,229 1274.6,222.11 1220.5,207.65 1181.6,196.05", + lp="1254.9,221.5", + pos="e,1151.6,195.39 2035.7,261.81 1749.2,258.28 1297.6,249.53 1221.4,229 1199.7,223.15 1177.4,211.43 1160.1,200.81", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "anatomical entity to anatomical entity association" -> publications [color=blue, label=publications, - lp="1499.4,221.5", - pos="e,1321.9,192.66 2251.6,262.88 1994,260.43 1602.8,252.77 1455.4,229 1412.5,222.09 1365.3,207.61 1331.5,196.01", + lp="1346.4,221.5", + pos="e,1286.4,196.26 2034.9,262.13 1756.6,258.95 1331.4,250.57 1302.4,229 1295.1,223.57 1290.9,214.84 1288.5,206.19", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,262 +110,262 @@ digraph { width=2.0943]; "anatomical entity to anatomical entity association" -> "has evidence" [color=blue, label="has evidence", - lp="1652.9,221.5", - pos="e,1479.4,193.55 2254.7,261.42 2035.5,257.79 1726.3,249.19 1606.4,229 1566,222.2 1521.6,208.38 1489.1,196.99", + lp="1444.9,221.5", + pos="e,1413.8,194.93 2034.1,262.51 1782.4,259.74 1420.3,251.78 1398.4,229 1390,220.25 1395.9,210.18 1405.7,201.37", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1643.4,178", - width=3.015]; + label=string, + pos="1573.4,178", + width=1.0652]; "anatomical entity to anatomical entity association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1802.9,221.5", - pos="e,1667.9,195.78 2250.2,264.12 2067,262.08 1831.5,254.31 1738.4,229 1716.6,223.09 1694.2,211.61 1676.7,201.13", + lp="1562.9,221.5", + pos="e,1543.3,189.28 2037.5,261.16 1816.2,257.32 1517.1,248.52 1498.4,229 1493.8,224.18 1494.8,219.62 1498.4,214 1502.8,207.12 1518,199.47 \ +1533.6,193.08", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1878.4,178", - width=3.015]; + label=string, + pos="1668.4,178", + width=1.0652]; "anatomical entity to anatomical entity association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1972.4,221.5", - pos="e,1872.6,196 2267.1,258.36 2097.2,252.96 1891.1,243.48 1877.4,229 1871.6,222.9 1870.4,214.27 1871,205.9", + lp="1729.4,221.5", + pos="e,1648.1,193.48 2046.1,258.84 1868.2,253.66 1648.8,244.23 1634.4,229 1626.3,220.46 1631.8,209.82 1640.6,200.55", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2113.4,178", - width=3.015]; + label=string, + pos="1810.4,178", + width=1.0652]; "anatomical entity to anatomical entity association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2180.9,221.5", - pos="e,2087.6,195.53 2268.4,258.07 2176.8,253.28 2088.8,244.63 2074.4,229 2066.7,220.62 2071.6,210.86 2080.1,202.2", + lp="1949.9,221.5", + pos="e,1816.9,195.93 2069.3,255.39 1968.3,249.69 1863.7,241.03 1843.4,229 1834,223.44 1826.8,214.03 1821.5,204.86", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2295.4,178", + pos="2037.4,178", width=1.5346]; "anatomical entity to anatomical entity association" -> timepoint [color=blue, label=timepoint, - lp="2332.4,221.5", - pos="e,2291.1,196.26 2348.6,250.43 2325,245.38 2305.6,238.47 2297.4,229 2292,222.83 2290.3,214.43 2290.3,206.27", + lp="2112.4,221.5", + pos="e,2046.6,196.08 2152.6,249.4 2120.6,244.01 2091.2,237.18 2077.4,229 2067.4,223.06 2058.9,213.63 2052.3,204.55", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2407.4,178", + pos="2149.4,178", width=1.0652]; "anatomical entity to anatomical entity association" -> "original subject" [color=blue, label="original subject", - lp="2430.4,221.5", - pos="e,2387.4,193.75 2397.2,248.35 2388.3,243.45 2380.5,237.13 2374.4,229 2367.7,220.01 2372.5,209.73 2380.3,200.83", + lp="2214.4,221.5", + pos="e,2148.2,196.23 2184.4,248.16 2174.6,243.34 2165.6,237.09 2158.4,229 2152.9,222.8 2150.2,214.39 2149,206.23", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2521.4,178", + pos="2274.4,178", width=1.5887]; "anatomical entity to anatomical entity association" -> "original predicate" [color=blue, label="original predicate", - lp="2556.9,221.5", - pos="e,2504.6,195.4 2490.1,246.84 2489.4,236.95 2489.6,224.45 2493.4,214 2494.7,210.42 2496.5,206.94 2498.6,203.64", + lp="2337.9,221.5", + pos="e,2274.4,196.18 2274.4,246.8 2274.4,235.16 2274.4,219.55 2274.4,206.24", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2635.4,178", + pos="2403.4,178", width=1.0652]; "anatomical entity to anatomical entity association" -> "original object" [color=blue, label="original object", - lp="2681.9,221.5", - pos="e,2634.3,196.46 2590.7,248.54 2601.6,243.65 2611.9,237.29 2620.4,229 2626.5,223.04 2630.2,214.69 2632.3,206.52", + lp="2459.9,221.5", + pos="e,2407.8,195.99 2362,248.17 2380.6,243.02 2396.4,236.63 2402.4,229 2407.4,222.62 2408.9,214.26 2408.7,206.21", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2768.4,178", + pos="2536.4,178", width=2.1304]; "anatomical entity to anatomical entity association" -> "subject category" [color=blue, label="subject category", - lp="2811.9,221.5", - pos="e,2762.2,196.16 2653.2,251.48 2689.6,246.29 2722,239.05 2737.4,229 2746.2,223.28 2752.9,214.13 2757.8,205.22", + lp="2586.9,221.5", + pos="e,2533.7,196.01 2440.2,251.84 2473.3,246.7 2502,239.38 2515.4,229 2522.8,223.28 2527.6,214.49 2530.7,205.86", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2939.4,178", + pos="2707.4,178", width=2.1304]; "anatomical entity to anatomical entity association" -> "object category" [color=blue, label="object category", - lp="2956.9,221.5", - pos="e,2923.4,195.77 2667.4,252.52 2758.7,245.72 2855.4,236.92 2875.4,229 2890.3,223.11 2904.5,212.62 2915.8,202.76", + lp="2728.9,221.5", + pos="e,2693.3,196.01 2450,252.56 2538.6,245.91 2631.3,237.23 2650.4,229 2663.9,223.19 2676.4,212.95 2686.3,203.24", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3072.4,178", + pos="2840.4,178", width=1.0652]; "anatomical entity to anatomical entity association" -> "subject closure" [color=blue, label="subject closure", - lp="3093.9,221.5", - pos="e,3059.6,195.17 2664.9,252.33 2691.5,250.54 2718.7,248.72 2744.4,247 2804.8,242.96 2960.5,252.45 3016.4,229 3030.2,223.21 3042.9,\ -212.57 3052.7,202.58", + lp="2864.9,221.5", + pos="e,2828.3,195.63 2447.1,252.32 2596.2,242.23 2787.9,229.22 2788.4,229 2801.2,223.32 2812.8,213.03 2821.7,203.26", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3172.4,178", + pos="2953.4,178", width=1.0652]; "anatomical entity to anatomical entity association" -> "object closure" [color=blue, label="object closure", - lp="3214.4,221.5", - pos="e,3170.3,196.32 2661.1,252.07 2688.9,250.26 2717.5,248.5 2744.4,247 2767,245.74 3133.9,242.13 3152.4,229 3160,223.63 3164.7,214.92 \ -3167.6,206.26", + lp="2988.4,221.5", + pos="e,2948,196.02 2443.5,252.08 2471.2,250.27 2499.6,248.51 2526.4,247 2570.5,244.51 2885.5,251.62 2923.4,229 2932.4,223.61 2939.1,214.36 \ +2943.8,205.27", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3305.4,178", + pos="3086.4,178", width=2.1304]; "anatomical entity to anatomical entity association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3372.9,221.5", - pos="e,3297.7,196.16 2659.8,251.93 2688,250.12 2717,248.39 2744.4,247 2773.5,245.52 3242.6,242.55 3268.4,229 3278.5,223.67 3286.6,214.17 \ -3292.6,204.87", + lp="3148.9,221.5", + pos="e,3076.5,196.23 2441.8,251.94 2470,250.13 2499,248.4 2526.4,247 2583.7,244.07 2990.5,253.54 3042.4,229 3053.7,223.64 3063.3,213.87 \ +3070.7,204.38", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3497.4,178", + pos="3279.4,178", width=2.1304]; "anatomical entity to anatomical entity association" -> "object category closure" [color=blue, label="object category closure", - lp="3563.9,221.5", - pos="e,3491.1,196.15 2658.1,251.82 2686.8,249.99 2716.5,248.29 2744.4,247 2784.4,245.15 3429.4,248.4 3464.4,229 3473.9,223.7 3481.2,214.34 \ -3486.5,205.14", + lp="3341.9,221.5", + pos="e,3271.1,196.22 2440.1,251.83 2468.8,250 2498.5,248.29 2526.4,247 2566,245.16 3205,246.86 3240.4,229 3250.8,223.74 3259.3,214.26 \ +3265.7,204.95", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3687.4,178", + pos="3469.4,178", width=1.0652]; "anatomical entity to anatomical entity association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3736.4,221.5", - pos="e,3680.3,195.72 2657,251.76 2686.1,249.92 2716.1,248.23 2744.4,247 2794.7,244.8 3606.8,252.42 3651.4,229 3661.6,223.65 3669.6,213.96 \ -3675.4,204.53", + lp="3515.4,221.5", + pos="e,3461.1,195.76 2439,251.77 2468.1,249.93 2498.1,248.23 2526.4,247 2576.5,244.81 3384.4,251.19 3429.4,229 3440.2,223.66 3449.1,213.83 \ +3455.7,204.3", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3846.4,178", + pos="3628.4,178", width=1.0652]; "anatomical entity to anatomical entity association" -> "object namespace" [color=blue, label="object namespace", - lp="3890.4,221.5", - pos="e,3838.7,195.75 2656.4,251.74 2685.7,249.89 2715.9,248.2 2744.4,247 2773.9,245.75 3782,242.36 3808.4,229 3818.9,223.7 3827.2,214.02 \ -3833.4,204.58", + lp="3669.4,221.5", + pos="e,3619.8,195.79 2438.4,251.74 2467.7,249.89 2497.9,248.2 2526.4,247 2585.3,244.52 3534.3,254.67 3587.4,229 3598.4,223.69 3607.4,\ +213.87 3614.2,204.33", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3997.4,178", + pos="3779.4,178", width=1.0652]; "anatomical entity to anatomical entity association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4050.4,221.5", - pos="e,3989.4,195.77 2656,251.71 2685.4,249.86 2715.8,248.18 2744.4,247 2778.1,245.61 3928.2,244.02 3958.4,229 3969.1,223.67 3977.8,213.85 \ -3984.2,204.31", + lp="3831.4,221.5", + pos="e,3770.5,195.81 2438,251.71 2467.4,249.86 2497.8,248.18 2526.4,247 2560,245.62 3707,243.44 3737.4,229 3748.5,223.71 3757.8,213.9 \ +3764.7,204.35", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4168.4,178", + pos="3950.4,178", width=1.0652]; "anatomical entity to anatomical entity association" -> "object label closure" [color=blue, label="object label closure", - lp="4215.9,221.5", - pos="e,4160.1,195.79 2655.7,251.69 2685.2,249.83 2715.7,248.15 2744.4,247 2782.8,245.46 4093.9,245.88 4128.4,229 4139.3,223.69 4148.1,\ -213.88 4154.7,204.34", + lp="3998.9,221.5", + pos="e,3941.8,195.8 2437.7,251.69 2467.2,249.83 2497.7,248.15 2526.4,247 2564.8,245.46 3874.8,245.66 3909.4,229 3920.4,223.71 3929.4,\ +213.89 3936.2,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4330.4,178", + pos="4112.4,178", width=2.347]; "anatomical entity to anatomical entity association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4378.9,221.5", - pos="e,4321.5,196.3 2655.7,251.65 2685.2,249.8 2715.7,248.13 2744.4,247 2787.3,245.3 4250.7,247.58 4289.4,229 4300.2,223.79 4309.2,214.18 \ -4315.9,204.76", + lp="4160.9,221.5", + pos="e,4103.8,196.29 2437.7,251.65 2467.2,249.8 2497.7,248.13 2526.4,247 2569.3,245.3 4033.8,247.83 4072.4,229 4083.1,223.78 4091.9,214.16 \ +4098.4,204.75", style=solid]; type [height=0.5, - pos="4464.4,178", + pos="4246.4,178", width=0.86659]; "anatomical entity to anatomical entity association" -> type [color=blue, label=type, - lp="4478.4,221.5", - pos="e,4465.2,196.18 2655.3,251.65 2685,249.79 2715.6,248.12 2744.4,247 2768.1,246.08 4433.8,243.79 4452.4,229 4459.2,223.54 4462.6,214.92 \ -4464.1,206.37", + lp="4260.4,221.5", + pos="e,4247.2,196.18 2437.3,251.65 2467,249.79 2497.6,248.12 2526.4,247 2550.1,246.08 4215.8,243.79 4234.4,229 4241.2,223.54 4244.6,214.92 \ +4246.1,206.37", style=solid]; category [height=0.5, - pos="4565.4,178", + pos="4347.4,178", width=1.4263]; "anatomical entity to anatomical entity association" -> category [color=blue, label=category, - lp="4558.9,221.5", - pos="e,4549.8,195.25 2655.3,251.64 2685,249.78 2715.6,248.12 2744.4,247 2793.1,245.11 4452.2,244.59 4498.4,229 4514.6,223.53 4530.1,212.5 \ -4542.1,202.2", + lp="4340.9,221.5", + pos="e,4331.8,195.25 2437.3,251.64 2467,249.78 2497.6,248.12 2526.4,247 2575.1,245.11 4234.2,244.59 4280.4,229 4296.6,223.53 4312.1,212.5 \ +4324.1,202.2", style=solid]; subject [height=0.5, - pos="4679.4,178", + pos="4461.4,178", width=1.2277]; "anatomical entity to anatomical entity association" -> subject [color=blue, label=subject, - lp="4655.4,221.5", - pos="e,4660.1,194.33 2655.3,251.63 2685,249.77 2715.6,248.11 2744.4,247 2847.1,243.04 4495.4,256.49 4594.4,229 4615.1,223.24 4636,211.08 \ -4651.9,200.2", + lp="4437.4,221.5", + pos="e,4442.1,194.33 2437.3,251.63 2467,249.77 2497.6,248.11 2526.4,247 2629.1,243.04 4277.4,256.49 4376.4,229 4397.1,223.24 4418,211.08 \ +4433.9,200.2", style=solid]; object [height=0.5, - pos="4722.4,91", + pos="4504.4,91", width=1.0832]; "anatomical entity to anatomical entity association" -> object [color=blue, label=object, - lp="4766.4,178", - pos="e,4735.8,108.09 2655,251.64 2684.7,249.78 2715.5,248.11 2744.4,247 2798.3,244.93 4634.1,245.49 4685.4,229 4709.7,221.2 4718,217.1 \ -4732.4,196 4746.3,175.59 4742.5,166.51 4745.4,142 4746.2,135.38 4747.3,133.39 4745.4,127 4744.4,123.55 4742.9,120.13 4741.1,116.85", + lp="4548.4,178", + pos="e,4517.8,108.09 2437,251.64 2466.7,249.78 2497.5,248.11 2526.4,247 2580.3,244.93 4416.1,245.49 4467.4,229 4491.7,221.2 4500,217.1 \ +4514.4,196 4528.3,175.59 4524.5,166.51 4527.4,142 4528.2,135.38 4529.3,133.39 4527.4,127 4526.4,123.55 4524.9,120.13 4523.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2791.4,265", + pos="2573.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2922.4,265", + pos="2704.4,265", width=2.0762]; subject -> object [label=relation, - lp="4717.4,134.5", - pos="e,4704.5,107.23 4680.5,159.55 4681.7,149.57 4684.2,137.07 4689.4,127 4691.6,122.68 4694.5,118.52 4697.7,114.66"]; + lp="4499.4,134.5", + pos="e,4486.5,107.23 4462.5,159.55 4463.7,149.57 4466.2,137.07 4471.4,127 4473.6,122.68 4476.5,118.52 4479.7,114.66"]; relation [height=0.5, - pos="4667.4,18", + pos="4449.4,18", width=1.2999]; - subject -> relation [pos="e,4668.7,36.188 4678.1,159.79 4676,132.48 4672,78.994 4669.5,46.38", + subject -> relation [pos="e,4450.7,36.188 4460.1,159.79 4458,132.48 4454,78.994 4451.5,46.38", style=dotted]; "anatomical entity to anatomical entity association_subject" [color=blue, height=0.5, label="anatomical entity", - pos="3106.4,265", + pos="2888.4,265", width=2.5456]; - object -> relation [pos="e,4680.2,35.54 4709.9,73.889 4703,64.939 4694.2,53.617 4686.4,43.584", + object -> relation [pos="e,4462.2,35.54 4491.9,73.889 4485,64.939 4476.2,53.617 4468.4,43.584", style=dotted]; "anatomical entity to anatomical entity association_object" [color=blue, height=0.5, label="anatomical entity", - pos="3307.4,265", + pos="3089.4,265", width=2.5456]; } diff --git a/graphviz/anatomical_entity_to_anatomical_entity_association.svg b/graphviz/anatomical_entity_to_anatomical_entity_association.svg index 1e9845e099..396efb592b 100644 --- a/graphviz/anatomical_entity_to_anatomical_entity_association.svg +++ b/graphviz/anatomical_entity_to_anatomical_entity_association.svg @@ -4,16 +4,16 @@ - + %3 - + anatomical entity to anatomical entity association - -anatomical entity to anatomical entity association + +anatomical entity to anatomical entity association @@ -24,9 +24,9 @@ anatomical entity to anatomical entity association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ anatomical entity to anatomical entity association->id - - -id + + +id @@ -50,9 +50,9 @@ anatomical entity to anatomical entity association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ anatomical entity to anatomical entity association->name - - -name + + +name @@ -76,9 +76,9 @@ anatomical entity to anatomical entity association->description - - -description + + +description @@ -89,9 +89,9 @@ anatomical entity to anatomical entity association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ anatomical entity to anatomical entity association->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ anatomical entity to anatomical entity association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ anatomical entity to anatomical entity association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ anatomical entity to anatomical entity association->publications - - -publications + + +publications @@ -154,344 +154,344 @@ anatomical entity to anatomical entity association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string anatomical entity to anatomical entity association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string anatomical entity to anatomical entity association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string anatomical entity to anatomical entity association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type anatomical entity to anatomical entity association->timepoint - - -timepoint + + +timepoint original subject - -string + +string anatomical entity to anatomical entity association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie anatomical entity to anatomical entity association->original predicate - - -original predicate + + +original predicate original object - -string + +string anatomical entity to anatomical entity association->original object - - -original object + + +original object subject category - -ontology class + +ontology class anatomical entity to anatomical entity association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class anatomical entity to anatomical entity association->object category - - -object category + + +object category subject closure - -string + +string anatomical entity to anatomical entity association->subject closure - - -subject closure + + +subject closure object closure - -string + +string anatomical entity to anatomical entity association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class anatomical entity to anatomical entity association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class anatomical entity to anatomical entity association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string anatomical entity to anatomical entity association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string anatomical entity to anatomical entity association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string anatomical entity to anatomical entity association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string anatomical entity to anatomical entity association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source anatomical entity to anatomical entity association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type anatomical entity to anatomical entity association->type - - -type + + +type category - -category + +category anatomical entity to anatomical entity association->category - - -category + + +category subject - -subject + +subject anatomical entity to anatomical entity association->subject - - -subject + + +subject object - -object + +object anatomical entity to anatomical entity association->object - - -object + + +object association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + anatomical entity to anatomical entity association_subject - -anatomical entity + +anatomical entity object->relation - - + + anatomical entity to anatomical entity association_object - -anatomical entity + +anatomical entity diff --git a/graphviz/anatomical_entity_to_anatomical_entity_ontogenic_association.gv b/graphviz/anatomical_entity_to_anatomical_entity_ontogenic_association.gv index b4be8a8da7..cdd2d51c19 100644 --- a/graphviz/anatomical_entity_to_anatomical_entity_ontogenic_association.gv +++ b/graphviz/anatomical_entity_to_anatomical_entity_ontogenic_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,5108,283"]; + graph [bb="0,0,4923,283"]; node [label="\N"]; "anatomical entity to anatomical entity ontogenic association" [height=0.5, label="anatomical entity to anatomical entity ontogenic association", - pos="2828.4,265", + pos="2643.4,265", width=8.0701]; "anatomical entity to anatomical entity association" [height=0.5, pos="242.43,178", width=6.7341]; "anatomical entity to anatomical entity ontogenic association" -> "anatomical entity to anatomical entity association" [label=is_a, lp="640.43,221.5", - pos="e,338.39,194.57 2538.8,263.49 2028.6,261.9 989.11,255.41 626.43,229 532.1,222.13 425.48,207.71 348.56,196.12"]; + pos="e,338.39,194.53 2354.5,262.98 1879.3,260.63 953.12,253.03 626.43,229 532.1,222.06 425.48,207.65 348.56,196.07"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "anatomical entity to anatomical entity ontogenic association" -> id [color=blue, label=id, - lp="756.43,221.5", - pos="e,570.42,189.98 2541.6,262.14 2012.7,258.28 922.27,248.11 749.43,229 677.26,221.02 659.37,215.5 589.43,196 586.32,195.13 583.12,\ -194.17 579.92,193.15", + lp="755.43,221.5", + pos="e,570.42,189.98 2357.6,261.65 1867.3,257.19 903.35,246.35 748.43,229 676.7,220.97 658.94,215.43 589.43,196 586.32,195.13 583.12,\ +194.17 579.93,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "anatomical entity to anatomical entity ontogenic association" -> iri [color=blue, label=iri, - lp="869.43,221.5", - pos="e,675.34,190.2 2542.3,261.73 2036.7,257.31 1023.4,246.4 861.43,229 786.64,220.97 768.25,214.85 695.43,196 692.05,195.13 688.57,194.16 \ -685.09,193.15", + lp="861.43,221.5", + pos="e,675.35,190.15 2352.5,264.89 1921.7,265.09 1134.7,260.84 853.43,229 782.15,220.93 764.79,214.31 695.43,196 692.06,195.11 688.58,\ +194.13 685.1,193.11", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "anatomical entity to anatomical entity ontogenic association" -> name [color=blue, label=name, - lp="976.43,221.5", - pos="e,799.39,191.54 2541.2,262.29 2055.2,258.85 1108.5,249.59 956.43,229 905.29,222.08 848.28,206.51 809.17,194.57", + lp="964.43,221.5", + pos="e,798.02,191.87 2356.8,261.94 1908.8,258.14 1079.7,248.56 944.43,229 897.05,222.15 844.49,206.96 807.9,195.11", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "anatomical entity to anatomical entity ontogenic association" -> description [color=blue, label=description, - lp="1096.9,221.5", - pos="e,945.48,194.14 2539.2,263.22 2074.2,261.21 1197.7,254.11 1056.4,229 1021.4,222.77 983.37,209.4 955.07,198.06", + lp="1077.9,221.5", + pos="e,941.81,194.62 2354,263.25 1926.3,261.3 1162.2,254.27 1037.4,229 1007.4,222.92 975.31,210.09 951.04,198.95", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "anatomical entity to anatomical entity ontogenic association" -> "has attribute" [color=blue, label="has attribute", - lp="1242.4,221.5", - pos="e,1086,192.82 2539.6,262.87 2105.8,260.41 1323.2,252.7 1195.4,229 1160.5,222.52 1122.6,208.39 1095.2,196.8", + lp="1212.4,221.5", + pos="e,1081.4,194.01 2353.9,263.42 1956.3,261.66 1277.4,254.85 1165.4,229 1138.9,222.88 1111.1,209.98 1090.2,198.82", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "anatomical entity to anatomical entity ontogenic association" -> negated [color=blue, label=negated, - lp="1398.4,221.5", - pos="e,1207.6,190.46 2537.9,264.1 2178.4,262.99 1587.1,256.79 1369.4,229 1316.1,222.2 1256.5,205.66 1217.2,193.46", + lp="1350.4,221.5", + pos="e,1203.1,191.96 2359.8,260.99 2001.8,256.49 1420.3,246.6 1321.4,229 1283.4,222.23 1241.9,207.52 1212.5,195.8", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "anatomical entity to anatomical entity ontogenic association" -> qualifiers [color=blue, label=qualifiers, - lp="1538.9,221.5", - pos="e,1356.7,193.07 2537.9,264.08 2210,262.8 1697.2,256.26 1505.4,229 1457.6,222.2 1404.6,207.74 1366.5,196.11", + lp="1460.9,221.5", + pos="e,1342.2,194.93 2357.9,261.56 2027,257.83 1515.4,248.91 1427.4,229 1400.8,222.97 1372.8,210.6 1351.3,199.66", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "anatomical entity to anatomical entity ontogenic association" -> publications [color=blue, label=publications, - lp="1686.4,221.5", - pos="e,1508.2,192.71 2538.2,263.89 2243.7,262.26 1808.2,255.25 1642.4,229 1599.3,222.18 1551.8,207.69 1517.8,196.06", + lp="1561.4,221.5", + pos="e,1481.6,195.77 2361.1,260.67 2040.1,256.07 1555.2,246.3 1517.4,229 1505.6,223.61 1495.5,213.64 1487.8,204.02", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,275 +100,275 @@ digraph { width=2.0943]; "anatomical entity to anatomical entity ontogenic association" -> "has evidence" [color=blue, label="has evidence", - lp="1840.9,221.5", - pos="e,1665.9,193.61 2540.4,262.5 2285.3,259.67 1932.5,251.61 1794.4,229 1753.6,222.3 1708.7,208.48 1675.7,197.06", + lp="1659.9,221.5", + pos="e,1615.5,195.85 2353.2,263.92 2057.6,262.37 1639,255.47 1613.4,229 1607.2,222.53 1607.9,213.49 1611.2,204.88", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1829.4,178", - width=3.015]; + label=string, + pos="1759.4,178", + width=1.0652]; "anatomical entity to anatomical entity ontogenic association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1995.9,221.5", - pos="e,1855.5,195.59 2554.3,259.02 2312.9,253.69 1990.6,243.94 1931.4,229 1907.9,223.07 1883.5,211.31 1864.4,200.68", + lp="1778.9,221.5", + pos="e,1735.1,191.96 2355.2,262.7 2090.8,260.04 1736.7,252.14 1714.4,229 1704.7,218.93 1714,207.33 1726.5,197.85", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2064.4,178", - width=3.015]; + label=string, + pos="1854.4,178", + width=1.0652]; "anatomical entity to anatomical entity ontogenic association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2167.4,221.5", - pos="e,2062.2,196.41 2552.7,259.33 2344.2,254.5 2090.7,245.32 2072.4,229 2066.1,223.34 2063.4,214.82 2062.5,206.41", + lp="1948.4,221.5", + pos="e,1848.6,196.04 2361.7,260.6 2142.1,256.51 1871.3,247.69 1853.4,229 1847.6,222.93 1846.3,214.32 1847,205.94", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2299.4,178", - width=3.015]; + label=string, + pos="2029.4,178", + width=1.0652]; "anatomical entity to anatomical entity ontogenic association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2375.9,221.5", - pos="e,2278.7,195.97 2577.8,255.88 2434.4,249.97 2280.6,240.92 2269.4,229 2262.4,221.54 2265.6,212.18 2272.1,203.58", + lp="2168.9,221.5", + pos="e,2035.8,196.01 2371.9,258.56 2234.3,253.84 2090.3,245.09 2062.4,229 2053,223.54 2045.7,214.14 2040.5,204.96", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2481.4,178", + pos="2256.4,178", width=1.5346]; "anatomical entity to anatomical entity ontogenic association" -> timepoint [color=blue, label=timepoint, - lp="2531.4,221.5", - pos="e,2482,196.47 2629,251.85 2565.3,246.23 2508.1,238.64 2496.4,229 2489.7,223.41 2485.9,214.91 2483.8,206.49", + lp="2331.4,221.5", + pos="e,2265.2,195.91 2412,254.06 2362.5,248.86 2318.4,240.97 2296.4,229 2286.1,223.36 2277.4,213.81 2270.9,204.56", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2593.4,178", + pos="2368.4,178", width=1.0652]; "anatomical entity to anatomical entity ontogenic association" -> "original subject" [color=blue, label="original subject", - lp="2630.4,221.5", - pos="e,2579.7,194.92 2626.9,251.96 2602.8,246.7 2583.4,239.32 2574.4,229 2568.2,221.83 2570,212.39 2574.4,203.65", + lp="2434.4,221.5", + pos="e,2367.2,196.24 2440.7,252.07 2412.6,246.86 2389.6,239.47 2378.4,229 2372.2,223.22 2369.3,214.78 2368,206.47", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2707.4,178", + pos="2493.4,178", width=1.5887]; "anatomical entity to anatomical entity ontogenic association" -> "original predicate" [color=blue, label="original predicate", - lp="2757.9,221.5", - pos="e,2696.4,195.76 2733.8,247.91 2715.6,242.88 2700.3,236.61 2694.4,229 2689.1,222.16 2689.7,213.39 2692.4,205.11", + lp="2564.9,221.5", + pos="e,2491.7,196.34 2545.2,248 2525.4,242.93 2508.4,236.61 2501.4,229 2495.8,222.91 2493.3,214.52 2492.3,206.36", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2821.4,178", + pos="2622.4,178", width=1.0652]; "anatomical entity to anatomical entity ontogenic association" -> "original object" [color=blue, label="original object", - lp="2876.9,221.5", - pos="e,2822.8,196.18 2827,246.8 2826.1,235.16 2824.8,219.55 2823.7,206.24", + lp="2685.9,221.5", + pos="e,2626.7,196.18 2639.2,246.8 2636.3,235.16 2632.4,219.55 2629.2,206.24", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2954.4,178", + pos="2755.4,178", width=2.1304]; "anatomical entity to anatomical entity ontogenic association" -> "subject category" [color=blue, label="subject category", - lp="3002.9,221.5", - pos="e,2950.6,196.4 2902.9,247.54 2913.6,242.83 2923.9,236.78 2932.4,229 2939.2,222.84 2944,214.24 2947.3,205.9", + lp="2809.9,221.5", + pos="e,2754.5,196.22 2715.8,247.33 2725.3,242.65 2734.3,236.66 2741.4,229 2747.2,222.79 2750.6,214.38 2752.7,206.22", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3125.4,178", + pos="2926.4,178", width=2.1304]; "anatomical entity to anatomical entity ontogenic association" -> "object category" [color=blue, label="object category", - lp="3145.9,221.5", - pos="e,3110.6,195.73 3000.4,250.44 3023.2,245.28 3045.8,238.33 3066.4,229 3080.1,222.83 3093,212.54 3103.3,202.9", + lp="2950.9,221.5", + pos="e,2913,196.2 2785.4,249.29 2822.5,243.92 2856.8,237.12 2873.4,229 2885.7,223.02 2897,213.21 2906,203.86", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3258.4,178", + pos="3059.4,178", width=1.0652]; "anatomical entity to anatomical entity ontogenic association" -> "subject closure" [color=blue, label="subject closure", - lp="3281.9,221.5", - pos="e,3246,195.51 3021.7,251.56 3105.1,245.16 3187.6,237.04 3205.4,229 3218.3,223.16 3230.1,212.86 3239.3,203.11", + lp="3085.9,221.5", + pos="e,3048.2,195.49 2876.8,254.28 2933.4,249.1 2984.9,241.16 3010.4,229 3022.6,223.19 3033.4,213.03 3041.8,203.37", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3358.4,178", + pos="3172.4,178", width=1.0652]; "anatomical entity to anatomical entity ontogenic association" -> "object closure" [color=blue, label="object closure", - lp="3402.4,221.5", - pos="e,3357,196.19 3035.9,252.37 3175.1,244.16 3334.1,233.8 3340.4,229 3347.7,223.49 3352.1,214.74 3354.7,206.09", + lp="3208.4,221.5", + pos="e,3167.6,195.9 2845.5,252.05 2981.7,243.64 3137.8,233.18 3144.4,229 3153.1,223.52 3159.3,214.38 3163.6,205.4", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3491.4,178", + pos="3305.4,178", width=2.1304]; "anatomical entity to anatomical entity ontogenic association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3559.9,221.5", - pos="e,3484.4,196.05 3034.2,252.29 3065.7,250.51 3098,248.7 3128.4,247 3164.9,244.97 3424.5,246.74 3456.4,229 3466.2,223.59 3473.8,214.21 \ -3479.4,205.02", + lp="3368.9,221.5", + pos="e,3295.8,196.13 2849.6,252.31 2881,250.53 2913.1,248.72 2943.4,247 2978.9,245 3230.6,244.71 3262.4,229 3273.4,223.57 3282.8,213.92 \ +3289.9,204.54", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3683.4,178", + pos="3498.4,178", width=2.1304]; "anatomical entity to anatomical entity ontogenic association" -> "object category closure" [color=blue, label="object category closure", - lp="3750.9,221.5", - pos="e,3677.4,196.09 3029.7,251.98 3062.7,250.18 3096.5,248.45 3128.4,247 3157.5,245.68 3626.2,243.39 3651.4,229 3660.8,223.64 3667.9,\ -214.27 3673,205.07", + lp="3560.9,221.5", + pos="e,3490.4,196.17 2844.7,251.99 2877.7,250.19 2911.5,248.46 2943.4,247 2972.1,245.69 3434.9,242.22 3460.4,229 3470.7,223.68 3479,214.18 \ +3485.2,204.88", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3873.4,178", + pos="3688.4,178", width=1.0652]; "anatomical entity to anatomical entity ontogenic association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3923.4,221.5", - pos="e,3866.4,196.17 3027.3,251.86 3061,250.05 3095.7,248.34 3128.4,247 3167.9,245.38 3803.7,247.66 3838.4,229 3848.2,223.74 3855.9,214.38 \ -3861.5,205.17", + lp="3734.4,221.5", + pos="e,3680.1,195.74 2842.3,251.86 2876,250.05 2910.7,248.34 2943.4,247 2982.6,245.39 3613.3,246.42 3648.4,229 3659.3,223.63 3668.1,213.8 \ +3674.7,204.27", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4032.4,178", + pos="3847.4,178", width=1.0652]; "anatomical entity to anatomical entity ontogenic association" -> "object namespace" [color=blue, label="object namespace", - lp="4076.4,221.5", - pos="e,4025.1,195.72 3026.1,251.79 3060.2,249.97 3095.3,248.28 3128.4,247 3176.6,245.14 3952.6,251.13 3995.4,229 4005.8,223.66 4013.9,\ -213.98 4019.9,204.54", + lp="3888.4,221.5", + pos="e,3838.8,195.77 2841.1,251.79 2875.2,249.97 2910.3,248.28 2943.4,247 2991.3,245.14 3763.3,249.96 3806.4,229 3817.4,223.66 3826.5,\ +213.84 3833.2,204.31", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4183.4,178", + pos="3998.4,178", width=1.0652]; "anatomical entity to anatomical entity ontogenic association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4236.4,221.5", - pos="e,4175.4,195.76 3025.3,251.75 3059.6,249.92 3095.1,248.24 3128.4,247 3156.6,245.95 4119.2,241.61 4144.4,229 4155.1,223.65 4163.8,\ -213.83 4170.2,204.3", + lp="4049.4,221.5", + pos="e,3989.5,195.79 2840.3,251.75 2874.6,249.92 2910.1,248.24 2943.4,247 2999.7,244.91 3905.6,253.23 3956.4,229 3967.6,223.7 3976.8,\ +213.88 3983.8,204.34", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4354.4,178", + pos="4169.4,178", width=1.0652]; "anatomical entity to anatomical entity ontogenic association" -> "object label closure" [color=blue, label="object label closure", - lp="4401.9,221.5", - pos="e,4346.1,195.78 3024.8,251.7 3059.4,249.87 3094.9,248.2 3128.4,247 3161.4,245.82 4284.8,243.5 4314.4,229 4325.3,223.68 4334.1,213.86 \ -4340.7,204.33", + lp="4216.9,221.5", + pos="e,4160.5,195.8 2839.8,251.7 2874.4,249.87 2909.9,248.2 2943.4,247 2976.3,245.82 4097.7,243.12 4127.4,229 4138.6,223.71 4147.8,213.89 \ +4154.8,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4507.4,178", + pos="4322.4,178", width=2.347]; "anatomical entity to anatomical entity ontogenic association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4560.9,221.5", - pos="e,4501.4,196.18 3024,251.69 3058.8,249.85 3094.7,248.18 3128.4,247 3165.8,245.69 4442.7,247.18 4475.4,229 4484.9,223.74 4492,214.39 \ -4497,205.18", + lp="4375.9,221.5", + pos="e,4316.4,196.18 2839,251.69 2873.8,249.85 2909.7,248.18 2943.4,247 2980.8,245.69 4257.7,247.18 4290.4,229 4299.9,223.74 4307,214.39 \ +4312,205.18", style=solid]; type [height=0.5, - pos="4641.4,178", + pos="4456.4,178", width=0.86659]; "anatomical entity to anatomical entity ontogenic association" -> type [color=blue, label=type, - lp="4659.4,221.5", - pos="e,4644.1,195.98 3024,251.65 3058.8,249.82 3094.7,248.16 3128.4,247 3149.3,246.28 4618.7,242.82 4634.4,229 4640.9,223.32 4643.4,214.65 \ -4644.1,206.11", + lp="4474.4,221.5", + pos="e,4459.1,195.98 2839,251.65 2873.8,249.82 2909.7,248.16 2943.4,247 2964.3,246.28 4433.7,242.82 4449.4,229 4455.9,223.32 4458.4,214.65 \ +4459.1,206.11", style=solid]; category [height=0.5, - pos="4742.4,178", + pos="4557.4,178", width=1.4263]; "anatomical entity to anatomical entity ontogenic association" -> category [color=blue, label=category, - lp="4737.9,221.5", - pos="e,4727.7,195.47 3023.6,251.66 3058.5,249.82 3094.5,248.16 3128.4,247 3171.5,245.53 4638.8,243.42 4679.4,229 4694.7,223.59 4709,212.83 \ -4720.2,202.67", + lp="4552.9,221.5", + pos="e,4542.7,195.47 2838.6,251.66 2873.5,249.82 2909.5,248.16 2943.4,247 2986.5,245.53 4453.8,243.42 4494.4,229 4509.7,223.59 4524,212.83 \ +4535.2,202.67", style=solid]; subject [height=0.5, - pos="4856.4,178", + pos="4671.4,178", width=1.2277]; "anatomical entity to anatomical entity ontogenic association" -> subject [color=blue, label=subject, - lp="4833.4,221.5", - pos="e,4837.7,194.32 3023.6,251.64 3058.5,249.8 3094.5,248.15 3128.4,247 3219.8,243.91 4685.5,253.96 4773.4,229 4793.6,223.28 4813.8,\ -211.29 4829.2,200.48", + lp="4648.4,221.5", + pos="e,4652.7,194.32 2838.6,251.64 2873.5,249.8 2909.5,248.15 2943.4,247 3034.8,243.91 4500.5,253.96 4588.4,229 4608.6,223.28 4628.8,\ +211.29 4644.2,200.48", style=solid]; object [height=0.5, - pos="4899.4,91", + pos="4714.4,91", width=1.0832]; "anatomical entity to anatomical entity ontogenic association" -> object [color=blue, label=object, - lp="4943.4,178", - pos="e,4912.8,108.09 3023.6,251.63 3058.5,249.79 3094.5,248.14 3128.4,247 3176.6,245.39 4817.6,243.99 4863.4,229 4887.3,221.17 4895.4,\ -216.87 4909.4,196 4923.2,175.52 4919.5,166.51 4922.4,142 4923.2,135.38 4924.3,133.39 4922.4,127 4921.4,123.55 4919.9,120.13 4918.2,\ + lp="4758.4,178", + pos="e,4727.8,108.09 2838.6,251.63 2873.5,249.79 2909.5,248.14 2943.4,247 2991.6,245.39 4632.6,243.99 4678.4,229 4702.3,221.17 4710.4,\ +216.87 4724.4,196 4738.2,175.52 4734.5,166.51 4737.4,142 4738.2,135.38 4739.3,133.39 4737.4,127 4736.4,123.55 4734.9,120.13 4733.2,\ 116.85", style=solid]; predicate [height=0.5, - pos="5053.4,178", + pos="4868.4,178", width=1.5165]; "anatomical entity to anatomical entity ontogenic association" -> predicate [color=blue, label=predicate, - lp="5026.4,221.5", - pos="e,5029.6,194.35 3023.2,251.63 3058.2,249.79 3094.4,248.13 3128.4,247 3229.6,243.64 4851.9,252.17 4950.4,229 4975.3,223.15 5001.2,\ -210.55 5020.8,199.47", + lp="4841.4,221.5", + pos="e,4844.6,194.35 2838.2,251.63 2873.2,249.79 2909.4,248.13 2943.4,247 3044.6,243.64 4666.9,252.17 4765.4,229 4790.3,223.15 4816.2,\ +210.55 4835.8,199.47", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3175.4,265", + pos="2990.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3306.4,265", + pos="3121.4,265", width=2.0762]; subject -> object [label=relation, - lp="4894.4,134.5", - pos="e,4881.5,107.23 4857.5,159.55 4858.7,149.57 4861.2,137.07 4866.4,127 4868.7,122.68 4871.6,118.52 4874.8,114.66"]; + lp="4709.4,134.5", + pos="e,4696.5,107.23 4672.5,159.55 4673.7,149.57 4676.2,137.07 4681.4,127 4683.7,122.68 4686.6,118.52 4689.8,114.66"]; relation [height=0.5, - pos="4844.4,18", + pos="4659.4,18", width=1.2999]; - subject -> relation [pos="e,4845.7,36.188 4855.1,159.79 4853,132.48 4849,78.994 4846.5,46.38", + subject -> relation [pos="e,4660.7,36.188 4670.1,159.79 4668,132.48 4664,78.994 4661.5,46.38", style=dotted]; "anatomical entity to anatomical entity ontogenic association_subject" [color=blue, height=0.5, label="anatomical entity", - pos="3490.4,265", + pos="3305.4,265", width=2.5456]; - object -> relation [pos="e,4857.2,35.54 4886.9,73.889 4880,64.939 4871.2,53.617 4863.5,43.584", + object -> relation [pos="e,4672.2,35.54 4701.9,73.889 4695,64.939 4686.2,53.617 4678.5,43.584", style=dotted]; "anatomical entity to anatomical entity ontogenic association_object" [color=blue, height=0.5, label="anatomical entity", - pos="3691.4,265", + pos="3506.4,265", width=2.5456]; "anatomical entity to anatomical entity ontogenic association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3879.4,265", + pos="3694.4,265", width=2.1665]; } diff --git a/graphviz/anatomical_entity_to_anatomical_entity_ontogenic_association.svg b/graphviz/anatomical_entity_to_anatomical_entity_ontogenic_association.svg index 8774e1c60f..71fa22f829 100644 --- a/graphviz/anatomical_entity_to_anatomical_entity_ontogenic_association.svg +++ b/graphviz/anatomical_entity_to_anatomical_entity_ontogenic_association.svg @@ -4,16 +4,16 @@ - + %3 - + anatomical entity to anatomical entity ontogenic association - -anatomical entity to anatomical entity ontogenic association + +anatomical entity to anatomical entity ontogenic association @@ -24,8 +24,8 @@ anatomical entity to anatomical entity ontogenic association->anatomical entity to anatomical entity association - - + + is_a @@ -37,9 +37,9 @@ anatomical entity to anatomical entity ontogenic association->id - + -id +id @@ -50,9 +50,9 @@ anatomical entity to anatomical entity ontogenic association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ anatomical entity to anatomical entity ontogenic association->name - - -name + + +name @@ -76,9 +76,9 @@ anatomical entity to anatomical entity ontogenic association->description - - -description + + +description @@ -89,9 +89,9 @@ anatomical entity to anatomical entity ontogenic association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ anatomical entity to anatomical entity ontogenic association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ anatomical entity to anatomical entity ontogenic association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ anatomical entity to anatomical entity ontogenic association->publications - - -publications + + +publications @@ -141,363 +141,363 @@ anatomical entity to anatomical entity ontogenic association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string anatomical entity to anatomical entity ontogenic association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string anatomical entity to anatomical entity ontogenic association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string anatomical entity to anatomical entity ontogenic association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type anatomical entity to anatomical entity ontogenic association->timepoint - - -timepoint + + +timepoint original subject - -string + +string anatomical entity to anatomical entity ontogenic association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie anatomical entity to anatomical entity ontogenic association->original predicate - - -original predicate + + +original predicate original object - -string + +string anatomical entity to anatomical entity ontogenic association->original object - - -original object + + +original object subject category - -ontology class + +ontology class anatomical entity to anatomical entity ontogenic association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class anatomical entity to anatomical entity ontogenic association->object category - - -object category + + +object category subject closure - -string + +string anatomical entity to anatomical entity ontogenic association->subject closure - - -subject closure + + +subject closure object closure - -string + +string anatomical entity to anatomical entity ontogenic association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class anatomical entity to anatomical entity ontogenic association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class anatomical entity to anatomical entity ontogenic association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string anatomical entity to anatomical entity ontogenic association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string anatomical entity to anatomical entity ontogenic association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string anatomical entity to anatomical entity ontogenic association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string anatomical entity to anatomical entity ontogenic association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source anatomical entity to anatomical entity ontogenic association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type anatomical entity to anatomical entity ontogenic association->type - - -type + + +type category - -category + +category anatomical entity to anatomical entity ontogenic association->category - - -category + + +category subject - -subject + +subject anatomical entity to anatomical entity ontogenic association->subject - - -subject + + +subject object - -object + +object anatomical entity to anatomical entity ontogenic association->object - - -object + + +object predicate - -predicate + +predicate anatomical entity to anatomical entity ontogenic association->predicate - - -predicate + + +predicate association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + anatomical entity to anatomical entity ontogenic association_subject - -anatomical entity + +anatomical entity object->relation - - + + anatomical entity to anatomical entity ontogenic association_object - -anatomical entity + +anatomical entity anatomical entity to anatomical entity ontogenic association_predicate - -predicate type + +predicate type diff --git a/graphviz/anatomical_entity_to_anatomical_entity_part_of_association.gv b/graphviz/anatomical_entity_to_anatomical_entity_part_of_association.gv index f24adaf247..65b88baa0e 100644 --- a/graphviz/anatomical_entity_to_anatomical_entity_part_of_association.gv +++ b/graphviz/anatomical_entity_to_anatomical_entity_part_of_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,5108,283"]; + graph [bb="0,0,4923,283"]; node [label="\N"]; "anatomical entity to anatomical entity part of association" [height=0.5, label="anatomical entity to anatomical entity part of association", - pos="2828.4,265", + pos="2643.4,265", width=7.6729]; "anatomical entity to anatomical entity association" [height=0.5, pos="242.43,178", width=6.7341]; "anatomical entity to anatomical entity part of association" -> "anatomical entity to anatomical entity association" [label=is_a, lp="640.43,221.5", - pos="e,338.39,194.57 2553,263.53 2048.1,262.02 992.51,255.66 626.43,229 532.1,222.13 425.48,207.71 348.56,196.12"]; + pos="e,338.39,194.53 2368.6,263.05 1898,260.78 956.39,253.27 626.43,229 532.1,222.06 425.48,207.65 348.56,196.07"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "anatomical entity to anatomical entity part of association" -> id [color=blue, label=id, - lp="756.43,221.5", - pos="e,570.42,189.98 2555.3,262.24 2031.9,258.46 923.78,248.28 749.43,229 677.26,221.02 659.37,215.5 589.43,196 586.32,195.13 583.12,\ -194.17 579.92,193.15", + lp="755.43,221.5", + pos="e,570.42,189.98 2371.5,261.78 1885.8,257.4 904.83,246.52 748.43,229 676.7,220.97 658.94,215.43 589.43,196 586.32,195.13 583.12,194.17 \ +579.93,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "anatomical entity to anatomical entity part of association" -> iri [color=blue, label=iri, - lp="869.43,221.5", - pos="e,675.34,190.2 2556,261.85 2055.4,257.51 1024.9,246.56 861.43,229 786.64,220.97 768.25,214.85 695.43,196 692.05,195.13 688.57,194.16 \ -685.09,193.15", + lp="861.43,221.5", + pos="e,675.35,190.15 2367,264.88 1939.6,265.18 1137.9,261.2 853.43,229 782.15,220.93 764.79,214.31 695.43,196 692.06,195.11 688.58,194.13 \ +685.1,193.11", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "anatomical entity to anatomical entity part of association" -> name [color=blue, label=name, - lp="976.43,221.5", - pos="e,799.39,191.54 2555,262.39 2073.4,259.03 1110,249.79 956.43,229 905.29,222.08 848.28,206.51 809.17,194.57", + lp="964.43,221.5", + pos="e,798.02,191.87 2370.8,262.06 1926.3,258.34 1081.1,248.77 944.43,229 897.05,222.15 844.49,206.96 807.9,195.11", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "anatomical entity to anatomical entity part of association" -> description [color=blue, label=description, - lp="1096.9,221.5", - pos="e,945.48,194.14 2553.1,263.27 2091.9,261.35 1199.1,254.37 1056.4,229 1021.4,222.77 983.37,209.4 955.07,198.06", + lp="1077.9,221.5", + pos="e,941.81,194.62 2368.4,263.31 1943.6,261.45 1163.6,254.55 1037.4,229 1007.4,222.92 975.31,210.09 951.04,198.95", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "anatomical entity to anatomical entity part of association" -> "has attribute" [color=blue, label="has attribute", - lp="1242.4,221.5", - pos="e,1086,192.82 2553.6,262.95 2123,260.57 1324.6,252.96 1195.4,229 1160.5,222.52 1122.6,208.39 1095.2,196.8", + lp="1212.4,221.5", + pos="e,1081.4,194.01 2368,263.48 1972.5,261.82 1278.8,255.16 1165.4,229 1138.9,222.88 1111.1,209.98 1090.2,198.82", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "anatomical entity to anatomical entity part of association" -> negated [color=blue, label=negated, - lp="1398.4,221.5", - pos="e,1207.6,190.46 2552.2,264.15 2194.3,263.16 1590.1,257.16 1369.4,229 1316.1,222.2 1256.5,205.66 1217.2,193.46", + lp="1350.4,221.5", + pos="e,1203.1,191.96 2373.5,261.16 2016.8,256.75 1421.6,246.83 1321.4,229 1283.4,222.23 1241.9,207.52 1212.5,195.8", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "anatomical entity to anatomical entity part of association" -> qualifiers [color=blue, label=qualifiers, - lp="1538.9,221.5", - pos="e,1356.7,193.07 2552.4,264.13 2225.3,262.99 1700,256.67 1505.4,229 1457.6,222.2 1404.6,207.74 1366.5,196.11", + lp="1460.9,221.5", + pos="e,1342.2,194.93 2371.7,261.72 2041.3,258.08 1516.6,249.19 1427.4,229 1400.8,222.97 1372.8,210.6 1351.3,199.66", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "anatomical entity to anatomical entity part of association" -> publications [color=blue, label=publications, - lp="1686.4,221.5", - pos="e,1508.2,192.71 2552.4,263.97 2257.8,262.48 1810.9,255.67 1642.4,229 1599.3,222.18 1551.8,207.69 1517.8,196.06", + lp="1561.4,221.5", + pos="e,1481.6,195.77 2374.4,260.86 2053.7,256.34 1555.8,246.54 1517.4,229 1505.6,223.61 1495.5,213.64 1487.8,204.02", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,274 +100,274 @@ digraph { width=2.0943]; "anatomical entity to anatomical entity part of association" -> "has evidence" [color=blue, label="has evidence", - lp="1840.9,221.5", - pos="e,1665.9,193.61 2554.5,262.66 2298.4,259.96 1935,252.03 1794.4,229 1753.6,222.3 1708.7,208.48 1675.7,197.06", + lp="1659.9,221.5", + pos="e,1615.5,195.85 2367.6,264 2071.4,262.59 1639.4,255.91 1613.4,229 1607.2,222.53 1607.9,213.49 1611.2,204.88", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1829.4,178", - width=3.015]; + label=string, + pos="1759.4,178", + width=1.0652]; "anatomical entity to anatomical entity part of association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1995.9,221.5", - pos="e,1855.5,195.59 2566.4,259.29 2323.8,254.02 1991.6,244.19 1931.4,229 1907.9,223.07 1883.5,211.31 1864.4,200.68", + lp="1778.9,221.5", + pos="e,1735.1,191.96 2369.1,262.83 2103.4,260.31 1737.1,252.55 1714.4,229 1704.7,218.93 1714,207.33 1726.5,197.85", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2064.4,178", - width=3.015]; + label=string, + pos="1854.4,178", + width=1.0652]; "anatomical entity to anatomical entity part of association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2167.4,221.5", - pos="e,2062.2,196.41 2564.7,259.6 2354.1,254.85 2091,245.63 2072.4,229 2066.1,223.34 2063.4,214.82 2062.5,206.41", + lp="1948.4,221.5", + pos="e,1848.6,196.04 2374.5,260.83 2152.7,256.85 1871.7,248.06 1853.4,229 1847.6,222.93 1846.3,214.32 1847,205.94", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2299.4,178", - width=3.015]; + label=string, + pos="2029.4,178", + width=1.0652]; "anatomical entity to anatomical entity part of association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2375.9,221.5", - pos="e,2278.7,195.97 2586.9,256.26 2441,250.36 2280.9,241.17 2269.4,229 2262.4,221.54 2265.6,212.18 2272.1,203.58", + lp="2168.9,221.5", + pos="e,2035.8,196.01 2383.2,258.94 2242.3,254.31 2091.1,245.54 2062.4,229 2053,223.54 2045.7,214.14 2040.5,204.96", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2481.4,178", + pos="2256.4,178", width=1.5346]; "anatomical entity to anatomical entity part of association" -> timepoint [color=blue, label=timepoint, - lp="2531.4,221.5", - pos="e,2482,196.47 2633.2,252.21 2567.8,246.56 2508.3,238.85 2496.4,229 2489.7,223.41 2485.9,214.91 2483.8,206.49", + lp="2331.4,221.5", + pos="e,2265.2,195.91 2417.4,254.61 2365.7,249.43 2319.2,241.41 2296.4,229 2286.1,223.36 2277.4,213.81 2270.9,204.56", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2593.4,178", + pos="2368.4,178", width=1.0652]; "anatomical entity to anatomical entity part of association" -> "original subject" [color=blue, label="original subject", - lp="2630.4,221.5", - pos="e,2579.7,194.92 2629.3,252.46 2604,247.18 2583.7,239.65 2574.4,229 2568.2,221.83 2570,212.39 2574.4,203.65", + lp="2434.4,221.5", + pos="e,2367.2,196.24 2443.2,252.54 2414,247.31 2389.9,239.78 2378.4,229 2372.2,223.22 2369.3,214.78 2368,206.47", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2707.4,178", + pos="2493.4,178", width=1.5887]; "anatomical entity to anatomical entity part of association" -> "original predicate" [color=blue, label="original predicate", - lp="2757.9,221.5", - pos="e,2696.4,195.76 2734.2,248.01 2715.8,242.96 2700.3,236.66 2694.4,229 2689.1,222.16 2689.7,213.39 2692.4,205.11", + lp="2564.9,221.5", + pos="e,2491.7,196.34 2545.6,248.09 2525.6,243 2508.5,236.66 2501.4,229 2495.8,222.91 2493.3,214.52 2492.3,206.36", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2821.4,178", + pos="2622.4,178", width=1.0652]; "anatomical entity to anatomical entity part of association" -> "original object" [color=blue, label="original object", - lp="2876.9,221.5", - pos="e,2822.8,196.18 2827,246.8 2826.1,235.16 2824.8,219.55 2823.7,206.24", + lp="2685.9,221.5", + pos="e,2626.7,196.18 2639.2,246.8 2636.3,235.16 2632.4,219.55 2629.2,206.24", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2954.4,178", + pos="2755.4,178", width=2.1304]; "anatomical entity to anatomical entity part of association" -> "subject category" [color=blue, label="subject category", - lp="3002.9,221.5", - pos="e,2950.6,196.4 2902.6,247.66 2913.5,242.93 2923.9,236.84 2932.4,229 2939.2,222.84 2944,214.24 2947.3,205.9", + lp="2809.9,221.5", + pos="e,2754.5,196.22 2715.3,247.57 2725,242.86 2734.2,236.8 2741.4,229 2747.2,222.79 2750.6,214.38 2752.7,206.22", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3125.4,178", + pos="2926.4,178", width=2.1304]; "anatomical entity to anatomical entity part of association" -> "object category" [color=blue, label="object category", - lp="3145.9,221.5", - pos="e,3110.6,195.73 2998.9,250.79 3022.2,245.6 3045.3,238.55 3066.4,229 3080.1,222.83 3093,212.54 3103.3,202.9", + lp="2950.9,221.5", + pos="e,2913,196.2 2784.2,249.47 2821.8,244.06 2856.6,237.21 2873.4,229 2885.7,223.02 2897,213.21 2906,203.86", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3258.4,178", + pos="3059.4,178", width=1.0652]; "anatomical entity to anatomical entity part of association" -> "subject closure" [color=blue, label="subject closure", - lp="3281.9,221.5", - pos="e,3246,195.51 3017.5,251.88 3102.3,245.44 3187.3,237.18 3205.4,229 3218.3,223.16 3230.1,212.86 3239.3,203.11", + lp="3085.9,221.5", + pos="e,3048.2,195.49 2830.7,251.76 2912.2,245.39 2993.2,237.23 3010.4,229 3022.6,223.19 3033.4,213.03 3041.8,203.37", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3358.4,178", + pos="3172.4,178", width=1.0652]; "anatomical entity to anatomical entity part of association" -> "object closure" [color=blue, label="object closure", - lp="3402.4,221.5", - pos="e,3357,196.19 3020.6,252.06 3164.5,242.93 3337.1,231.5 3340.4,229 3347.7,223.49 3352.1,214.74 3354.7,206.09", + lp="3208.4,221.5", + pos="e,3167.6,195.9 2840.6,252.35 2977.9,243.9 3137.8,233.23 3144.4,229 3153.1,223.52 3159.3,214.38 3163.6,205.4", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3491.4,178", + pos="3305.4,178", width=2.1304]; "anatomical entity to anatomical entity part of association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3560.9,221.5", - pos="e,3484.4,196.06 3023.4,252.23 3053.9,250.45 3085,248.65 3114.4,247 3152.4,244.87 3423.2,247.45 3456.4,229 3466.2,223.6 3473.8,214.22 \ -3479.4,205.03", + lp="3368.9,221.5", + pos="e,3295.8,196.14 2838.8,252.25 2869.1,250.46 2900.1,248.66 2929.4,247 2966.4,244.9 3229.2,245.36 3262.4,229 3273.4,223.58 3282.8,\ +213.94 3289.9,204.55", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3683.4,178", + pos="3498.4,178", width=2.1304]; "anatomical entity to anatomical entity part of association" -> "object category closure" [color=blue, label="object category closure", - lp="3750.9,221.5", - pos="e,3677.7,196.08 3019.2,251.97 3051,250.17 3083.6,248.43 3114.4,247 3144.3,245.61 3626.5,243.98 3652.4,229 3661.6,223.68 3668.4,214.45 \ -3673.3,205.35", + lp="3560.9,221.5", + pos="e,3490.4,196.17 2834.5,251.96 2866.2,250.16 2898.7,248.43 2929.4,247 2958.9,245.62 3434.2,242.56 3460.4,229 3470.7,223.69 3479,214.19 \ +3485.2,204.89", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3873.4,178", + pos="3688.4,178", width=1.0652]; "anatomical entity to anatomical entity part of association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3923.4,221.5", - pos="e,3866.4,196.17 3017.2,251.85 3049.6,250.03 3083,248.32 3114.4,247 3154.6,245.31 3803,248.02 3838.4,229 3848.2,223.74 3855.9,214.38 \ -3861.5,205.18", + lp="3734.4,221.5", + pos="e,3680.1,195.74 2832.2,251.86 2864.6,250.04 2898,248.33 2929.4,247 2969.3,245.31 3612.6,246.76 3648.4,229 3659.3,223.63 3668.1,213.8 \ +3674.7,204.27", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4032.4,178", + pos="3847.4,178", width=1.0652]; "anatomical entity to anatomical entity part of association" -> "object namespace" [color=blue, label="object namespace", - lp="4076.4,221.5", - pos="e,4025.1,195.73 3016.4,251.78 3049.1,249.95 3082.7,248.26 3114.4,247 3163.3,245.05 3951.9,251.48 3995.4,229 4005.8,223.66 4013.9,\ -213.98 4020,204.54", + lp="3888.4,221.5", + pos="e,3838.8,195.77 2831.4,251.78 2864.1,249.96 2897.7,248.27 2929.4,247 2978.1,245.05 3762.6,250.3 3806.4,229 3817.4,223.67 3826.5,\ +213.85 3833.2,204.31", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4183.4,178", + pos="3998.4,178", width=1.0652]; "anatomical entity to anatomical entity part of association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4236.4,221.5", - pos="e,4175.4,195.76 3015.7,251.74 3048.6,249.91 3082.5,248.23 3114.4,247 3143,245.9 4118.8,241.78 4144.4,229 4155.1,223.66 4163.8,213.83 \ -4170.2,204.3", + lp="4049.4,221.5", + pos="e,3989.5,195.79 2830.7,251.74 2863.6,249.91 2897.5,248.23 2929.4,247 2986.5,244.81 3904.9,253.56 3956.4,229 3967.6,223.7 3976.8,\ +213.88 3983.8,204.34", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4354.4,178", + pos="4169.4,178", width=1.0652]; "anatomical entity to anatomical entity part of association" -> "object label closure" [color=blue, label="object label closure", - lp="4401.9,221.5", - pos="e,4346.1,195.78 3014.9,251.72 3048,249.88 3082.2,248.2 3114.4,247 3147.7,245.76 4284.5,243.67 4314.4,229 4325.3,223.68 4334.1,213.86 \ -4340.7,204.33", + lp="4216.9,221.5", + pos="e,4160.5,195.8 2829.9,251.72 2863,249.88 2897.2,248.2 2929.4,247 2962.7,245.76 4097.4,243.28 4127.4,229 4138.6,223.71 4147.8,213.9 \ +4154.8,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4507.4,178", + pos="4322.4,178", width=2.347]; "anatomical entity to anatomical entity part of association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4560.9,221.5", - pos="e,4501.4,196.18 3014.5,251.69 3047.8,249.85 3082.1,248.17 3114.4,247 3152.2,245.63 4442.4,247.37 4475.4,229 4484.9,223.74 4492,214.39 \ -4497,205.18", + lp="4375.9,221.5", + pos="e,4316.4,196.18 2829.5,251.69 2862.8,249.85 2897.1,248.17 2929.4,247 2967.2,245.63 4257.4,247.37 4290.4,229 4299.9,223.74 4307,214.39 \ +4312,205.18", style=solid]; type [height=0.5, - pos="4641.4,178", + pos="4456.4,178", width=0.86659]; "anatomical entity to anatomical entity part of association" -> type [color=blue, label=type, - lp="4659.4,221.5", - pos="e,4644.1,195.98 3014.1,251.67 3047.5,249.83 3082,248.16 3114.4,247 3135.5,246.25 4618.6,242.95 4634.4,229 4640.9,223.32 4643.4,214.65 \ -4644.1,206.11", + lp="4474.4,221.5", + pos="e,4459.1,195.98 2829.1,251.67 2862.5,249.83 2897,248.16 2929.4,247 2950.5,246.25 4433.6,242.95 4449.4,229 4455.9,223.32 4458.4,214.65 \ +4459.1,206.11", style=solid]; category [height=0.5, - pos="4742.4,178", + pos="4557.4,178", width=1.4263]; "anatomical entity to anatomical entity part of association" -> category [color=blue, label=category, - lp="4737.9,221.5", - pos="e,4727.7,195.47 3014.1,251.67 3047.5,249.82 3082,248.15 3114.4,247 3157.9,245.46 4638.5,243.55 4679.4,229 4694.7,223.59 4709,212.83 \ -4720.2,202.68", + lp="4552.9,221.5", + pos="e,4542.7,195.47 2829.1,251.67 2862.5,249.82 2897,248.15 2929.4,247 2972.9,245.46 4453.5,243.55 4494.4,229 4509.7,223.59 4524,212.83 \ +4535.2,202.68", style=solid]; subject [height=0.5, - pos="4856.4,178", + pos="4671.4,178", width=1.2277]; "anatomical entity to anatomical entity part of association" -> subject [color=blue, label=subject, - lp="4833.4,221.5", - pos="e,4837.7,194.32 3014.1,251.65 3047.5,249.8 3082,248.14 3114.4,247 3206.5,243.76 4684.8,254.16 4773.4,229 4793.6,223.28 4813.8,211.29 \ -4829.2,200.48", + lp="4648.4,221.5", + pos="e,4652.7,194.32 2829.1,251.65 2862.5,249.8 2897,248.14 2929.4,247 3021.5,243.76 4499.8,254.16 4588.4,229 4608.6,223.28 4628.8,211.29 \ +4644.2,200.48", style=solid]; object [height=0.5, - pos="4899.4,91", + pos="4714.4,91", width=1.0832]; "anatomical entity to anatomical entity part of association" -> object [color=blue, label=object, - lp="4943.4,178", - pos="e,4912.8,108.09 3014.1,251.63 3047.5,249.79 3082,248.13 3114.4,247 3163,245.31 4817.3,244.11 4863.4,229 4887.3,221.17 4895.4,216.87 \ -4909.4,196 4923.2,175.52 4919.5,166.51 4922.4,142 4923.2,135.38 4924.3,133.39 4922.4,127 4921.4,123.55 4919.9,120.13 4918.2,116.85", + lp="4758.4,178", + pos="e,4727.8,108.09 2829.1,251.63 2862.5,249.79 2897,248.13 2929.4,247 2978,245.31 4632.3,244.11 4678.4,229 4702.3,221.17 4710.4,216.87 \ +4724.4,196 4738.2,175.52 4734.5,166.51 4737.4,142 4738.2,135.38 4739.3,133.39 4737.4,127 4736.4,123.55 4734.9,120.13 4733.2,116.85", style=solid]; predicate [height=0.5, - pos="5053.4,178", + pos="4868.4,178", width=1.5165]; "anatomical entity to anatomical entity part of association" -> predicate [color=blue, label=predicate, - lp="5026.4,221.5", - pos="e,5029.6,194.35 3013.8,251.64 3047.2,249.79 3081.9,248.13 3114.4,247 3216.4,243.47 4851.1,252.34 4950.4,229 4975.3,223.15 5001.2,\ -210.56 5020.8,199.47", + lp="4841.4,221.5", + pos="e,4844.6,194.35 2828.8,251.64 2862.2,249.79 2896.9,248.13 2929.4,247 3031.4,243.47 4666.1,252.34 4765.4,229 4790.3,223.15 4816.2,\ +210.56 4835.8,199.47", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3161.4,265", + pos="2976.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3292.4,265", + pos="3107.4,265", width=2.0762]; subject -> object [label=relation, - lp="4894.4,134.5", - pos="e,4881.5,107.23 4857.5,159.55 4858.7,149.57 4861.2,137.07 4866.4,127 4868.7,122.68 4871.6,118.52 4874.8,114.66"]; + lp="4709.4,134.5", + pos="e,4696.5,107.23 4672.5,159.55 4673.7,149.57 4676.2,137.07 4681.4,127 4683.7,122.68 4686.6,118.52 4689.8,114.66"]; relation [height=0.5, - pos="4844.4,18", + pos="4659.4,18", width=1.2999]; - subject -> relation [pos="e,4845.7,36.188 4855.1,159.79 4853,132.48 4849,78.994 4846.5,46.38", + subject -> relation [pos="e,4660.7,36.188 4670.1,159.79 4668,132.48 4664,78.994 4661.5,46.38", style=dotted]; "anatomical entity to anatomical entity part of association_subject" [color=blue, height=0.5, label="anatomical entity", - pos="3476.4,265", + pos="3291.4,265", width=2.5456]; - object -> relation [pos="e,4857.2,35.54 4886.9,73.889 4880,64.939 4871.2,53.617 4863.5,43.584", + object -> relation [pos="e,4672.2,35.54 4701.9,73.889 4695,64.939 4686.2,53.617 4678.5,43.584", style=dotted]; "anatomical entity to anatomical entity part of association_object" [color=blue, height=0.5, label="anatomical entity", - pos="3677.4,265", + pos="3492.4,265", width=2.5456]; "anatomical entity to anatomical entity part of association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3865.4,265", + pos="3680.4,265", width=2.1665]; } diff --git a/graphviz/anatomical_entity_to_anatomical_entity_part_of_association.svg b/graphviz/anatomical_entity_to_anatomical_entity_part_of_association.svg index 15a5f53802..c80eda8dc1 100644 --- a/graphviz/anatomical_entity_to_anatomical_entity_part_of_association.svg +++ b/graphviz/anatomical_entity_to_anatomical_entity_part_of_association.svg @@ -4,16 +4,16 @@ - + %3 - + anatomical entity to anatomical entity part of association - -anatomical entity to anatomical entity part of association + +anatomical entity to anatomical entity part of association @@ -24,8 +24,8 @@ anatomical entity to anatomical entity part of association->anatomical entity to anatomical entity association - - + + is_a @@ -37,9 +37,9 @@ anatomical entity to anatomical entity part of association->id - + -id +id @@ -50,9 +50,9 @@ anatomical entity to anatomical entity part of association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ anatomical entity to anatomical entity part of association->name - - -name + + +name @@ -76,9 +76,9 @@ anatomical entity to anatomical entity part of association->description - - -description + + +description @@ -89,9 +89,9 @@ anatomical entity to anatomical entity part of association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ anatomical entity to anatomical entity part of association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ anatomical entity to anatomical entity part of association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ anatomical entity to anatomical entity part of association->publications - - -publications + + +publications @@ -141,363 +141,363 @@ anatomical entity to anatomical entity part of association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string anatomical entity to anatomical entity part of association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string anatomical entity to anatomical entity part of association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string anatomical entity to anatomical entity part of association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type anatomical entity to anatomical entity part of association->timepoint - - -timepoint + + +timepoint original subject - -string + +string anatomical entity to anatomical entity part of association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie anatomical entity to anatomical entity part of association->original predicate - - -original predicate + + +original predicate original object - -string + +string anatomical entity to anatomical entity part of association->original object - - -original object + + +original object subject category - -ontology class + +ontology class anatomical entity to anatomical entity part of association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class anatomical entity to anatomical entity part of association->object category - - -object category + + +object category subject closure - -string + +string anatomical entity to anatomical entity part of association->subject closure - - -subject closure + + +subject closure object closure - -string + +string anatomical entity to anatomical entity part of association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class anatomical entity to anatomical entity part of association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class anatomical entity to anatomical entity part of association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string anatomical entity to anatomical entity part of association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string anatomical entity to anatomical entity part of association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string anatomical entity to anatomical entity part of association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string anatomical entity to anatomical entity part of association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source anatomical entity to anatomical entity part of association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type anatomical entity to anatomical entity part of association->type - - -type + + +type category - -category + +category anatomical entity to anatomical entity part of association->category - - -category + + +category subject - -subject + +subject anatomical entity to anatomical entity part of association->subject - - -subject + + +subject object - -object + +object anatomical entity to anatomical entity part of association->object - - -object + + +object predicate - -predicate + +predicate anatomical entity to anatomical entity part of association->predicate - - -predicate + + +predicate association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + anatomical entity to anatomical entity part of association_subject - -anatomical entity + +anatomical entity object->relation - - + + anatomical entity to anatomical entity part of association_object - -anatomical entity + +anatomical entity anatomical entity to anatomical entity part of association_predicate - -predicate type + +predicate type diff --git a/graphviz/association.gv b/graphviz/association.gv index 379f7a969f..7b0d34b5a7 100644 --- a/graphviz/association.gv +++ b/graphviz/association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4830.7,283"]; + graph [bb="0,0,4592.7,283"]; node [label="\N"]; association [height=0.5, label=association, - pos="2450.3,265", + pos="2212.3,265", width=1.7332]; entity [height=0.5, pos="38.347,178", width=1.0652]; association -> entity [label=is_a, lp="232.35,221.5", - pos="e,67.441,189.82 2387.9,263.88 2049,263.08 438.22,257.82 218.35,229 168.52,222.47 113.08,205.53 77.063,193.17"]; + pos="e,67.443,189.8 2149.9,263.75 1833.4,262.36 413.36,254.75 218.35,229 168.53,222.42 113.08,205.49 77.066,193.15"]; id [color=blue, height=0.5, label=string, @@ -19,7 +19,7 @@ digraph { association -> id [color=blue, label=id, lp="348.35,221.5", - pos="e,162.33,189.98 2387.9,263.66 2060.4,261.78 548.87,251.92 341.35,229 269.18,221.03 251.29,215.5 181.35,196 178.24,195.13 175.04,\ + pos="e,162.33,189.98 2150.1,263.52 1845.9,261.08 524.03,249.37 341.35,229 269.19,220.95 251.29,215.5 181.35,196 178.24,195.13 175.04,\ 194.17 171.84,193.15", style=solid]; iri [color=blue, @@ -30,7 +30,7 @@ digraph { association -> iri [color=blue, label=iri, lp="455.35,221.5", - pos="e,267.26,190.16 2387.9,263.6 2070.6,261.48 643.79,250.78 447.35,229 375.18,221 357.57,214.45 287.35,196 283.97,195.11 280.5,194.14 \ + pos="e,267.26,190.16 2149.8,264.3 1876.6,265.37 787.33,267.1 447.35,229 375.19,220.91 357.57,214.45 287.35,196 283.97,195.11 280.5,194.14 \ 277.02,193.12", style=solid]; name [color=blue, @@ -41,7 +41,7 @@ digraph { association -> name [color=blue, label=name, lp="559.35,221.5", - pos="e,390.2,191.77 2388,263.76 2079.7,262.47 725.5,255.32 539.35,229 490.87,222.15 437,206.78 399.77,194.87", + pos="e,390.2,191.75 2149.9,263.59 1865.7,261.59 700.76,252.04 539.35,229 490.88,222.08 437.01,206.72 399.77,194.84", style=solid]; description [color=blue, height=0.5, @@ -51,7 +51,7 @@ digraph { association -> description [color=blue, label=description, lp="675.85,221.5", - pos="e,534.72,194.4 2387.6,264.06 2088,264.18 809.99,262.71 635.35,229 603.66,222.88 569.65,209.83 544.09,198.6", + pos="e,534.73,194.37 2149.8,263.86 1875.5,263.1 785.55,258.22 635.35,229 603.67,222.84 569.66,209.79 544.09,198.56", style=solid]; "has attribute" [color=blue, height=0.5, @@ -61,7 +61,7 @@ digraph { association -> "has attribute" [color=blue, label="has attribute", lp="814.35,221.5", - pos="e,674.81,193.55 2387.9,264.09 2102.4,264.3 927.88,263.1 767.35,229 738.06,222.78 706.94,209.44 683.86,198.1", + pos="e,674.82,193.52 2149.9,263.86 1890.2,263.07 903.53,258.17 767.35,229 738.07,222.73 706.95,209.39 683.87,198.06", style=solid]; subject [color=blue, height=0.5, @@ -71,7 +71,7 @@ digraph { association -> subject [color=blue, label=subject, lp="941.35,221.5", - pos="e,818.47,194.37 2387.7,263.87 2117.7,263.13 1061,258.37 915.35,229 884.89,222.86 852.33,209.9 827.79,198.71", + pos="e,818.48,194.33 2149.8,263.59 1907.4,261.81 1036.7,253.74 915.35,229 884.91,222.8 852.34,209.84 827.8,198.66", style=solid]; predicate [color=blue, height=0.5, @@ -81,7 +81,7 @@ digraph { association -> predicate [color=blue, label=predicate, lp="1020.3,221.5", - pos="e,960.36,196.14 2387.6,264.14 2115.5,264.52 1048.2,263.8 986.35,229 976.92,223.69 969.84,214.33 964.77,205.13", + pos="e,960.37,196.12 2149.9,263.83 1907.1,262.97 1037.3,257.86 986.35,229 976.93,223.67 969.85,214.3 964.78,205.1", style=solid]; object [color=blue, height=0.5, @@ -91,7 +91,7 @@ digraph { association -> object [color=blue, label=object, lp="1099.3,178", - pos="e,927.99,105.47 2388.2,263.11 2180.1,259.97 1509.6,248.55 1294.3,229 1197.2,220.17 1164.4,240.02 1077.3,196 1057.2,185.79 1060,172.77 \ + pos="e,927.99,105.47 2150.1,263.04 1965.2,260 1420.8,249.49 1244.3,229 1169.2,220.27 1144.1,231.62 1077.3,196 1057.4,185.35 1060,172.77 \ 1041.3,160 1009.2,138.07 968.92,120.64 937.45,108.92", style=solid]; negated [color=blue, @@ -101,8 +101,8 @@ digraph { width=1.2999]; association -> negated [color=blue, label=negated, - lp="1404.3,221.5", - pos="e,1211.9,190.37 2388,263.56 2189.4,261.91 1573.1,254.79 1375.3,229 1321.5,221.98 1261.3,205.49 1221.6,193.36", + lp="1323.3,221.5", + pos="e,1202.9,193.17 2149.9,264.57 1970.8,265.74 1457.7,265.71 1294.3,229 1265.5,222.52 1234.8,209.14 1212.1,197.85", style=solid]; qualifiers [color=blue, height=0.5, @@ -111,8 +111,8 @@ digraph { width=2.1304]; association -> qualifiers [color=blue, label=qualifiers, - lp="1537.8,221.5", - pos="e,1360.2,193.18 2387.9,263.53 2205.4,261.85 1675.5,254.83 1504.3,229 1458.1,222.01 1406.8,207.72 1369.8,196.19", + lp="1413.8,221.5", + pos="e,1333.3,195.8 2149.9,263.62 1968.8,262.21 1451.6,255.84 1380.3,229 1365.6,223.43 1351.6,212.87 1340.7,202.88", style=solid]; publications [color=blue, height=0.5, @@ -121,8 +121,8 @@ digraph { width=1.7332]; association -> publications [color=blue, label=publications, - lp="1675.3,221.5", - pos="e,1510,193.06 2388.1,263.49 2222.9,261.79 1776.4,254.87 1631.3,229 1592.7,222.11 1550.4,208.11 1519.6,196.67", + lp="1499.3,221.5", + pos="e,1460.5,195.6 2150.1,263.44 1973.3,261.53 1479.2,253.98 1455.3,229 1448.8,222.17 1450.6,212.96 1455,204.3", style=solid]; "has evidence" [color=blue, height=0.5, @@ -131,219 +131,221 @@ digraph { width=2.0943]; association -> "has evidence" [color=blue, label="has evidence", - lp="1821.8,221.5", - pos="e,1665.8,194.06 2388.2,263.01 2244.2,260.37 1891.6,251.72 1775.3,229 1740.8,222.26 1703.4,209.05 1675.3,197.9", + lp="1597.8,221.5", + pos="e,1582.7,191.79 2150.1,262.99 1989.3,260.1 1571.8,250.52 1551.3,229 1538.4,215.4 1553.1,203.96 1573.2,195.48", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1833.3,178", - width=3.015]; + label=string, + pos="1763.3,178", + width=1.0652]; association -> "knowledge source" [color=blue, label="knowledge source", - lp="1961.8,221.5", - pos="e,1849.2,195.93 2387.5,264.66 2262.1,265.21 1985.4,262.45 1897.3,229 1882.4,223.32 1868.1,212.85 1856.9,202.96", + lp="1715.8,221.5", + pos="e,1734,189.74 2150.5,262.39 2008.2,258.38 1668.2,246.97 1651.3,229 1646.8,224.14 1647.3,219.31 1651.3,214 1669.2,190.45 1687.2,204.94 \ +1715.3,196 1718.3,195.07 1721.3,194.07 1724.4,193.05", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2068.3,178", - width=3.015]; + label=string, + pos="1858.3,178", + width=1.0652]; association -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2128.3,221.5", - pos="e,2045,195.58 2387.9,263.32 2277.4,261.45 2056.8,254.54 2033.3,229 2026,221.04 2030.1,211.47 2037.7,202.85", + lp="1882.3,221.5", + pos="e,1829,189.79 2150,263.43 2037.9,261.74 1811.4,255.1 1787.3,229 1782.8,224.1 1783.8,219.66 1787.3,214 1791.4,207.54 1805.2,200.12 \ +1819.6,193.78", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2303.3,178", - width=3.015]; + label=string, + pos="1976.3,178", + width=1.0652]; association -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2337.8,221.5", - pos="e,2254.9,194.15 2388.4,262.76 2330.9,260.15 2251.2,252.29 2231.3,229 2221.3,217.19 2230.7,206.86 2245.6,198.69", + lp="2096.8,221.5", + pos="e,1976.7,196.29 2150.9,261.61 2093.5,258.13 2013.5,249.62 1990.3,229 1983.8,223.21 1980.2,214.66 1978.3,206.26", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2485.3,178", + pos="2202.3,178", width=1.5346]; association -> timepoint [color=blue, label=timepoint, - lp="2486.3,221.5", - pos="e,2465.1,194.83 2447.6,246.69 2446.8,236.76 2447.1,224.26 2451.3,214 2453,209.95 2455.4,206.11 2458.2,202.56", + lp="2243.3,221.5", + pos="e,2204.4,196.18 2210.3,246.8 2209,235.16 2207.1,219.55 2205.6,206.24", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2597.3,178", + pos="2314.3,178", width=1.0652]; association -> "original subject" [color=blue, label="original subject", - lp="2599.3,221.5", - pos="e,2575.9,193.16 2482.2,249.32 2494.6,243.35 2508.8,236.17 2521.3,229 2522.6,228.29 2546.6,212.48 2567.3,198.82", + lp="2351.3,221.5", + pos="e,2306.5,195.95 2248.8,250.3 2260.4,244.83 2272.6,237.72 2282.3,229 2289.9,222.22 2296.4,213.26 2301.5,204.8", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2711.3,178", + pos="2440.3,178", width=1.5887]; association -> "original predicate" [color=blue, label="original predicate", - lp="2742.8,221.5", - pos="e,2697.8,195.8 2495.9,252.53 2504.7,250.53 2513.8,248.59 2522.3,247 2581.4,236.08 2601.9,254.36 2656.3,229 2669.3,222.98 2681.3,\ -212.85 2690.8,203.27", + lp="2488.8,221.5", + pos="e,2434.9,196.14 2257.9,252.58 2266.7,250.58 2275.8,248.62 2284.3,247 2340.4,236.44 2364.1,260.86 2411.3,229 2419.8,223.32 2426.1,\ +214.3 2430.6,205.47", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2825.3,178", + pos="2574.3,178", width=1.0652]; association -> "original object" [color=blue, label="original object", - lp="2869.8,221.5", - pos="e,2823.5,196.23 2494.7,252.3 2503.8,250.25 2513.3,248.34 2522.3,247 2553.6,242.35 2780.9,247.77 2806.3,229 2813.8,223.53 2818.3,\ -214.8 2821,206.14", + lp="2619.8,221.5", + pos="e,2572.9,196.19 2256.7,252.32 2265.8,250.26 2275.3,248.35 2284.3,247 2314.3,242.5 2532.2,247.23 2556.3,229 2563.7,223.49 2568,214.75 \ +2570.6,206.1", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2958.3,178", + pos="2707.3,178", width=2.1304]; association -> "subject category" [color=blue, label="subject category", - lp="3000.8,221.5", - pos="e,2952,196.07 2494.7,252.17 2503.8,250.12 2513.3,248.26 2522.3,247 2566.7,240.82 2886.4,251.12 2925.3,229 2934.8,223.61 2942.1,214.23 \ -2947.4,205.04", + lp="2750.8,221.5", + pos="e,2701.3,196.05 2256.7,252.18 2265.8,250.13 2275.3,248.26 2284.3,247 2327.4,240.98 2637.7,250.75 2675.3,229 2684.6,223.64 2691.6,\ +214.4 2696.7,205.3", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3129.3,178", + pos="2878.3,178", width=2.1304]; association -> "object category" [color=blue, label="object category", - lp="3147.8,221.5", - pos="e,3113.5,195.85 2494.3,252.17 2503.5,250.1 2513.2,248.22 2522.3,247 2582.1,239.04 3007.6,249.35 3064.3,229 3079.8,223.45 3094.5,\ -212.75 3106.1,202.67", + lp="2897.8,221.5", + pos="e,2862.8,195.85 2256.3,252.18 2265.5,250.11 2275.2,248.23 2284.3,247 2342.7,239.19 2759,249.13 2814.3,229 2829.5,223.5 2843.9,212.95 \ +2855.1,202.95", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3262.3,178", + pos="3011.3,178", width=1.0652]; association -> "subject closure" [color=blue, label="subject closure", - lp="3285.8,221.5", - pos="e,3249.9,195.36 2494.3,252.12 2503.5,250.06 2513.2,248.19 2522.3,247 2597.9,237.2 3136.7,257.39 3207.3,229 3221.1,223.48 3233.6,\ -212.86 3243.1,202.83", + lp="3035.8,221.5", + pos="e,2999.2,195.35 2256.3,252.13 2265.5,250.06 2275.2,248.19 2284.3,247 2358.5,237.35 2888.1,257.22 2957.3,229 2970.8,223.52 2982.9,\ +213.06 2992.3,203.11", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3360.3,178", + pos="3119.3,178", width=1.0652]; association -> "object closure" [color=blue, label="object closure", - lp="3402.3,221.5", - pos="e,3358.3,196.39 2494.2,252.09 2503.5,250.03 2513.2,248.17 2522.3,247 2567.4,241.25 3303,254.9 3340.3,229 3348.1,223.66 3352.8,214.83 \ -3355.7,206.07", + lp="3158.3,221.5", + pos="e,3115.7,196.02 2256.2,252.09 2265.5,250.03 2275.2,248.17 2284.3,247 2329,241.3 3056.3,253.09 3094.3,229 3102.8,223.66 3108.5,214.54 \ +3112.3,205.55", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3493.3,178", + pos="3252.3,178", width=2.1304]; association -> "subject category closure" [color=blue, label="subject category closure", - lp="3560.8,221.5", - pos="e,3485.7,196.22 2494.2,252.07 2503.5,250.01 2513.2,248.16 2522.3,247 2573.8,240.5 3410.2,252.8 3456.3,229 3466.5,223.75 3474.6,214.26 \ -3480.6,204.95", + lp="3317.8,221.5", + pos="e,3243.8,196.26 2256.2,252.07 2265.5,250.01 2275.2,248.16 2284.3,247 2335.5,240.54 3166.1,251.79 3212.3,229 3223,223.73 3231.8,214.11 \ +3238.3,204.71", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3683.3,178", + pos="3445.3,178", width=2.1304]; association -> "object category closure" [color=blue, label="object category closure", - lp="3750.8,221.5", - pos="e,3677.7,196.15 2494.2,252.05 2503.5,249.99 2513.2,248.14 2522.3,247 2584.7,239.24 3597.7,259.97 3652.3,229 3661.6,223.76 3668.4,\ -214.54 3673.3,205.43", + lp="3509.8,221.5", + pos="e,3438,196.22 2256.2,252.05 2265.5,249.99 2275.2,248.14 2284.3,247 2346.4,239.27 3353.9,257.94 3409.3,229 3419.4,223.75 3427.3,214.26 \ +3433.1,204.95", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3873.3,178", + pos="3635.3,178", width=1.0652]; association -> "subject namespace" [color=blue, label="subject namespace", - lp="3923.3,221.5", - pos="e,3866.6,195.73 2494.2,252.03 2503.5,249.97 2513.2,248.13 2522.3,247 2558.6,242.52 3806,246.1 3838.3,229 3848.4,223.67 3856.2,213.98 \ -3861.9,204.55", + lp="3683.3,221.5", + pos="e,3627.7,195.77 2256.2,252.03 2265.5,249.97 2275.2,248.13 2284.3,247 2320.5,242.53 3564.8,245.43 3597.3,229 3607.8,223.71 3616.2,\ +214.04 3622.4,204.6", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4032.3,178", + pos="3794.3,178", width=1.0652]; association -> "object namespace" [color=blue, label="object namespace", - lp="4076.3,221.5", - pos="e,4025,195.76 2494.2,252.02 2503.5,249.96 2513.2,248.13 2522.3,247 2563,242.02 3958.9,247.64 3995.3,229 4005.7,223.71 4013.9,214.03 \ -4019.9,204.59", + lp="3837.3,221.5", + pos="e,3786.4,195.78 2256.2,252.02 2265.5,249.96 2275.2,248.13 2284.3,247 2324.9,242.02 3718.7,247.15 3755.3,229 3766.1,223.68 3774.7,\ +213.86 3781.1,204.33", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4183.3,178", + pos="3945.3,178", width=1.0652]; association -> "subject label closure" [color=blue, label="subject label closure", - lp="4236.3,221.5", - pos="e,4175.4,195.79 2494.2,252.01 2503.5,249.96 2513.2,248.12 2522.3,247 2567.1,241.54 4104,248.99 4144.3,229 4155.1,223.69 4163.7,213.87 \ -4170.1,204.33", + lp="3998.3,221.5", + pos="e,3937.1,195.8 2256.2,252.01 2265.5,249.96 2275.2,248.12 2284.3,247 2329,241.54 3864.9,248.73 3905.3,229 3916.2,223.7 3925.1,213.89 \ +3931.6,204.35", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4354.3,178", + pos="4116.3,178", width=1.0652]; association -> "object label closure" [color=blue, label="object label closure", - lp="4402.8,221.5", - pos="e,4346.1,195.8 2493.9,252.09 2503.2,250 2513,248.13 2522.3,247 2571.8,240.99 4269.6,250.79 4314.3,229 4325.2,223.71 4334.1,213.9 \ -4340.7,204.35", + lp="4164.8,221.5", + pos="e,4108.1,195.8 2255.9,252.09 2265.2,250 2275,248.13 2284.3,247 2333.8,240.99 4031.6,250.79 4076.3,229 4087.2,223.71 4096.1,213.9 \ +4102.7,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4516.3,178", + pos="4278.3,178", width=2.347]; association -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4564.8,221.5", - pos="e,4507.8,196.3 2493.9,252.09 2503.2,249.99 2513,248.13 2522.3,247 2576.2,240.47 4427.5,252.74 4476.3,229 4487.1,223.79 4495.8,214.18 \ -4502.4,204.76", + lp="4326.8,221.5", + pos="e,4269.8,196.3 2255.9,252.09 2265.2,249.99 2275,248.13 2284.3,247 2338.2,240.47 4189.5,252.74 4238.3,229 4249.1,223.79 4257.8,214.18 \ +4264.4,204.76", style=solid]; type [height=0.5, - pos="4678.3,178", + pos="4440.3,178", width=0.86659]; association -> type [color=blue, label=type, - lp="4673.3,221.5", - pos="e,4670.1,195.81 2493.9,252.08 2503.2,249.99 2513,248.12 2522.3,247 2580.7,239.95 4585.5,254.69 4638.3,229 4649.2,223.72 4658.1,213.9 \ -4664.7,204.36", + lp="4435.3,221.5", + pos="e,4432.1,195.81 2255.9,252.08 2265.2,249.99 2275,248.12 2284.3,247 2342.7,239.95 4347.5,254.69 4400.3,229 4411.2,223.72 4420.1,213.9 \ +4426.7,204.36", style=solid]; category [height=0.5, - pos="4779.3,178", + pos="4541.3,178", width=1.4263]; association -> category [color=blue, label=category, - lp="4759.8,221.5", - pos="e,4759.2,194.83 2493.9,252.08 2503.2,249.99 2513,248.12 2522.3,247 2642.1,232.55 4577,260.88 4693.3,229 4714,223.34 4734.8,211.43 \ -4750.8,200.65", + lp="4521.8,221.5", + pos="e,4521.2,194.83 2255.9,252.08 2265.2,249.99 2275,248.12 2284.3,247 2404.1,232.55 4339,260.88 4455.3,229 4476,223.34 4496.8,211.43 \ +4512.8,200.65", style=solid]; subject -> object [label=relation, lp="871.35,134.5", @@ -358,11 +360,11 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="2569.3,265", + pos="2331.3,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2700.3,265", + pos="2462.3,265", width=2.0762]; } diff --git a/graphviz/association.svg b/graphviz/association.svg index a9152ecd21..edd8072bd5 100644 --- a/graphviz/association.svg +++ b/graphviz/association.svg @@ -4,16 +4,16 @@ - + %3 - + association - -association + +association @@ -24,8 +24,8 @@ association->entity - - + + is_a @@ -37,7 +37,7 @@ association->id - + id @@ -50,7 +50,7 @@ association->iri - + iri @@ -63,8 +63,8 @@ association->name - - + + name @@ -76,8 +76,8 @@ association->description - - + + description @@ -89,8 +89,8 @@ association->has attribute - - + + has attribute @@ -102,8 +102,8 @@ association->subject - - + + subject @@ -115,8 +115,8 @@ association->predicate - - + + predicate @@ -128,7 +128,7 @@ association->object - + object @@ -141,9 +141,9 @@ association->negated - - -negated + + +negated @@ -154,9 +154,9 @@ association->qualifiers - - -qualifiers + + +qualifiers @@ -167,9 +167,9 @@ association->publications - - -publications + + +publications @@ -180,269 +180,269 @@ association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type association->timepoint - - -timepoint + + +timepoint original subject - -string + +string association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie association->original predicate - - -original predicate + + +original predicate original object - -string + +string association->original object - - -original object + + +original object subject category - -ontology class + +ontology class association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class association->object category - - -object category + + +object category subject closure - -string + +string association->subject closure - - -subject closure + + +subject closure object closure - -string + +string association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type association->type - - -type + + +type category - -category + +category association->category - - -category + + +category @@ -472,14 +472,14 @@ association_type - -string + +string association_category - -category type + +category type diff --git a/graphviz/behavior_to_behavioral_feature_association.gv b/graphviz/behavior_to_behavioral_feature_association.gv index 524771e1e0..5a8f4dfe28 100644 --- a/graphviz/behavior_to_behavioral_feature_association.gv +++ b/graphviz/behavior_to_behavioral_feature_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,6284.4,283"]; + graph [bb="0,0,6066.4,283"]; node [label="\N"]; "behavior to behavioral feature association" [height=0.5, label="behavior to behavioral feature association", - pos="3444.4,265", + pos="3226.4,265", width=5.7231]; association [height=0.5, pos="62.394,178", width=1.7332]; "behavior to behavioral feature association" -> association [label=is_a, - lp="572.39,221.5", - pos="e,107.12,190.69 3239.1,263.26 2670.2,260.94 1080.9,252.47 558.39,229 369.57,220.52 321.15,225.14 134.39,196 128.7,195.11 122.8,194.01 \ -116.93,192.81"]; + lp="571.39,221.5", + pos="e,107.12,190.69 3021.2,263.03 2482.4,260.21 1035.9,250.78 557.39,229 369.02,220.43 320.71,225.09 134.39,196 128.7,195.11 122.8,194.01 \ +116.93,192.8"]; "entity to phenotypic feature association mixin" [height=0.5, pos="367.39,178", width=6.2286]; "behavior to behavioral feature association" -> "entity to phenotypic feature association mixin" [label=uses, - lp="745.89,221.5", - pos="e,457.07,194.55 3238,264.66 2691.7,265.89 1216.1,265.6 729.39,229 640.27,222.3 539.61,207.83 467.11,196.17"]; + lp="744.89,221.5", + pos="e,456.82,194.52 3020.3,264.4 2505.2,264.86 1171.4,262.65 728.39,229 639.52,222.25 539.14,207.79 466.83,196.14"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "behavior to behavioral feature association" -> id [color=blue, label=id, - lp="865.39,221.5", - pos="e,677.38,190 3239,263.43 2668.6,261.55 1091.7,254.12 858.39,229 785.34,221.13 767.2,215.65 696.39,196 693.29,195.14 690.09,194.17 \ -686.89,193.16", + lp="863.39,221.5", + pos="e,677.38,189.98 3021,263.19 2484.4,260.74 1067.9,252.16 856.39,229 784.22,221.1 766.34,215.5 696.39,196 693.29,195.13 690.09,194.17 \ +686.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,9 @@ digraph { width=1.2277]; "behavior to behavioral feature association" -> iri [color=blue, label=iri, - lp="982.39,221.5", - pos="e,782.29,190.23 3239.4,263.16 2687.3,260.6 1196.2,251.67 974.39,229 896.96,221.08 877.81,215.26 802.39,196 799.02,195.14 795.54,\ -194.18 792.05,193.17", + lp="976.39,221.5", + pos="e,782.3,190.2 3021.3,262.94 2503.2,259.96 1168.7,250.29 968.39,229 893.59,221.05 875.22,214.85 802.39,196 799.02,195.13 795.54,194.16 \ +792.06,193.15", style=solid]; name [color=blue, height=0.5, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "behavior to behavioral feature association" -> name [color=blue, label=name, - lp="1093.4,221.5", - pos="e,907.19,191.31 3238.8,263.53 2702,261.95 1284.6,255.31 1073.4,229 1019,222.22 958.13,206.28 916.96,194.21", + lp="1084.4,221.5", + pos="e,906.18,191.46 3020.8,263.39 2518.2,261.51 1254.5,254.31 1064.4,229 1012.7,222.12 955.09,206.41 915.77,194.42", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "behavior to behavioral feature association" -> description [color=blue, label=description, - lp="1220.9,221.5", - pos="e,1055.3,193.7 3238.1,264.15 2718,264.04 1379.9,260.66 1180.4,229 1140.5,222.66 1096.8,208.74 1064.8,197.19", + lp="1206.9,221.5", + pos="e,1052.9,194.05 3020.6,264.1 2535.1,263.83 1345.2,259.95 1166.4,229 1130.4,222.77 1091.3,209.24 1062.3,197.83", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "behavior to behavioral feature association" -> "has attribute" [color=blue, label="has attribute", - lp="1377.4,221.5", - pos="e,1196.7,191.92 3238.8,263.8 2744.2,262.85 1515.1,257.62 1330.4,229 1287.1,222.29 1239.4,207.19 1206.1,195.33", + lp="1354.4,221.5", + pos="e,1193.8,192.73 3020.7,263.91 2559.9,263.18 1472.1,258.34 1307.4,229 1271.2,222.55 1231.8,208.34 1203.4,196.72", style=solid]; predicate [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=2.1665]; "behavior to behavioral feature association" -> predicate [color=blue, label=predicate, - lp="1536.4,221.5", - pos="e,1353.7,193.17 3239.4,263.06 2775.1,260.55 1670.5,252.18 1502.4,229 1454.5,222.4 1401.5,207.92 1363.5,196.23", + lp="1499.4,221.5", + pos="e,1347.4,194.02 3021.2,263.31 2589.5,261.35 1614.9,254.19 1465.4,229 1427.9,222.68 1387,209.07 1356.8,197.64", style=solid]; negated [color=blue, height=0.5, @@ -87,8 +87,8 @@ digraph { width=1.2999]; "behavior to behavioral feature association" -> negated [color=blue, label=negated, - lp="1678.4,221.5", - pos="e,1488.4,190.5 3240.3,262.46 2803.2,258.8 1803.3,248.41 1649.4,229 1596.4,222.32 1537.3,205.82 1498.2,193.59", + lp="1619.4,221.5", + pos="e,1482.5,192.47 3021.1,263.39 2612.9,261.63 1727.1,254.85 1590.4,229 1555.9,222.49 1518.7,208.24 1491.9,196.62", style=solid]; qualifiers [color=blue, height=0.5, @@ -97,8 +97,8 @@ digraph { width=2.1304]; "behavior to behavioral feature association" -> qualifiers [color=blue, label=qualifiers, - lp="1817.9,221.5", - pos="e,1637.2,193.14 3240.2,262.41 2828.2,258.8 1924.7,248.75 1784.4,229 1737,222.33 1684.6,207.86 1646.9,196.19", + lp="1722.9,221.5", + pos="e,1618.5,195.22 3020.1,264.6 2630.6,264.96 1814.5,261.71 1689.4,229 1667.3,223.22 1644.7,211.39 1627.1,200.68", style=solid]; publications [color=blue, height=0.5, @@ -107,8 +107,8 @@ digraph { width=1.7332]; "behavior to behavioral feature association" -> publications [color=blue, label=publications, - lp="1964.4,221.5", - pos="e,1788.5,192.78 3240.3,262.33 2854.9,258.74 2047,248.93 1920.4,229 1878,222.33 1831.3,207.82 1797.9,196.15", + lp="1815.4,221.5", + pos="e,1754.1,196.36 3023,262.02 2628.7,257.8 1796.5,246.8 1771.4,229 1763.9,223.68 1759.3,214.98 1756.6,206.31", style=solid]; "has evidence" [color=blue, height=0.5, @@ -117,347 +117,348 @@ digraph { width=2.0943]; "behavior to behavioral feature association" -> "has evidence" [color=blue, label="has evidence", - lp="2124.9,221.5", - pos="e,1947.2,193.58 3241.7,261.72 2889.2,257.31 2189.8,246.5 2078.4,229 2036.5,222.42 1990.4,208.42 1956.8,196.9", + lp="1913.9,221.5", + pos="e,1882.2,194.9 3022.5,262.38 2648.1,258.91 1887.2,249.37 1867.4,229 1859,220.42 1864.8,210.29 1874.3,201.41", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2110.4,178", - width=3.015]; + label=string, + pos="2040.4,178", + width=1.0652]; "behavior to behavioral feature association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2282.9,221.5", - pos="e,2137.7,195.42 3239.8,262.66 2916.7,259.85 2314.6,251.64 2218.4,229 2193.3,223.09 2167,211.05 2146.6,200.26", + lp="2031.9,221.5", + pos="e,2010.7,189.53 3023.1,261.94 2671.6,257.9 1985.5,247.63 1967.4,229 1962.7,224.22 1963.8,219.64 1967.4,214 1971.6,207.3 1986.2,199.72 \ +2001.3,193.34", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2345.4,178", - width=3.015]; + label=string, + pos="2135.4,178", + width=1.0652]; "behavior to behavioral feature association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2456.4,221.5", - pos="e,2346.1,196.25 3239.1,263.41 2934.8,261.68 2395.7,254.94 2361.4,229 2354.2,223.55 2350.2,214.82 2347.9,206.17", + lp="2199.4,221.5", + pos="e,2116.4,193.72 3020.4,264.89 2705,265.21 2135.7,261.28 2104.4,229 2096.5,220.86 2101.3,210.39 2109.2,201.13", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2580.4,178", - width=3.015]; + label=string, + pos="2277.4,178", + width=1.0652]; "behavior to behavioral feature association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2665.9,221.5", - pos="e,2564.7,196.05 3239.5,262.97 2985.4,260.66 2582.6,253.18 2559.4,229 2552.9,222.25 2554.6,213.2 2559.2,204.65", + lp="2420.9,221.5", + pos="e,2285.1,196.14 3026.1,260.69 2767.1,255.78 2345.3,245.33 2314.4,229 2304.3,223.65 2296.2,214.14 2290.2,204.85", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2762.4,178", + pos="2503.4,178", width=1.5346]; "behavior to behavioral feature association" -> timepoint [color=blue, label=timepoint, - lp="2824.4,221.5", - pos="e,2766.8,195.94 3239.4,263.02 3061.6,260.55 2826.9,252.74 2789.4,229 2780.8,223.57 2774.8,214.44 2770.6,205.45", + lp="2586.4,221.5", + pos="e,2514.2,195.69 3025.2,261.04 2842,257.13 2593.6,248.32 2551.4,229 2539.3,223.45 2528.6,213.32 2520.5,203.62", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2874.4,178", + pos="2615.4,178", width=1.0652]; "behavior to behavioral feature association" -> "original subject" [color=blue, label="original subject", - lp="2924.4,221.5", - pos="e,2866.3,195.95 3252,258.54 3089.7,252.97 2881.7,243.12 2868.4,229 2862.6,222.84 2862,214.21 2863.6,205.84", + lp="2692.4,221.5", + pos="e,2617.9,196.29 3022.5,262.4 2864.6,259.42 2667.8,251.22 2636.4,229 2628.7,223.54 2623.8,214.69 2620.7,205.94", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2988.4,178", + pos="2741.4,178", width=1.5887]; "behavior to behavioral feature association" -> "original predicate" [color=blue, label="original predicate", - lp="3053.9,221.5", - pos="e,2983.9,196.05 3244.3,260.67 3131.1,256.68 3008.7,247.98 2990.4,229 2984.6,223.02 2982.9,214.53 2983,206.24", + lp="2827.9,221.5", + pos="e,2744.6,196.28 3034.1,258.53 2917.5,253.63 2787,244.71 2764.4,229 2756.5,223.53 2751.3,214.68 2747.8,205.93", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3102.4,178", + pos="2870.4,178", width=1.0652]; "behavior to behavioral feature association" -> "original object" [color=blue, label="original object", - lp="3187.9,221.5", - pos="e,3109.3,195.81 3264.7,256.2 3210.4,251.13 3159.2,242.77 3136.4,229 3127,223.3 3119.5,213.87 3114.1,204.72", + lp="2964.9,221.5", + pos="e,2880.1,195.88 3050.9,255.49 2993.6,250.35 2938.2,242.12 2913.4,229 2902.5,223.27 2893.2,213.57 2886.1,204.23", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3235.4,178", + pos="3003.4,178", width=2.1304]; "behavior to behavioral feature association" -> "subject category" [color=blue, label="subject category", - lp="3312.9,221.5", - pos="e,3237.2,196.31 3318.7,250.69 3289.9,245.48 3264.5,238.43 3253.4,229 3246.6,223.23 3242.4,214.69 3239.7,206.29", + lp="3093.9,221.5", + pos="e,3009.7,196.02 3107.6,250.25 3076.2,244.88 3047.4,237.85 3034.4,229 3025.7,223.11 3019.1,213.93 3014.1,205.03", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3406.4,178", + pos="3174.4,178", width=2.1304]; "behavior to behavioral feature association" -> "object category" [color=blue, label="object category", - lp="3433.9,221.5", - pos="e,3387.5,195.82 3397.2,247.32 3389.7,242.57 3382.9,236.56 3378.4,229 3373.5,220.9 3376.1,211.93 3381.3,203.84", + lp="3215.9,221.5", + pos="e,3163.2,196.12 3179.2,247.32 3171.7,242.57 3164.9,236.56 3160.4,229 3156.1,221.86 3156.7,213.36 3159.3,205.41", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3539.4,178", + pos="3307.4,178", width=1.0652]; "behavior to behavioral feature association" -> "subject closure" [color=blue, label="subject closure", - lp="3559.9,221.5", - pos="e,3524.6,194.83 3467.3,247.09 3474.5,241.51 3482.4,235.16 3489.4,229 3498.9,220.58 3508.9,210.78 3517.5,202.1", + lp="3338.9,221.5", + pos="e,3297.1,195.67 3250.8,247.03 3257.8,241.64 3265.2,235.41 3271.4,229 3278.7,221.45 3285.6,212.36 3291.5,204.01", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3639.4,178", + pos="3420.4,178", width=1.0652]; "behavior to behavioral feature association" -> "object closure" [color=blue, label="object closure", - lp="3680.4,221.5", - pos="e,3636.4,196.31 3556.4,249.84 3583.5,244.56 3607.8,237.68 3618.4,229 3625.5,223.17 3630.3,214.5 3633.4,206.02", + lp="3460.4,221.5", + pos="e,3416.7,196.33 3335.4,249.63 3362.4,244.32 3386.7,237.48 3397.4,229 3404.7,223.19 3409.8,214.53 3413.3,206.04", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3772.4,178", + pos="3553.4,178", width=2.1304]; "behavior to behavioral feature association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3838.9,221.5", - pos="e,3763.9,196.31 3585.7,251.88 3652.6,245.24 3720.8,236.8 3734.4,229 3744.3,223.33 3752.4,213.95 3758.6,204.83", + lp="3619.9,221.5", + pos="e,3544.6,196.31 3366.7,251.77 3433.1,245.1 3500.8,236.67 3514.4,229 3524.4,223.33 3532.8,213.95 3539.1,204.84", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3964.4,178", + pos="3746.4,178", width=2.1304]; "behavior to behavioral feature association" -> "object category closure" [color=blue, label="object category closure", - lp="4029.9,221.5", - pos="e,3957.6,196 3590.1,252.23 3613.3,250.43 3637,248.63 3659.4,247 3689.5,244.81 3904.2,243.99 3930.4,229 3940,223.52 3947.4,214.13 \ -3952.8,204.95", + lp="3810.9,221.5", + pos="e,3739.3,196.01 3372.1,252.23 3395.3,250.43 3419,248.63 3441.4,247 3471.4,244.81 3685.2,243.76 3711.4,229 3721.1,223.54 3728.7,214.14 \ +3734.3,204.96", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4154.4,178", + pos="3936.4,178", width=1.0652]; "behavior to behavioral feature association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4202.4,221.5", - pos="e,4146.7,196.14 3586.6,251.96 3610.9,250.13 3635.8,248.39 3659.4,247 3710.2,243.99 4072.4,252.81 4117.4,229 4127.5,223.64 4135.6,\ -214.14 4141.6,204.85", + lp="3983.4,221.5", + pos="e,3928.7,195.66 3368.6,251.96 3392.9,250.13 3417.8,248.39 3441.4,247 3492.1,244 3853.3,252.47 3898.4,229 3908.8,223.58 3917.2,213.88 \ +3923.4,204.46", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4313.4,178", + pos="4095.4,178", width=1.0652]; "behavior to behavioral feature association" -> "object namespace" [color=blue, label="object namespace", - lp="4356.4,221.5", - pos="e,4305.4,195.71 3585.4,251.84 3610.1,250.01 3635.5,248.3 3659.4,247 3693.5,245.15 4243.9,244.44 4274.4,229 4285.1,223.59 4293.7,\ -213.76 4300.1,204.24", + lp="4137.4,221.5", + pos="e,4087.1,195.72 3367.4,251.84 3392.1,250.01 3417.5,248.3 3441.4,247 3475.5,245.15 4024.9,244.23 4055.4,229 4066.2,223.61 4075.1,\ +213.78 4081.6,204.25", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4464.4,178", + pos="4246.4,178", width=1.0652]; "behavior to behavioral feature association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4516.4,221.5", - pos="e,4456.1,195.75 3584.5,251.79 3609.5,249.94 3635.2,248.24 3659.4,247 3701.9,244.82 4386.3,247.87 4424.4,229 4435.2,223.64 4444.1,\ -213.81 4450.7,204.28", + lp="4297.4,221.5", + pos="e,4237.8,195.76 3366.5,251.79 3391.5,249.94 3417.2,248.24 3441.4,247 3483.8,244.83 4167.2,247.61 4205.4,229 4216.4,223.65 4225.4,\ +213.83 4232.2,204.29", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4603.4,178", + pos="4385.4,178", width=1.0652]; "behavior to behavioral feature association" -> "object label closure" [color=blue, label="object label closure", - lp="4672.9,221.5", - pos="e,4605.3,196.04 3584,251.75 3609.1,249.89 3635,248.2 3659.4,247 3685.3,245.73 4574.6,245.85 4594.4,229 4601,223.39 4603.8,214.73 \ -4604.9,206.19", + lp="4454.9,221.5", + pos="e,4387,196.08 3366,251.75 3391.1,249.89 3417,248.2 3441.4,247 3467.3,245.73 4355.5,245.64 4375.4,229 4382.1,223.43 4385.1,214.78 \ +4386.3,206.24", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4744.4,178", + pos="4526.4,178", width=2.347]; "behavior to behavioral feature association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4822.9,221.5", - pos="e,4750.8,196.11 3583.7,251.71 3608.9,249.85 3634.9,248.17 3659.4,247 3689.6,245.56 4725.2,250.53 4746.4,229 4752.3,223.01 4753.4,\ -214.41 4752.6,206.03", + lp="4604.9,221.5", + pos="e,4532.8,196.11 3365.7,251.71 3390.9,249.85 3416.9,248.17 3441.4,247 3471.6,245.56 4507.2,250.53 4528.4,229 4534.3,223.01 4535.4,\ +214.41 4534.6,206.03", style=solid]; type [height=0.5, - pos="4878.4,178", + pos="4660.4,178", width=0.86659]; "behavior to behavioral feature association" -> type [color=blue, label=type, - lp="4917.4,221.5", - pos="e,4891.4,194.36 3583.4,251.69 3608.7,249.83 3634.8,248.15 3659.4,247 3676.6,246.2 4884.3,241.24 4896.4,229 4903.3,222 4901.3,212.17 \ -4896.7,203.08", + lp="4699.4,221.5", + pos="e,4673.4,194.36 3365.4,251.69 3390.7,249.83 3416.8,248.15 3441.4,247 3458.6,246.2 4666.3,241.24 4678.4,229 4685.3,222 4683.3,212.17 \ +4678.7,203.08", style=solid]; category [height=0.5, - pos="4979.4,178", + pos="4761.4,178", width=1.4263]; "behavior to behavioral feature association" -> category [color=blue, label=category, - lp="4988.9,221.5", - pos="e,4970.5,195.81 3583.4,251.68 3608.7,249.82 3634.8,248.14 3659.4,247 3694.9,245.35 4905.3,244.22 4937.4,229 4948.5,223.72 4957.8,\ -213.9 4964.7,204.36", + lp="4770.9,221.5", + pos="e,4752.5,195.81 3365.4,251.68 3390.7,249.82 3416.8,248.14 3441.4,247 3476.9,245.35 4687.3,244.22 4719.4,229 4730.5,223.72 4739.8,\ +213.9 4746.7,204.36", style=solid]; subject [height=0.5, - pos="5093.4,178", + pos="4875.4,178", width=1.2277]; "behavior to behavioral feature association" -> subject [color=blue, label=subject, - lp="5079.4,221.5", - pos="e,5077.5,195 3583.1,251.69 3608.5,249.82 3634.7,248.14 3659.4,247 3735.2,243.51 4952.4,252.87 5024.4,229 5041.2,223.42 5057.4,212.12 \ -5069.9,201.67", + lp="4861.4,221.5", + pos="e,4859.5,195 3365.1,251.69 3390.5,249.82 3416.7,248.14 3441.4,247 3517.2,243.51 4734.4,252.87 4806.4,229 4823.2,223.42 4839.4,212.12 \ +4851.9,201.67", style=solid]; object [height=0.5, - pos="5136.4,91", + pos="4918.4,91", width=1.0832]; "behavior to behavioral feature association" -> object [color=blue, label=object, - lp="5179.4,178", - pos="e,5149.8,108.09 3583.1,251.67 3608.5,249.8 3634.7,248.13 3659.4,247 3699.6,245.16 5071.8,243.58 5109.4,229 5151,212.86 5154.1,186.29 \ -5159.4,142 5160.2,135.38 5161.3,133.39 5159.4,127 5158.4,123.55 5156.9,120.13 5155.1,116.85", + lp="4961.4,178", + pos="e,4931.8,108.09 3365.1,251.67 3390.5,249.8 3416.7,248.13 3441.4,247 3481.6,245.16 4853.8,243.58 4891.4,229 4933,212.86 4936.1,186.29 \ +4941.4,142 4942.2,135.38 4943.3,133.39 4941.4,127 4940.4,123.55 4938.9,120.13 4937.1,116.85", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="5320.4,178", + pos="5102.4,178", width=2.3651]; "behavior to behavioral feature association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="5308.4,221.5", - pos="e,5288.2,194.71 3583.1,251.66 3608.5,249.79 3634.7,248.12 3659.4,247 3829,239.3 5020.5,260.35 5187.4,229 5219.1,223.04 5253.1,210.12 \ -5278.8,198.91", + lp="5090.4,221.5", + pos="e,5070.2,194.71 3365.1,251.66 3390.5,249.79 3416.7,248.12 3441.4,247 3611,239.3 4802.5,260.35 4969.4,229 5001.1,223.04 5035.1,210.12 \ +5060.8,198.91", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="5499.4,178", + pos="5281.4,178", width=2.1123]; "behavior to behavioral feature association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="5489.4,221.5", - pos="e,5470.6,194.84 3582.8,251.65 3608.3,249.78 3634.6,248.11 3659.4,247 3754.9,242.73 5286.8,248.38 5380.4,229 5408.7,223.13 5438.8,\ -210.45 5461.6,199.33", + lp="5271.4,221.5", + pos="e,5252.6,194.84 3364.8,251.65 3390.3,249.78 3416.6,248.11 3441.4,247 3536.9,242.73 5068.8,248.38 5162.4,229 5190.7,223.13 5220.8,\ +210.45 5243.6,199.33", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="5629.4,178", + pos="5411.4,178", width=1.011]; "behavior to behavioral feature association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="5637.9,221.5", - pos="e,5612.7,194.31 3582.8,251.63 3608.3,249.76 3634.6,248.1 3659.4,247 3712,244.67 5504.1,244.49 5554.4,229 5572.8,223.32 5590.9,211.5 \ -5604.7,200.77", + lp="5419.9,221.5", + pos="e,5394.7,194.31 3364.8,251.63 3390.3,249.76 3416.6,248.1 3441.4,247 3494,244.67 5286.1,244.49 5336.4,229 5354.8,223.32 5372.9,211.5 \ +5386.7,200.77", style=solid]; "sex qualifier" [color=blue, height=0.5, label="biological sex", - pos="5757.4,178", + pos="5539.4,178", width=2.0401]; "behavior to behavioral feature association" -> "sex qualifier" [color=blue, label="sex qualifier", - lp="5765.4,221.5", - pos="e,5742.1,195.74 3582.5,251.64 3608.1,249.76 3634.5,248.09 3659.4,247 3715.8,244.52 5640.1,247.63 5693.4,229 5708.9,223.6 5723.5,\ -212.8 5734.8,202.62", + lp="5547.4,221.5", + pos="e,5524.1,195.74 3364.5,251.64 3390.1,249.76 3416.5,248.09 3441.4,247 3497.8,244.52 5422.1,247.63 5475.4,229 5490.9,223.6 5505.5,\ +212.8 5516.8,202.62", style=solid]; "has count" [color=blue, height=0.5, label=integer, - pos="5893.4,178", + pos="5675.4,178", width=1.2277]; "behavior to behavioral feature association" -> "has count" [color=blue, label="has count", - lp="5881.4,221.5", - pos="e,5875.1,194.57 3582.5,251.63 3608.1,249.75 3634.5,248.09 3659.4,247 3719.2,244.39 5755.9,245.74 5813.4,229 5832.8,223.33 5852.2,\ -211.47 5867,200.71", + lp="5663.4,221.5", + pos="e,5657.1,194.57 3364.5,251.63 3390.1,249.75 3416.5,248.09 3441.4,247 3501.2,244.39 5537.9,245.74 5595.4,229 5614.8,223.33 5634.2,\ +211.47 5649,200.71", style=solid]; "has total" [color=blue, height=0.5, label=integer, - pos="5999.4,178", + pos="5781.4,178", width=1.2277]; "behavior to behavioral feature association" -> "has total" [color=blue, label="has total", - lp="5984.9,221.5", - pos="e,5981.4,194.57 3582.5,251.62 3608.1,249.75 3634.5,248.08 3659.4,247 3722.1,244.27 5860.1,246.73 5920.4,229 5939.7,223.33 5958.8,\ -211.47 5973.3,200.71", + lp="5766.9,221.5", + pos="e,5763.4,194.57 3364.5,251.62 3390.1,249.75 3416.5,248.08 3441.4,247 3504.1,244.27 5642.1,246.73 5702.4,229 5721.7,223.33 5740.8,\ +211.47 5755.3,200.71", style=solid]; "has quotient" [color=blue, height=0.5, label=double, - pos="6103.4,178", + pos="5885.4,178", width=1.1735]; "behavior to behavioral feature association" -> "has quotient" [color=blue, label="has quotient", - lp="6099.4,221.5", - pos="e,6084.7,194.34 3582.5,251.62 3608.1,249.74 3634.5,248.08 3659.4,247 3724.9,244.16 5957.3,246.8 6020.4,229 6040.6,223.31 6060.8,\ -211.32 6076.2,200.51", + lp="5881.4,221.5", + pos="e,5866.7,194.34 3364.5,251.62 3390.1,249.74 3416.5,248.08 3441.4,247 3506.9,244.16 5739.3,246.8 5802.4,229 5822.6,223.31 5842.8,\ +211.32 5858.2,200.51", style=solid]; "has percentage" [color=blue, height=0.5, label=double, - pos="6210.4,178", + pos="5992.4,178", width=1.1735]; "behavior to behavioral feature association" -> "has percentage" [color=blue, label="has percentage", - lp="6229.4,221.5", - pos="e,6196.4,195 3582.5,251.61 3608.1,249.73 3634.5,248.07 3659.4,247 3728.5,244.02 6083.3,252.25 6148.4,229 6163.7,223.54 6178,212.56 \ -6189,202.28", + lp="6011.4,221.5", + pos="e,5978.4,195 3364.5,251.61 3390.1,249.73 3416.5,248.07 3441.4,247 3510.5,244.02 5865.3,252.25 5930.4,229 5945.7,223.54 5960,212.56 \ +5971,202.28", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3706.4,265", + pos="3488.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3837.4,265", + pos="3619.4,265", width=2.0762]; subject -> object [label=relation, - lp="5131.4,134.5", - pos="e,5118.5,107.23 5094.5,159.55 5095.7,149.57 5098.2,137.07 5103.4,127 5105.6,122.68 5108.5,118.52 5111.7,114.66"]; + lp="4913.4,134.5", + pos="e,4900.5,107.23 4876.5,159.55 4877.7,149.57 4880.2,137.07 4885.4,127 4887.6,122.68 4890.5,118.52 4893.7,114.66"]; relation [height=0.5, - pos="5081.4,18", + pos="4863.4,18", width=1.2999]; - subject -> relation [pos="e,5082.7,36.188 5092.1,159.79 5090,132.48 5086,78.994 5083.5,46.38", + subject -> relation [pos="e,4864.7,36.188 4874.1,159.79 4872,132.48 4868,78.994 4865.5,46.38", style=dotted]; "behavior to behavioral feature association_subject" [color=blue, height=0.5, label=behavior, - pos="3981.4,265", + pos="3763.4,265", width=1.4263]; - object -> relation [pos="e,5094.2,35.54 5123.9,73.889 5117,64.939 5108.2,53.617 5100.4,43.584", + object -> relation [pos="e,4876.2,35.54 4905.9,73.889 4899,64.939 4890.2,53.617 4882.4,43.584", style=dotted]; "behavior to behavioral feature association_object" [color=blue, height=0.5, label="behavioral feature", - pos="4147.4,265", + pos="3929.4,265", width=2.672]; } diff --git a/graphviz/behavior_to_behavioral_feature_association.svg b/graphviz/behavior_to_behavioral_feature_association.svg index 7bb9c0d068..e46f6d6265 100644 --- a/graphviz/behavior_to_behavioral_feature_association.svg +++ b/graphviz/behavior_to_behavioral_feature_association.svg @@ -4,16 +4,16 @@ - + %3 - + behavior to behavioral feature association - -behavior to behavioral feature association + +behavior to behavioral feature association @@ -24,9 +24,9 @@ behavior to behavioral feature association->association - + -is_a +is_a @@ -37,9 +37,9 @@ behavior to behavioral feature association->entity to phenotypic feature association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ behavior to behavioral feature association->id - - -id + + +id @@ -63,9 +63,9 @@ behavior to behavioral feature association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ behavior to behavioral feature association->name - - -name + + +name @@ -89,9 +89,9 @@ behavior to behavioral feature association->description - - -description + + +description @@ -102,9 +102,9 @@ behavior to behavioral feature association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ behavior to behavioral feature association->predicate - - -predicate + + +predicate @@ -128,9 +128,9 @@ behavior to behavioral feature association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ behavior to behavioral feature association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ behavior to behavioral feature association->publications - - -publications + + +publications @@ -167,448 +167,448 @@ behavior to behavioral feature association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string behavior to behavioral feature association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string behavior to behavioral feature association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string behavior to behavioral feature association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type behavior to behavioral feature association->timepoint - - -timepoint + + +timepoint original subject - -string + +string behavior to behavioral feature association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie behavior to behavioral feature association->original predicate - - -original predicate + + +original predicate original object - -string + +string behavior to behavioral feature association->original object - - -original object + + +original object subject category - -ontology class + +ontology class behavior to behavioral feature association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class behavior to behavioral feature association->object category - - -object category + + +object category subject closure - -string + +string behavior to behavioral feature association->subject closure - - -subject closure + + +subject closure object closure - -string + +string behavior to behavioral feature association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class behavior to behavioral feature association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class behavior to behavioral feature association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string behavior to behavioral feature association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string behavior to behavioral feature association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string behavior to behavioral feature association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string behavior to behavioral feature association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source behavior to behavioral feature association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type behavior to behavioral feature association->type - - -type + + +type category - -category + +category behavior to behavioral feature association->category - - -category + + +category subject - -subject + +subject behavior to behavioral feature association->subject - - -subject + + +subject object - -object + +object behavior to behavioral feature association->object - - -object + + +object frequency qualifier - -frequency value + +frequency value behavior to behavioral feature association->frequency qualifier - - -frequency qualifier + + +frequency qualifier severity qualifier - -severity value + +severity value behavior to behavioral feature association->severity qualifier - - -severity qualifier + + +severity qualifier onset qualifier - -onset + +onset behavior to behavioral feature association->onset qualifier - - -onset qualifier + + +onset qualifier sex qualifier - -biological sex + +biological sex behavior to behavioral feature association->sex qualifier - - -sex qualifier + + +sex qualifier has count - -integer + +integer behavior to behavioral feature association->has count - - -has count + + +has count has total - -integer + +integer behavior to behavioral feature association->has total - - -has total + + +has total has quotient - -double + +double behavior to behavioral feature association->has quotient - - -has quotient + + +has quotient has percentage - -double + +double behavior to behavioral feature association->has percentage - - -has percentage + + +has percentage association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + behavior to behavioral feature association_subject - -behavior + +behavior object->relation - - + + behavior to behavioral feature association_object - -behavioral feature + +behavioral feature diff --git a/graphviz/case_to_phenotypic_feature_association.gv b/graphviz/case_to_phenotypic_feature_association.gv index 6c1f59bc54..21c0cf789a 100644 --- a/graphviz/case_to_phenotypic_feature_association.gv +++ b/graphviz/case_to_phenotypic_feature_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,6661.4,283"]; + graph [bb="0,0,6396.4,283"]; node [label="\N"]; "case to phenotypic feature association" [height=0.5, label="case to phenotypic feature association", - pos="3673.4,265", + pos="3408.4,265", width=5.2356]; association [height=0.5, pos="62.394,178", width=1.7332]; "case to phenotypic feature association" -> association [label=is_a, lp="699.39,221.5", - pos="e,106.72,190.73 3485.9,262.99 2920,259.74 1234.4,248.64 685.39,229 440.22,220.23 377.12,231.65 134.39,196 128.61,195.15 122.62,194.07 \ -116.66,192.86"]; + pos="e,106.72,190.73 3219.7,264.62 2777.1,265.42 1637.1,263.6 685.39,229 440.23,220.09 377.12,231.65 134.39,196 128.61,195.15 122.62,\ +194.07 116.66,192.86"]; "entity to phenotypic feature association mixin" [height=0.5, pos="367.39,178", width=6.2286]; "case to phenotypic feature association" -> "entity to phenotypic feature association mixin" [label=uses, lp="927.89,221.5", - pos="e,490.35,193.09 3485.2,263.55 2947.9,261.97 1413.8,255.23 911.39,229 770.87,221.66 610.5,206.04 500.5,194.19"]; + pos="e,490.62,193.08 3220.5,263.26 2719.6,260.98 1360.2,252.73 911.39,229 770.99,221.57 610.77,205.98 500.77,194.17"]; "case to entity association mixin" [height=0.5, pos="767.39,178", width=4.3691]; "case to phenotypic feature association" -> "case to entity association mixin" [label=uses, lp="1077.9,221.5", - pos="e,837.68,194.11 3485.7,263.17 2927.3,260.46 1300.2,250.77 1061.4,229 988.53,222.36 906.51,207.81 847.66,196.11"]; + pos="e,837.98,194.14 3221.1,262.86 2702.7,259.48 1273.4,248.49 1061.4,229 988.65,222.31 906.79,207.81 847.96,196.14"]; id [color=blue, height=0.5, label=string, @@ -32,7 +32,7 @@ digraph { "case to phenotypic feature association" -> id [color=blue, label=id, lp="1196.4,221.5", - pos="e,1010.4,189.98 3485.3,263.4 2945.4,261.4 1414.8,253.6 1189.4,229 1117.2,221.12 1099.3,215.5 1029.4,196 1026.3,195.13 1023.1,194.17 \ + pos="e,1010.4,189.98 3220.6,263.06 2721.7,260.27 1388,250.85 1189.4,229 1117.2,221.06 1099.3,215.5 1029.4,196 1026.3,195.13 1023.1,194.17 \ 1019.9,193.15", style=solid]; iri [color=blue, @@ -43,7 +43,7 @@ digraph { "case to phenotypic feature association" -> iri [color=blue, label=iri, lp="1303.4,221.5", - pos="e,1115.3,190.16 3485.5,263.27 2961.7,260.97 1510,252.5 1295.4,229 1223.2,221.1 1205.6,214.45 1135.4,196 1132,195.11 1128.5,194.14 \ + pos="e,1115.3,190.16 3220.9,262.9 2739.3,259.78 1483.4,249.76 1295.4,229 1223.2,221.03 1205.6,214.45 1135.4,196 1132,195.11 1128.5,194.14 \ 1125.1,193.12", style=solid]; name [color=blue, @@ -54,7 +54,7 @@ digraph { "case to phenotypic feature association" -> name [color=blue, label=name, lp="1407.4,221.5", - pos="e,1238.2,191.81 3484.9,263.79 2974.8,262.83 1591.9,257.61 1387.4,229 1338.9,222.22 1285,206.84 1247.8,194.91", + pos="e,1238.2,191.79 3220.5,263.37 2753.6,261.44 1565.4,254.08 1387.4,229 1338.9,222.17 1285,206.8 1247.8,194.89", style=solid]; description [color=blue, height=0.5, @@ -64,7 +64,7 @@ digraph { "case to phenotypic feature association" -> description [color=blue, label=description, lp="1523.9,221.5", - pos="e,1382.8,194.43 3486.2,262.76 2973.9,259.14 1580.8,247.63 1483.4,229 1451.7,222.94 1417.7,209.88 1392.1,198.63", + pos="e,1382.8,194.41 3219.8,264.24 2768.3,264.3 1650.4,261.14 1483.4,229 1451.7,222.9 1417.7,209.85 1392.1,198.61", style=solid]; "has attribute" [color=blue, height=0.5, @@ -74,7 +74,7 @@ digraph { "case to phenotypic feature association" -> "has attribute" [color=blue, label="has attribute", lp="1662.4,221.5", - pos="e,1522.9,193.58 3486,262.74 2995.6,259.17 1705.9,248.04 1615.4,229 1586.1,222.84 1555,209.49 1531.9,198.13", + pos="e,1522.9,193.56 3219.7,264.33 2790.9,264.51 1768.8,261.48 1615.4,229 1586.1,222.8 1555,209.45 1531.9,198.11", style=solid]; subject [color=blue, height=0.5, @@ -84,7 +84,7 @@ digraph { "case to phenotypic feature association" -> subject [color=blue, label=subject, lp="1789.4,221.5", - pos="e,1666.3,194.29 3485,264.35 3036.2,264.64 1928.7,261.94 1763.4,229 1732.8,222.91 1700.1,209.88 1675.6,198.64", + pos="e,1666.3,194.26 3220,263.73 2818.3,262.6 1902.6,256.96 1763.4,229 1732.8,222.86 1700.2,209.83 1675.6,198.61", style=solid]; predicate [color=blue, height=0.5, @@ -94,7 +94,7 @@ digraph { "case to phenotypic feature association" -> predicate [color=blue, label=predicate, lp="1868.4,221.5", - pos="e,1808.4,196.15 3486.1,262.75 3025.1,259.38 1870.1,248.96 1834.4,229 1825,223.71 1817.9,214.35 1812.8,205.15", + pos="e,1808.4,196.14 3219.8,264.52 2814.8,264.99 1893.8,262.35 1834.4,229 1825,223.7 1817.9,214.34 1812.8,205.13", style=solid]; object [color=blue, height=0.5, @@ -104,7 +104,7 @@ digraph { "case to phenotypic feature association" -> object [color=blue, label=object, lp="1947.4,178", - pos="e,1776,105.47 3486.2,262.74 3136.6,259.88 2396.9,251.34 2141.4,229 2044.6,220.54 2012,239.85 1925.4,196 1905.2,185.78 1908.1,172.77 \ + pos="e,1776,105.47 3220.6,263.26 2908.5,261.33 2296,254.32 2081.4,229 2011,220.7 1987.7,229.78 1925.4,196 1905.5,185.21 1908.1,172.77 \ 1889.4,160 1857.3,138.07 1817,120.64 1785.5,108.92", style=solid]; negated [color=blue, @@ -114,8 +114,8 @@ digraph { width=1.2999]; "case to phenotypic feature association" -> negated [color=blue, label=negated, - lp="2250.4,221.5", - pos="e,2059.6,190.46 3485,264.27 3149.2,263.96 2460,259.46 2221.4,229 2168.1,222.19 2108.5,205.66 2069.1,193.46", + lp="2154.4,221.5", + pos="e,2048.1,193.98 3220.6,263.37 2889.8,261.59 2228.4,254.81 2125.4,229 2101.1,222.92 2075.9,210.29 2056.9,199.24", style=solid]; qualifiers [color=blue, height=0.5, @@ -124,8 +124,8 @@ digraph { width=2.1304]; "case to phenotypic feature association" -> qualifiers [color=blue, label=qualifiers, - lp="2389.9,221.5", - pos="e,2208.5,193.07 3485,264.34 3174.5,263.99 2568.3,259.29 2356.4,229 2308.8,222.2 2256.1,207.74 2218.2,196.11", + lp="2236.9,221.5", + pos="e,2174,196.18 3221.1,262.83 2893.7,260.19 2247.6,252.08 2203.4,229 2193.2,223.7 2185.1,214.2 2179.2,204.9", style=solid]; publications [color=blue, height=0.5, @@ -134,8 +134,8 @@ digraph { width=1.7332]; "case to phenotypic feature association" -> publications [color=blue, label=publications, - lp="2537.4,221.5", - pos="e,2359.9,192.71 3484.9,264.28 3201.3,263.69 2678.5,258.46 2493.4,229 2450.5,222.18 2403.3,207.69 2369.5,196.06", + lp="2322.4,221.5", + pos="e,2295.7,194.14 3219.6,264.91 2906.4,265.48 2310.5,262.16 2278.4,229 2269.4,219.73 2276.6,209.15 2287.6,200.12", style=solid]; "has evidence" [color=blue, height=0.5, @@ -144,302 +144,304 @@ digraph { width=2.0943]; "case to phenotypic feature association" -> "has evidence" [color=blue, label="has evidence", - lp="2691.9,221.5", - pos="e,2517.6,193.61 3485.5,263.4 3234,261.6 2801.5,254.72 2645.4,229 2604.8,222.3 2560.1,208.48 2527.4,197.06", + lp="2421.9,221.5", + pos="e,2419.1,188.92 3219.9,264.3 2929.8,263.82 2404.2,258.8 2375.4,229 2358.5,211.53 2381,199.39 2409.3,191.45", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2681.4,178", - width=3.015]; + label=string, + pos="2611.4,178", + width=1.0652]; "case to phenotypic feature association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2846.9,221.5", - pos="e,2707.2,195.59 3489.7,260.88 3248.7,256.16 2848.7,245.9 2782.4,229 2759.1,223.06 2734.9,211.3 2716,200.68", + lp="2550.9,221.5", + pos="e,2582.4,189.86 3220.6,263.45 2958.3,261.74 2511.4,255 2486.4,229 2444.1,185.03 2449.4,229.4 2563.4,196 2566.5,195.09 2569.7,194.1 \ +2572.9,193.06", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2916.4,178", - width=3.015]; + label=string, + pos="2706.4,178", + width=1.0652]; "case to phenotypic feature association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="3018.4,221.5", - pos="e,2913.8,196.37 3488.9,261.23 3273.6,257.14 2944,247.82 2923.4,229 2917.2,223.35 2914.7,214.95 2913.9,206.63", + lp="2717.4,221.5", + pos="e,2676.8,189.5 3222,262.1 2996.1,258.86 2642.9,250.39 2622.4,229 2617.8,224.18 2618.7,219.55 2622.4,214 2625.2,209.74 2646.7,200.84 \ +2667.2,193.08", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="3151.4,178", - width=3.015]; + label=string, + pos="2801.4,178", + width=1.0652]; "case to phenotypic feature association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="3226.9,221.5", - pos="e,3130.1,195.91 3484.7,264.54 3334.4,262.95 3145.3,255.56 3120.4,229 3113.3,221.47 3116.7,212.1 3123.3,203.51", + lp="2935.9,221.5", + pos="e,2806.2,195.93 3223.1,261.61 3066.4,258.14 2862.3,249.67 2829.4,229 2820.7,223.56 2814.5,214.43 2810.2,205.44", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="3333.4,178", + pos="3021.4,178", width=1.5346]; "case to phenotypic feature association" -> timepoint [color=blue, label=timepoint, - lp="3381.4,221.5", - pos="e,3333.2,196.41 3515.7,255.11 3438.8,249.34 3360,240.7 3346.4,229 3339.8,223.34 3336.4,214.82 3334.6,206.41", + lp="3099.4,221.5", + pos="e,3031.1,195.93 3234,258.09 3164.7,253.31 3094.4,244.66 3064.4,229 3053.5,223.32 3044.2,213.63 3037.1,204.29", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="3445.4,178", + pos="3133.4,178", width=1.0652]; "case to phenotypic feature association" -> "original subject" [color=blue, label="original subject", - lp="3479.4,221.5", - pos="e,3430.2,194.78 3504.8,256.92 3467.7,251.73 3435.7,243.14 3423.4,229 3417,221.59 3419.3,212 3424.4,203.21", + lp="3204.4,221.5", + pos="e,3134,196.38 3244.6,256.06 3202.4,250.95 3164.3,242.6 3148.4,229 3141.7,223.31 3138,214.79 3135.8,206.38", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3559.4,178", + pos="3258.4,178", width=1.5887]; "case to phenotypic feature association" -> "original predicate" [color=blue, label="original predicate", - lp="3605.9,221.5", - pos="e,3546.4,195.6 3585.7,249 3565.8,243.77 3548.6,237.12 3542.4,229 3537,221.92 3538.1,212.99 3541.6,204.65", + lp="3335.9,221.5", + pos="e,3259,196.01 3304.9,249.93 3292.9,244.84 3281.6,238.04 3272.4,229 3266.2,222.9 3262.6,214.28 3260.7,205.91", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3673.4,178", + pos="3399.4,178", width=1.0652]; "case to phenotypic feature association" -> "original object" [color=blue, label="original object", - lp="3724.9,221.5", - pos="e,3673.4,196.18 3673.4,246.8 3673.4,235.16 3673.4,219.55 3673.4,206.24", + lp="3456.9,221.5", + pos="e,3401.2,196.18 3406.6,246.8 3405.3,235.16 3403.7,219.55 3402.3,206.24", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3806.4,178", + pos="3532.4,178", width=2.1304]; "case to phenotypic feature association" -> "subject category" [color=blue, label="subject category", - lp="3849.9,221.5", - pos="e,3800.2,195.97 3743.3,248.25 3755.5,243.41 3767.4,237.13 3777.4,229 3785.2,222.66 3791.3,213.66 3795.9,205.03", + lp="3582.9,221.5", + pos="e,3529.3,196.38 3481.7,248.38 3492.9,243.55 3503.7,237.25 3512.4,229 3518.9,222.88 3523.3,214.39 3526.3,206.14", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3977.4,178", + pos="3703.4,178", width=2.1304]; "case to phenotypic feature association" -> "object category" [color=blue, label="object category", - lp="3993.9,221.5", - pos="e,3961.1,195.71 3824.2,254.16 3854.6,248.85 3885.6,240.88 3913.4,229 3928,222.76 3942.1,212.32 3953.4,202.6", + lp="3724.9,221.5", + pos="e,3689.2,195.73 3562.3,254.56 3591.1,249.15 3620.3,241.05 3646.4,229 3659.7,222.84 3672.3,212.55 3682.2,202.9", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="4110.4,178", + pos="3836.4,178", width=1.0652]; "case to phenotypic feature association" -> "subject closure" [color=blue, label="subject closure", - lp="4127.9,221.5", - pos="e,4094.9,194.58 3806.5,252.22 3914.9,242.55 4050.5,230.25 4053.4,229 4061.1,225.69 4075.3,213.26 4087.6,201.63", + lp="3860.9,221.5", + pos="e,3824.3,195.51 3543.7,252.44 3649.2,243.27 3778.8,231.57 3784.4,229 3797.2,223.16 3808.7,212.85 3817.7,203.11", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="4206.4,178", + pos="3935.4,178", width=1.0652]; "case to phenotypic feature association" -> "object closure" [color=blue, label="object closure", - lp="4247.4,221.5", - pos="e,4203.9,196.3 3805.4,252.14 3827.4,250.31 3850.1,248.53 3871.4,247 3906.3,244.51 4156.9,249.17 4185.4,229 4193.1,223.55 4198,214.7 \ -4201.1,205.95", + lp="3980.4,221.5", + pos="e,3934.7,196.17 3540.4,252.14 3562.4,250.31 3585.1,248.53 3606.4,247 3641.1,244.51 3891.9,250.34 3919.4,229 3926.5,223.46 3930.6,\ +214.71 3932.8,206.07", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="4339.4,178", + pos="4068.4,178", width=2.1304]; "case to phenotypic feature association" -> "subject category closure" [color=blue, label="subject category closure", - lp="4405.9,221.5", - pos="e,4331.4,196.14 3803.8,251.99 3826.3,250.14 3849.5,248.4 3871.4,247 3919.1,243.95 4259,251.14 4301.4,229 4311.6,223.64 4319.9,214.14 \ -4326.1,204.85", + lp="4137.9,221.5", + pos="e,4061.7,196.09 3538.8,251.99 3561.3,250.15 3584.5,248.4 3606.4,247 3653.9,243.96 3992.8,252.15 4034.4,229 4044,223.64 4051.5,214.27 \ +4056.9,205.07", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="4528.4,178", + pos="4263.4,178", width=2.1304]; "case to phenotypic feature association" -> "object category closure" [color=blue, label="object category closure", - lp="4595.9,221.5", - pos="e,4522.7,196.1 3802.5,251.85 3825.4,250 3849.1,248.28 3871.4,247 3906.1,245.01 4467.2,246.36 4497.4,229 4506.6,223.71 4513.4,214.47 \ -4518.3,205.37", + lp="4328.9,221.5", + pos="e,4256.7,196.14 3537.5,251.85 3560.4,250 3584.1,248.28 3606.4,247 3641,245.02 4199,245.64 4229.4,229 4239.1,223.7 4246.5,214.34 \ +4252,205.14", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4718.4,178", + pos="4453.4,178", width=1.0652]; "case to phenotypic feature association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4768.4,221.5", - pos="e,4711.4,196.19 3801.7,251.79 3824.8,249.93 3848.8,248.22 3871.4,247 3916.5,244.57 4643.6,250.28 4683.4,229 4693.2,223.75 4700.9,\ -214.4 4706.5,205.19", + lp="4501.4,221.5", + pos="e,4446,195.72 3536.7,251.79 3559.8,249.93 3583.8,248.22 3606.4,247 3651.3,244.57 4376.4,249.7 4416.4,229 4426.7,223.65 4434.9,213.97 \ +4440.9,204.54", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4877.4,178", + pos="4612.4,178", width=1.0652]; "case to phenotypic feature association" -> "object namespace" [color=blue, label="object namespace", - lp="4921.4,221.5", - pos="e,4870,195.73 3801.4,251.75 3824.7,249.88 3848.7,248.18 3871.4,247 3925.2,244.2 4792.5,253.68 4840.4,229 4850.7,223.67 4858.9,213.99 \ -4864.9,204.55", + lp="4655.4,221.5", + pos="e,4604.4,195.76 3536.4,251.75 3559.7,249.88 3583.7,248.18 3606.4,247 3660.1,244.2 4525.3,253.02 4573.4,229 4584.1,223.65 4592.7,\ +213.83 4599.2,204.29", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="5028.4,178", + pos="4763.4,178", width=1.0652]; "case to phenotypic feature association" -> "subject label closure" [color=blue, label="subject label closure", - lp="5081.4,221.5", - pos="e,5020.4,195.77 3801.1,251.72 3824.5,249.85 3848.7,248.16 3871.4,247 3902.4,245.42 4961.6,242.85 4989.4,229 5000.1,223.66 5008.8,\ -213.84 5015.2,204.31", + lp="4815.4,221.5", + pos="e,4755.1,195.78 3536.1,251.72 3559.5,249.85 3583.7,248.16 3606.4,247 3637.4,245.42 4695.5,242.67 4723.4,229 4734.2,223.68 4743.1,\ +213.86 4749.7,204.32", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="5166.4,178", + pos="4901.4,178", width=1.0652]; "case to phenotypic feature association" -> "object label closure" [color=blue, label="object label closure", - lp="5237.9,221.5", - pos="e,5169.1,195.98 3800.9,251.7 3824.3,249.83 3848.6,248.14 3871.4,247 3907.1,245.22 5132.6,252.67 5159.4,229 5165.8,223.31 5168.4,\ -214.64 5169.1,206.11", + lp="4971.9,221.5", + pos="e,4903.7,196.02 3535.9,251.7 3559.3,249.83 3583.6,248.14 3606.4,247 3642.1,245.22 4866.4,252.39 4893.4,229 4899.9,223.36 4902.6,\ +214.7 4903.5,206.16", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="5307.4,178", + pos="5042.4,178", width=2.347]; "case to phenotypic feature association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="5386.9,221.5", - pos="e,5314.7,196.1 3800.6,251.7 3824.1,249.81 3848.5,248.13 3871.4,247 3891.4,246.02 5297.3,243.23 5311.4,229 5317.3,223.01 5318.2,214.41 \ -5317,206.03", + lp="5121.9,221.5", + pos="e,5049.2,196.11 3535.6,251.7 3559.1,249.81 3583.5,248.13 3606.4,247 3626.4,246.02 5031.3,243.22 5045.4,229 5051.3,223.02 5052.3,\ +214.42 5051.3,206.04", style=solid]; type [height=0.5, - pos="5441.4,178", + pos="5176.4,178", width=0.86659]; "case to phenotypic feature association" -> type [color=blue, label=type, - lp="5481.4,221.5", - pos="e,5454.9,194.34 3800.6,251.67 3824.1,249.79 3848.5,248.11 3871.4,247 3893.4,245.93 5444.9,244.69 5460.4,229 5467.3,221.97 5465.2,\ -212.13 5460.4,203.04", + lp="5216.4,221.5", + pos="e,5189.9,194.34 3535.6,251.67 3559.1,249.79 3583.5,248.11 3606.4,247 3628.4,245.93 5179.9,244.69 5195.4,229 5202.3,221.97 5200.2,\ +212.13 5195.4,203.04", style=solid]; category [height=0.5, - pos="5542.4,178", + pos="5277.4,178", width=1.4263]; "case to phenotypic feature association" -> category [color=blue, label=category, - lp="5552.9,221.5", - pos="e,5533.8,195.81 3800.3,251.69 3823.9,249.8 3848.4,248.11 3871.4,247 3916.6,244.81 5460.6,248.59 5501.4,229 5512.4,223.72 5521.4,\ -213.91 5528.2,204.36", + lp="5287.9,221.5", + pos="e,5268.8,195.81 3535.3,251.69 3558.9,249.8 3583.4,248.11 3606.4,247 3651.6,244.81 5195.6,248.59 5236.4,229 5247.4,223.72 5256.4,\ +213.91 5263.2,204.36", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="5696.4,178", + pos="5431.4,178", width=2.3651]; "case to phenotypic feature association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="5700.4,221.5", - pos="e,5669.6,195.33 3800.3,251.68 3823.9,249.79 3848.4,248.11 3871.4,247 3966.7,242.42 5495.3,250.01 5588.4,229 5613.7,223.28 5640.2,\ -211.11 5660.6,200.22", + lp="5435.4,221.5", + pos="e,5404.6,195.33 3535.3,251.68 3558.9,249.79 3583.4,248.11 3606.4,247 3701.7,242.42 5230.3,250.01 5323.4,229 5348.7,223.28 5375.2,\ +211.11 5395.6,200.22", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="5875.4,178", + pos="5610.4,178", width=2.1123]; "case to phenotypic feature association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="5875.4,221.5", - pos="e,5850.3,195.09 3800.3,251.66 3823.9,249.77 3848.4,248.09 3871.4,247 3976.9,241.98 5669.6,253.15 5772.4,229 5796.8,223.27 5822.1,\ -211.06 5841.6,200.15", + lp="5610.4,221.5", + pos="e,5585.3,195.09 3535.3,251.66 3558.9,249.77 3583.4,248.09 3606.4,247 3711.9,241.98 5404.6,253.15 5507.4,229 5531.8,223.27 5557.1,\ +211.06 5576.6,200.15", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="6005.4,178", + pos="5740.4,178", width=1.011]; "case to phenotypic feature association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="6019.9,221.5", - pos="e,5990.6,195.01 3800,251.67 3823.7,249.77 3848.3,248.09 3871.4,247 3928.8,244.29 5886.1,247.74 5940.4,229 5956.4,223.49 5971.5,212.35 \ -5983.1,201.98", + lp="5754.9,221.5", + pos="e,5725.6,195.01 3535,251.67 3558.7,249.77 3583.3,248.09 3606.4,247 3663.8,244.29 5621.1,247.74 5675.4,229 5691.4,223.49 5706.5,212.35 \ +5718.1,201.98", style=solid]; "sex qualifier" [color=blue, height=0.5, label="biological sex", - pos="6133.4,178", + pos="5868.4,178", width=2.0401]; "case to phenotypic feature association" -> "sex qualifier" [color=blue, label="sex qualifier", - lp="6144.4,221.5", - pos="e,6119.6,195.96 3800,251.66 3823.7,249.76 3848.3,248.08 3871.4,247 3932.6,244.13 6018.1,250.56 6075.4,229 6089.5,223.7 6102.4,213.32 \ -6112.5,203.38", + lp="5879.4,221.5", + pos="e,5854.6,195.96 3535,251.66 3558.7,249.76 3583.3,248.08 3606.4,247 3667.6,244.13 5753.1,250.56 5810.4,229 5824.5,223.7 5837.4,213.32 \ +5847.5,203.38", style=solid]; "has count" [color=blue, height=0.5, label=integer, - pos="6269.4,178", + pos="6004.4,178", width=1.2277]; "case to phenotypic feature association" -> "has count" [color=blue, label="has count", - lp="6259.4,221.5", - pos="e,6251.9,194.56 3800,251.65 3823.7,249.76 3848.3,248.08 3871.4,247 3935.8,243.99 6130.6,247.55 6192.4,229 6211.1,223.38 6229.5,211.68 \ -6243.7,201.01", + lp="5994.4,221.5", + pos="e,5986.9,194.56 3535,251.65 3558.7,249.76 3583.3,248.08 3606.4,247 3670.8,243.99 5865.6,247.55 5927.4,229 5946.1,223.38 5964.5,211.68 \ +5978.7,201.01", style=solid]; "has total" [color=blue, height=0.5, label=integer, - pos="6375.4,178", + pos="6110.4,178", width=1.2277]; "case to phenotypic feature association" -> "has total" [color=blue, label="has total", - lp="6361.9,221.5", - pos="e,6357.9,194.57 3800,251.64 3823.7,249.75 3848.3,248.08 3871.4,247 3938.7,243.86 6233.8,248.39 6298.4,229 6317.1,223.38 6335.5,211.68 \ -6349.7,201.01", + lp="6096.9,221.5", + pos="e,6092.9,194.57 3535,251.64 3558.7,249.75 3583.3,248.08 3606.4,247 3673.7,243.86 5968.8,248.39 6033.4,229 6052.1,223.38 6070.5,211.68 \ +6084.7,201.01", style=solid]; "has quotient" [color=blue, height=0.5, label=double, - pos="6479.4,178", + pos="6214.4,178", width=1.1735]; "case to phenotypic feature association" -> "has quotient" [color=blue, label="has quotient", - lp="6476.4,221.5", - pos="e,6460.9,194.34 3800,251.64 3823.7,249.75 3848.3,248.07 3871.4,247 3941.5,243.75 6329.9,248.21 6397.4,229 6417.4,223.31 6437.3,211.32 \ -6452.5,200.51", + lp="6211.4,221.5", + pos="e,6195.9,194.34 3535,251.64 3558.7,249.75 3583.3,248.07 3606.4,247 3676.5,243.75 6064.9,248.21 6132.4,229 6152.4,223.31 6172.3,211.32 \ +6187.5,200.51", style=solid]; "has percentage" [color=blue, height=0.5, label=double, - pos="6586.4,178", + pos="6321.4,178", width=1.1735]; "case to phenotypic feature association" -> "has percentage" [color=blue, label="has percentage", - lp="6606.4,221.5", - pos="e,6572.2,195.49 3800,251.63 3823.7,249.74 3848.3,248.07 3871.4,247 3945,243.59 6456.1,254.05 6525.4,229 6540.3,223.61 6554.2,212.85 \ -6565,202.7", + lp="6341.4,221.5", + pos="e,6307.2,195.49 3535,251.63 3558.7,249.74 3583.3,248.07 3606.4,247 3680,243.59 6191.1,254.05 6260.4,229 6275.3,223.61 6289.2,212.85 \ +6300,202.7", style=solid]; subject -> object [label=relation, lp="1719.4,134.5", @@ -454,11 +456,11 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="3918.4,265", + pos="3653.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="4049.4,265", + pos="3784.4,265", width=2.0762]; } diff --git a/graphviz/case_to_phenotypic_feature_association.svg b/graphviz/case_to_phenotypic_feature_association.svg index 3c1c5b0a60..39bf89f470 100644 --- a/graphviz/case_to_phenotypic_feature_association.svg +++ b/graphviz/case_to_phenotypic_feature_association.svg @@ -4,16 +4,16 @@ - + %3 - + case to phenotypic feature association - -case to phenotypic feature association + +case to phenotypic feature association @@ -24,7 +24,7 @@ case to phenotypic feature association->association - + is_a @@ -37,8 +37,8 @@ case to phenotypic feature association->entity to phenotypic feature association mixin - - + + uses @@ -50,8 +50,8 @@ case to phenotypic feature association->case to entity association mixin - - + + uses @@ -63,7 +63,7 @@ case to phenotypic feature association->id - + id @@ -76,7 +76,7 @@ case to phenotypic feature association->iri - + iri @@ -89,8 +89,8 @@ case to phenotypic feature association->name - - + + name @@ -102,8 +102,8 @@ case to phenotypic feature association->description - - + + description @@ -115,8 +115,8 @@ case to phenotypic feature association->has attribute - - + + has attribute @@ -128,8 +128,8 @@ case to phenotypic feature association->subject - - + + subject @@ -141,8 +141,8 @@ case to phenotypic feature association->predicate - - + + predicate @@ -154,7 +154,7 @@ case to phenotypic feature association->object - + object @@ -167,9 +167,9 @@ case to phenotypic feature association->negated - - -negated + + +negated @@ -180,9 +180,9 @@ case to phenotypic feature association->qualifiers - - -qualifiers + + +qualifiers @@ -193,9 +193,9 @@ case to phenotypic feature association->publications - - -publications + + +publications @@ -206,373 +206,373 @@ case to phenotypic feature association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string case to phenotypic feature association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string case to phenotypic feature association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string case to phenotypic feature association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type case to phenotypic feature association->timepoint - - -timepoint + + +timepoint original subject - -string + +string case to phenotypic feature association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie case to phenotypic feature association->original predicate - - -original predicate + + +original predicate original object - -string + +string case to phenotypic feature association->original object - - -original object + + +original object subject category - -ontology class + +ontology class case to phenotypic feature association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class case to phenotypic feature association->object category - - -object category + + +object category subject closure - -string + +string case to phenotypic feature association->subject closure - - -subject closure + + +subject closure object closure - -string + +string case to phenotypic feature association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class case to phenotypic feature association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class case to phenotypic feature association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string case to phenotypic feature association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string case to phenotypic feature association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string case to phenotypic feature association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string case to phenotypic feature association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source case to phenotypic feature association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type case to phenotypic feature association->type - - -type + + +type category - -category + +category case to phenotypic feature association->category - - -category + + +category frequency qualifier - -frequency value + +frequency value case to phenotypic feature association->frequency qualifier - - -frequency qualifier + + +frequency qualifier severity qualifier - -severity value + +severity value case to phenotypic feature association->severity qualifier - - -severity qualifier + + +severity qualifier onset qualifier - -onset + +onset case to phenotypic feature association->onset qualifier - - -onset qualifier + + +onset qualifier sex qualifier - -biological sex + +biological sex case to phenotypic feature association->sex qualifier - - -sex qualifier + + +sex qualifier has count - -integer + +integer case to phenotypic feature association->has count - - -has count + + +has count has total - -integer + +integer case to phenotypic feature association->has total - - -has total + + +has total has quotient - -double + +double case to phenotypic feature association->has quotient - - -has quotient + + +has quotient has percentage - -double + +double case to phenotypic feature association->has percentage - - -has percentage + + +has percentage @@ -602,14 +602,14 @@ association_type - -string + +string association_category - -category type + +category type diff --git a/graphviz/causal_gene_to_disease_association.gv b/graphviz/causal_gene_to_disease_association.gv new file mode 100644 index 0000000000..607221780f --- /dev/null +++ b/graphviz/causal_gene_to_disease_association.gv @@ -0,0 +1,501 @@ +digraph { + graph [bb="0,0,6813.8,283"]; + node [label="\N"]; + "causal gene to disease association" [height=0.5, + label="causal gene to disease association", + pos="3631.8,265", + width=4.7121]; + "gene to disease association" [height=0.5, + pos="137.79,178", + width=3.8274]; + "causal gene to disease association" -> "gene to disease association" [label=is_a, + lp="762.79,221.5", + pos="e,234.98,190.85 3462.5,263.26 2928.4,260.7 1282.2,251.19 748.79,229 542.22,220.41 490.64,215.21 284.79,196 271.95,194.8 258.49,193.42 \ +245.15,191.97"]; + "entity to disease association mixin" [height=0.5, + pos="464.79,178", + width=4.7482]; + "causal gene to disease association" -> "entity to disease association mixin" [label=uses, + lp="973.29,221.5", + pos="e,569.19,192.31 3462.3,263.74 2954,262.65 1447.3,257.08 956.79,229 827.1,221.58 678.84,205.46 579.27,193.52"]; + "gene to entity association mixin" [height=0.5, + pos="812.79,178", + width=4.4232]; + "causal gene to disease association" -> "gene to entity association mixin" [label=uses, + lp="1124.3,221.5", + pos="e,883.62,194.16 3462.7,263.17 2935,260.36 1340.3,250.19 1107.8,229 1034.8,222.35 952.66,207.84 893.63,196.16"]; + id [color=blue, + height=0.5, + label=string, + pos="1028.8,178", + width=1.0652]; + "causal gene to disease association" -> id [color=blue, + label=id, + lp="1241.8,221.5", + pos="e,1057.8,189.97 3462.7,263.4 2953.1,261.34 1454,253.26 1234.8,229 1163.5,221.11 1145.9,215.35 1076.8,196 1073.7,195.13 1070.5,194.16 \ +1067.3,193.14", + style=solid]; + iri [color=blue, + height=0.5, + label="iri type", + pos="1129.8,178", + width=1.2277]; + "causal gene to disease association" -> iri [color=blue, + label=iri, + lp="1346.8,221.5", + pos="e,1162.7,190.13 3462.6,263.3 2968.2,261.01 1547.4,252.43 1338.8,229 1268.4,221.09 1251.3,214.18 1182.8,196 1179.4,195.11 1175.9,\ +194.12 1172.5,193.1", + style=solid]; + name [color=blue, + height=0.5, + label="label type", + pos="1248.8,178", + width=1.5707]; + "causal gene to disease association" -> name [color=blue, + label=name, + lp="1448.8,221.5", + pos="e,1284.7,191.92 3462.4,263.79 2981,262.86 1627.4,257.69 1428.8,229 1382.1,222.26 1330.4,207.06 1294.5,195.18", + style=solid]; + description [color=blue, + height=0.5, + label="narrative text", + pos="1398.8,178", + width=2.0943]; + "causal gene to disease association" -> description [color=blue, + label=description, + lp="1561.3,221.5", + pos="e,1428.4,194.79 3463.1,262.91 2979.2,259.55 1615.2,248.41 1520.8,229 1491.8,223.04 1461,210.36 1437.6,199.27", + style=solid]; + "has attribute" [color=blue, + height=0.5, + label=attribute, + pos="1543.8,178", + width=1.4443]; + "causal gene to disease association" -> "has attribute" [color=blue, + label="has attribute", + lp="1693.8,221.5", + pos="e,1567.6,194.29 3462.8,263 2999,260 1734.3,249.92 1646.8,229 1621.9,223.05 1596,210.46 1576.4,199.4", + style=solid]; + negated [color=blue, + height=0.5, + label=boolean, + pos="1660.8,178", + width=1.2999]; + "causal gene to disease association" -> negated [color=blue, + label=negated, + lp="1826.8,221.5", + pos="e,1689.1,192.49 3462.3,263.95 3039.1,263.38 1958.3,258.96 1797.8,229 1763.1,222.53 1725.6,208.28 1698.6,196.64", + style=solid]; + qualifiers [color=blue, + height=0.5, + label="ontology class", + pos="1801.8,178", + width=2.1304]; + "causal gene to disease association" -> qualifiers [color=blue, + label=qualifiers, + lp="1931.3,221.5", + pos="e,1825.4,195.24 3463.2,262.67 3042.1,259.08 1972.6,248.13 1897.8,229 1875.3,223.26 1852.2,211.42 1834.3,200.71", + style=solid]; + publications [color=blue, + height=0.5, + label=publication, + pos="1958.8,178", + width=1.7332]; + "causal gene to disease association" -> publications [color=blue, + label=publications, + lp="2024.8,221.5", + pos="e,1961.6,196.44 3463.1,262.8 3048.5,259.54 2011.3,249.37 1980.8,229 1972.9,223.72 1967.8,214.91 1964.5,206.14", + style=solid]; + "has evidence" [color=blue, + height=0.5, + label="evidence type", + pos="2114.8,178", + width=2.0943]; + "causal gene to disease association" -> "has evidence" [color=blue, + label="has evidence", + lp="2123.3,221.5", + pos="e,2090.2,195.13 3462.9,263.27 3065.1,261.16 2100.7,253.5 2076.8,229 2068.7,220.76 2073.8,210.79 2082.5,201.94", + style=solid]; + "knowledge source" [color=blue, + height=0.5, + label=string, + pos="2246.8,178", + width=1.0652]; + "causal gene to disease association" -> "knowledge source" [color=blue, + label="knowledge source", + lp="2241.3,221.5", + pos="e,2217.9,189.84 3462.9,263 3084.4,260.35 2199,251.73 2176.8,229 2172.1,224.23 2173.3,219.67 2176.8,214 2180.7,207.6 2194.4,200.19 \ +2208.6,193.84", + style=solid]; + "primary knowledge source" [color=blue, + height=0.5, + label=string, + pos="2341.8,178", + width=1.0652]; + "causal gene to disease association" -> "primary knowledge source" [color=blue, + label="primary knowledge source", + lp="2408.8,221.5", + pos="e,2323.8,194.35 3463.5,262.56 3112.7,259.15 2333.6,249.31 2313.8,229 2306.3,221.28 2310.1,211.15 2317.1,202.02", + style=solid]; + "aggregator knowledge source" [color=blue, + height=0.5, + label=string, + pos="2483.8,178", + width=1.0652]; + "causal gene to disease association" -> "aggregator knowledge source" [color=blue, + label="aggregator knowledge source", + lp="2631.3,221.5", + pos="e,2492.4,195.72 3464,262.32 3164.7,258.83 2566.1,249.34 2524.8,229 2513.8,223.61 2504.8,213.78 2498,204.25", + style=solid]; + timepoint [color=blue, + height=0.5, + label="time type", + pos="2710.8,178", + width=1.5346]; + "causal gene to disease association" -> timepoint [color=blue, + label=timepoint, + lp="2797.8,221.5", + pos="e,2722.8,195.77 3462.6,263.61 3227.8,262.1 2825.2,255.59 2762.8,229 2749.9,223.5 2738.3,213.23 2729.4,203.43", + style=solid]; + "original subject" [color=blue, + height=0.5, + label=string, + pos="2822.8,178", + width=1.0652]; + "causal gene to disease association" -> "original subject" [color=blue, + label="original subject", + lp="2905.8,221.5", + pos="e,2827.2,195.97 3466.8,260.74 3245,255.76 2875.5,245.1 2849.8,229 2841.2,223.61 2835.1,214.49 2831,205.49", + style=solid]; + "original predicate" [color=blue, + height=0.5, + label=uriorcurie, + pos="2947.8,178", + width=1.5887]; + "causal gene to disease association" -> "original predicate" [color=blue, + label="original predicate", + lp="3044.3,221.5", + pos="e,2954.2,196.03 3463.3,262.74 3284.3,260.18 3021.6,252.42 2980.8,229 2971.3,223.57 2964.1,214.18 2958.8,205", + style=solid]; + "original object" [color=blue, + height=0.5, + label=string, + pos="3076.8,178", + width=1.0652]; + "causal gene to disease association" -> "original object" [color=blue, + label="original object", + lp="3186.3,221.5", + pos="e,3090.2,195.15 3462.7,263.39 3342.4,260.84 3192.4,252.73 3134.8,229 3120.7,223.19 3107.6,212.54 3097.4,202.56", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3209.8,178", + width=2.1304]; + "causal gene to disease association" -> "subject category" [color=blue, + label="subject category", + lp="3322.3,221.5", + pos="e,3222.6,195.99 3471.5,259.03 3389.7,254.47 3299.7,245.73 3262.8,229 3250.1,223.23 3238.4,213.13 3229.4,203.51", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3380.8,178", + width=2.1304]; + "causal gene to disease association" -> "object category" [color=blue, + label="object category", + lp="3451.3,221.5", + pos="e,3381.4,196.34 3488.4,255.36 3448,250.23 3410.9,242.04 3395.8,229 3389.2,223.27 3385.4,214.73 3383.3,206.33", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3513.8,178", + width=1.0652]; + "causal gene to disease association" -> "subject closure" [color=blue, + label="subject closure", + lp="3571.3,221.5", + pos="e,3510.3,196.01 3543,249.55 3532.9,244.52 3523.8,237.85 3516.8,229 3511.8,222.64 3510,214.28 3509.8,206.23", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3626.8,178", + width=1.0652]; + "causal gene to disease association" -> "object closure" [color=blue, + label="object closure", + lp="3679.8,221.5", + pos="e,3627.8,196.18 3630.8,246.8 3630.1,235.16 3629.2,219.55 3628.4,206.24", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3759.8,178", + width=2.1304]; + "causal gene to disease association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3832.3,221.5", + pos="e,3754.1,196.41 3699.4,248.43 3711.4,243.57 3723.1,237.23 3732.8,229 3740.1,222.78 3745.8,214.06 3750,205.64", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3952.8,178", + width=2.1304]; + "causal gene to disease association" -> "object category closure" [color=blue, + label="object category closure", + lp="4022.3,221.5", + pos="e,3947.4,196.22 3751.1,252.15 3828.5,244.06 3916.3,233.95 3923.8,229 3932.3,223.41 3938.6,214.41 3943.1,205.57", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4142.8,178", + width=1.0652]; + "causal gene to disease association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4193.8,221.5", + pos="e,4136.4,196.01 3750.7,252.13 3770.7,250.29 3791.3,248.51 3810.8,247 3844,244.43 4081,245.65 4109.8,229 4119.2,223.54 4126.5,214.15 \ +4131.8,204.96", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4301.8,178", + width=1.0652]; + "causal gene to disease association" -> "object namespace" [color=blue, + label="object namespace", + lp="4346.8,221.5", + pos="e,4294.4,196.13 3749.2,251.92 3769.7,250.07 3790.9,248.34 3810.8,247 3861.3,243.61 4221.2,252.95 4265.8,229 4275.8,223.63 4283.7,\ +214.12 4289.5,204.83", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4412.8,178", + width=1.0652]; + "causal gene to disease association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4495.8,221.5", + pos="e,4419.1,196.07 3748.2,251.84 3769,249.98 3790.5,248.26 3810.8,247 3844.3,244.91 4391.4,253.09 4414.8,229 4420.6,222.97 4421.8,214.37 \ +4420.9,205.99", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4507.8,178", + width=1.0652]; + "causal gene to disease association" -> "object label closure" [color=blue, + label="object label closure", + lp="4648.3,221.5", + pos="e,4538.2,188.94 3747.7,251.78 3768.7,249.91 3790.4,248.21 3810.8,247 3832,245.75 4559,244.17 4573.8,229 4587.3,215.2 4568.5,202.14 \ +4547.6,192.82", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4648.8,178", + width=2.347]; + "causal gene to disease association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4796.3,221.5", + pos="e,4694.8,193.16 3747.2,251.75 3768.4,249.88 3790.2,248.18 3810.8,247 3836.1,245.55 4704.1,247.07 4721.8,229 4733.6,216.9 4721.7,\ +205.95 4704.3,197.4", + style=solid]; + type [height=0.5, + pos="4782.8,178", + width=0.86659]; + "causal gene to disease association" -> type [color=blue, + label=type, + lp="4889.8,221.5", + pos="e,4807.5,189.33 3746.8,251.75 3768,249.86 3790.1,248.16 3810.8,247 3840.2,245.36 4849.2,249.98 4869.8,229 4874.5,224.25 4873.5,219.51 \ +4869.8,214 4857.4,195.87 4844.2,204.2 4823.8,196 4821.6,195.1 4819.3,194.17 4816.9,193.22", + style=solid]; + category [height=0.5, + pos="4883.8,178", + width=1.4263]; + "causal gene to disease association" -> category [color=blue, + label=category, + lp="4946.3,221.5", + pos="e,4901.3,194.94 3746.8,251.74 3768,249.85 3790.1,248.15 3810.8,247 3841.3,245.31 4888.4,250.77 4909.8,229 4917,221.63 4913.9,211.83 \ +4907.7,202.85", + style=solid]; + "subject aspect qualifier" [height=0.5, + pos="5071.8,178", + width=3.3039]; + "causal gene to disease association" -> "subject aspect qualifier" [color=blue, + label="subject aspect qualifier", + lp="5102.3,221.5", + pos="e,5049.1,195.77 3746.8,251.72 3768,249.84 3790.1,248.14 3810.8,247 3875.8,243.42 4918.9,245.8 4981.8,229 5002.6,223.43 5023.8,212 \ +5040.4,201.48", + style=solid]; + "object direction qualifier" [height=0.5, + pos="5333.8,178", + width=3.4664]; + "causal gene to disease association" -> "object direction qualifier" [color=blue, + label="object direction qualifier", + lp="5334.8,221.5", + pos="e,5297.4,195.31 3746.8,251.68 3768,249.8 3790.1,248.12 3810.8,247 3963.8,238.75 5038.9,255.47 5189.8,229 5223.6,223.07 5260.1,210.31 \ +5287.9,199.17", + style=solid]; + predicate [height=0.5, + pos="5530.8,178", + width=1.5165]; + "causal gene to disease association" -> predicate [color=blue, + label=predicate, + lp="5502.8,221.5", + pos="e,5506.7,194.34 3746.3,251.69 3767.7,249.8 3789.9,248.11 3810.8,247 3900.4,242.25 5339.4,249.44 5426.8,229 5451.9,223.13 5478,210.54 \ +5497.8,199.46", + style=solid]; + "frequency qualifier" [color=blue, + height=0.5, + label="frequency value", + pos="5688.8,178", + width=2.3651]; + "causal gene to disease association" -> "frequency qualifier" [color=blue, + label="frequency qualifier", + lp="5667.8,221.5", + pos="e,5653.4,194.48 3746.3,251.68 3767.7,249.79 3789.9,248.1 3810.8,247 4002.8,236.9 5351.3,261.16 5540.8,229 5576.5,222.95 5615.2,209.62 \ +5644,198.25", + style=solid]; + "severity qualifier" [color=blue, + height=0.5, + label="severity value", + pos="5867.8,178", + width=2.1123]; + "causal gene to disease association" -> "severity qualifier" [color=blue, + label="severity qualifier", + lp="5851.8,221.5", + pos="e,5837.2,194.61 3746.3,251.66 3767.7,249.77 3789.9,248.09 3810.8,247 3917.8,241.43 5634.6,249.33 5739.8,229 5770.4,223.09 5803.1,\ +210.19 5827.8,198.97", + style=solid]; + "onset qualifier" [color=blue, + height=0.5, + label=onset, + pos="5997.8,178", + width=1.011]; + "causal gene to disease association" -> "onset qualifier" [color=blue, + label="onset qualifier", + lp="6002.3,221.5", + pos="e,5980.2,193.84 3746.3,251.65 3767.7,249.76 3789.9,248.08 3810.8,247 3869.2,243.98 5860.6,245.21 5916.8,229 5936.8,223.22 5956.8,\ +210.98 5971.9,200.06", + style=solid]; + "sex qualifier" [color=blue, + height=0.5, + label="biological sex", + pos="6125.8,178", + width=2.0401]; + "causal gene to disease association" -> "sex qualifier" [color=blue, + label="sex qualifier", + lp="6130.8,221.5", + pos="e,6109.4,195.76 3746.3,251.64 3767.7,249.75 3789.9,248.07 3810.8,247 3873.1,243.8 5998.6,248.7 6057.8,229 6073.9,223.63 6089.4,212.83 \ +6101.6,202.64", + style=solid]; + "has count" [color=blue, + height=0.5, + label=integer, + pos="6261.8,178", + width=1.2277]; + "causal gene to disease association" -> "has count" [color=blue, + label="has count", + lp="6247.8,221.5", + pos="e,6243.1,194.34 3746.3,251.63 3767.7,249.74 3789.9,248.07 3810.8,247 3876.5,243.64 6115.5,246.86 6178.8,229 6199,223.31 6219.1,211.32 \ +6234.6,200.51", + style=solid]; + "has total" [color=blue, + height=0.5, + label=integer, + pos="6367.8,178", + width=1.2277]; + "causal gene to disease association" -> "has total" [color=blue, + label="has total", + lp="6352.3,221.5", + pos="e,6349.3,194.58 3745.8,251.67 3767.4,249.76 3789.7,248.07 3810.8,247 3879.5,243.5 6220.7,248.02 6286.8,229 6306.4,223.35 6326,211.48 \ +6341,200.73", + style=solid]; + "has quotient" [color=blue, + height=0.5, + label=double, + pos="6471.8,178", + width=1.1735]; + "causal gene to disease association" -> "has quotient" [color=blue, + label="has quotient", + lp="6467.8,221.5", + pos="e,6452.8,194.34 3745.8,251.66 3767.4,249.76 3789.7,248.07 3810.8,247 3882.3,243.36 6318.8,248.23 6387.8,229 6408.3,223.27 6429,211.11 \ +6444.6,200.22", + style=solid]; + "has percentage" [color=blue, + height=0.5, + label=double, + pos="6573.8,178", + width=1.1735]; + "causal gene to disease association" -> "has percentage" [color=blue, + label="has percentage", + lp="6596.8,221.5", + pos="e,6560.8,195.47 3745.8,251.66 3767.4,249.75 3789.7,248.07 3810.8,247 3885.9,243.19 6446.5,255.72 6516.8,229 6530.9,223.63 6543.8,\ +213.03 6553.8,202.96", + style=solid]; + subject [height=0.5, + pos="6695.8,178", + width=1.2277]; + "causal gene to disease association" -> subject [color=blue, + label=subject, + lp="6700.8,221.5", + pos="e,6687.5,195.82 3745.8,251.65 3767.4,249.75 3789.7,248.06 3810.8,247 3850.3,245.01 6620.2,246.23 6655.8,229 6666.7,223.73 6675.5,\ +213.92 6682.1,204.37", + style=solid]; + object [height=0.5, + pos="6738.8,91", + width=1.0832]; + "causal gene to disease association" -> object [color=blue, + label=object, + lp="6791.8,178", + pos="e,6752.2,108.09 3745.8,251.65 3767.4,249.75 3789.7,248.06 3810.8,247 3851.3,244.96 6696,249.81 6730.8,229 6771.5,204.69 6775.4,172.39 \ +6761.8,127 6760.8,123.55 6759.3,120.13 6757.5,116.85", + style=solid]; + association_type [color=blue, + height=0.5, + label=string, + pos="3857.8,265", + width=1.0652]; + association_category [color=blue, + height=0.5, + label="category type", + pos="3988.8,265", + width=2.0762]; + "gene to disease or phenotypic feature association_subject aspect qualifier" [color=blue, + height=0.5, + label=GeneOrGeneProductOrChemicalEntityAspectEnum, + pos="4330.8,265", + width=6.9147]; + "gene to disease or phenotypic feature association_object direction qualifier" [color=blue, + height=0.5, + label=DirectionQualifierEnum, + pos="4718.8,265", + width=3.358]; + "gene to disease or phenotypic feature association_predicate" [color=blue, + height=0.5, + label="predicate type", + pos="4935.8,265", + width=2.1665]; + subject -> object [label=relation, + lp="6733.8,134.5", + pos="e,6720.9,107.23 6696.9,159.55 6698.1,149.57 6700.6,137.07 6705.8,127 6708,122.68 6710.9,118.52 6714.1,114.66"]; + relation [height=0.5, + pos="6683.8,18", + width=1.2999]; + subject -> relation [pos="e,6685.1,36.188 6694.5,159.79 6692.4,132.48 6688.3,78.994 6685.9,46.38", + style=dotted]; + "causal gene to disease association_subject" [color=blue, + height=0.5, + label="gene or gene product", + pos="5141.8,265", + width=3.0692]; + object -> relation [pos="e,6696.6,35.54 6726.3,73.889 6719.4,64.939 6710.6,53.617 6702.8,43.584", + style=dotted]; + "causal gene to disease association_object" [color=blue, + height=0.5, + label=disease, + pos="5315.8,265", + width=1.2638]; +} diff --git a/graphviz/causal_gene_to_disease_association.svg b/graphviz/causal_gene_to_disease_association.svg new file mode 100644 index 0000000000..81fbdbe3e2 --- /dev/null +++ b/graphviz/causal_gene_to_disease_association.svg @@ -0,0 +1,671 @@ + + + + + + +%3 + + + +causal gene to disease association + +causal gene to disease association + + + +gene to disease association + +gene to disease association + + + +causal gene to disease association->gene to disease association + + +is_a + + + +entity to disease association mixin + +entity to disease association mixin + + + +causal gene to disease association->entity to disease association mixin + + +uses + + + +gene to entity association mixin + +gene to entity association mixin + + + +causal gene to disease association->gene to entity association mixin + + +uses + + + +id + +string + + + +causal gene to disease association->id + + +id + + + +iri + +iri type + + + +causal gene to disease association->iri + + +iri + + + +name + +label type + + + +causal gene to disease association->name + + +name + + + +description + +narrative text + + + +causal gene to disease association->description + + +description + + + +has attribute + +attribute + + + +causal gene to disease association->has attribute + + +has attribute + + + +negated + +boolean + + + +causal gene to disease association->negated + + +negated + + + +qualifiers + +ontology class + + + +causal gene to disease association->qualifiers + + +qualifiers + + + +publications + +publication + + + +causal gene to disease association->publications + + +publications + + + +has evidence + +evidence type + + + +causal gene to disease association->has evidence + + +has evidence + + + +knowledge source + +string + + + +causal gene to disease association->knowledge source + + +knowledge source + + + +primary knowledge source + +string + + + +causal gene to disease association->primary knowledge source + + +primary knowledge source + + + +aggregator knowledge source + +string + + + +causal gene to disease association->aggregator knowledge source + + +aggregator knowledge source + + + +timepoint + +time type + + + +causal gene to disease association->timepoint + + +timepoint + + + +original subject + +string + + + +causal gene to disease association->original subject + + +original subject + + + +original predicate + +uriorcurie + + + +causal gene to disease association->original predicate + + +original predicate + + + +original object + +string + + + +causal gene to disease association->original object + + +original object + + + +subject category + +ontology class + + + +causal gene to disease association->subject category + + +subject category + + + +object category + +ontology class + + + +causal gene to disease association->object category + + +object category + + + +subject closure + +string + + + +causal gene to disease association->subject closure + + +subject closure + + + +object closure + +string + + + +causal gene to disease association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +causal gene to disease association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +causal gene to disease association->object category closure + + +object category closure + + + +subject namespace + +string + + + +causal gene to disease association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +causal gene to disease association->object namespace + + +object namespace + + + +subject label closure + +string + + + +causal gene to disease association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +causal gene to disease association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +causal gene to disease association->retrieval source ids + + +retrieval source ids + + + +type + +type + + + +causal gene to disease association->type + + +type + + + +category + +category + + + +causal gene to disease association->category + + +category + + + +subject aspect qualifier + +subject aspect qualifier + + + +causal gene to disease association->subject aspect qualifier + + +subject aspect qualifier + + + +object direction qualifier + +object direction qualifier + + + +causal gene to disease association->object direction qualifier + + +object direction qualifier + + + +predicate + +predicate + + + +causal gene to disease association->predicate + + +predicate + + + +frequency qualifier + +frequency value + + + +causal gene to disease association->frequency qualifier + + +frequency qualifier + + + +severity qualifier + +severity value + + + +causal gene to disease association->severity qualifier + + +severity qualifier + + + +onset qualifier + +onset + + + +causal gene to disease association->onset qualifier + + +onset qualifier + + + +sex qualifier + +biological sex + + + +causal gene to disease association->sex qualifier + + +sex qualifier + + + +has count + +integer + + + +causal gene to disease association->has count + + +has count + + + +has total + +integer + + + +causal gene to disease association->has total + + +has total + + + +has quotient + +double + + + +causal gene to disease association->has quotient + + +has quotient + + + +has percentage + +double + + + +causal gene to disease association->has percentage + + +has percentage + + + +subject + +subject + + + +causal gene to disease association->subject + + +subject + + + +object + +object + + + +causal gene to disease association->object + + +object + + + +association_type + +string + + + +association_category + +category type + + + +gene to disease or phenotypic feature association_subject aspect qualifier + +GeneOrGeneProductOrChemicalEntityAspectEnum + + + +gene to disease or phenotypic feature association_object direction qualifier + +DirectionQualifierEnum + + + +gene to disease or phenotypic feature association_predicate + +predicate type + + + +subject->object + + +relation + + + +relation + +relation + + + +subject->relation + + + + + +causal gene to disease association_subject + +gene or gene product + + + +object->relation + + + + + +causal gene to disease association_object + +disease + + + diff --git a/graphviz/cell_line_as_a_model_of_disease_association.gv b/graphviz/cell_line_as_a_model_of_disease_association.gv index 5b3cb6781b..8e1f5a530d 100644 --- a/graphviz/cell_line_as_a_model_of_disease_association.gv +++ b/graphviz/cell_line_as_a_model_of_disease_association.gv @@ -1,28 +1,28 @@ digraph { - graph [bb="0,0,6356.8,283"]; + graph [bb="0,0,6091.8,283"]; node [label="\N"]; "cell line as a model of disease association" [height=0.5, label="cell line as a model of disease association", - pos="3603.8,265", + pos="3338.8,265", width=5.6509]; "cell line to disease or phenotypic feature association" [height=0.5, pos="254.78,178", width=7.0771]; "cell line as a model of disease association" -> "cell line to disease or phenotypic feature association" [label=is_a, lp="1010.8,221.5", - pos="e,412.78,192.12 3401.9,262.7 2874.5,259.07 1463.9,247.86 996.78,229 799.57,221.04 573.32,204.76 423.02,192.93"]; + pos="e,413.5,192.11 3135.1,264.54 2728.4,264.82 1787,261.51 996.78,229 799.9,220.9 574.05,204.69 423.74,192.91"]; "model to disease association mixin" [height=0.5, pos="699.78,178", width=4.7843]; "cell line as a model of disease association" -> "model to disease association mixin" [label=uses, lp="1228.3,221.5", - pos="e,807.45,192.13 3401.1,263.19 2904.1,260.87 1635,252.72 1211.8,229 1076.3,221.41 921.27,205.21 817.63,193.3"]; + pos="e,807.46,192.07 3136.9,262.76 2680.9,259.63 1582.1,250.1 1211.8,229 1076.3,221.28 921.28,205.11 817.64,193.24"]; "entity to disease association mixin" [height=0.5, pos="1060.8,178", width=4.7482]; "cell line as a model of disease association" -> "entity to disease association mixin" [label=uses, lp="1383.3,221.5", - pos="e,1134.9,194.23 3400.2,264.63 2925.9,265.47 1757.8,263.81 1366.8,229 1291.2,222.27 1206.1,207.8 1144.9,196.15"]; + pos="e,1135.2,194.25 3135.4,264.11 2703.2,263.74 1705,259.48 1366.8,229 1291.4,222.21 1206.4,207.78 1145.2,196.16"]; id [color=blue, height=0.5, label=string, @@ -31,8 +31,8 @@ digraph { "cell line as a model of disease association" -> id [color=blue, label=id, lp="1500.8,221.5", - pos="e,1316.8,189.97 3401.4,262.82 2909.8,259.66 1679.5,249.75 1493.8,229 1422.5,221.04 1404.9,215.35 1335.8,196 1332.7,195.13 1329.5,\ -194.16 1326.3,193.14", + pos="e,1316.8,189.97 3137.5,262.31 2692.8,258.26 1653.2,247 1493.8,229 1422.5,220.95 1404.9,215.35 1335.8,196 1332.7,195.13 1329.5,194.16 \ +1326.3,193.14", style=solid]; iri [color=blue, height=0.5, @@ -42,7 +42,7 @@ digraph { "cell line as a model of disease association" -> iri [color=blue, label=iri, lp="1597.8,221.5", - pos="e,1422.1,190.02 3401.5,262.8 2926.3,259.66 1765.8,249.93 1589.8,229 1534.3,222.4 1472.2,205.4 1431.8,193.05", + pos="e,1422.1,189.99 3137.6,262.23 2710.4,258.15 1739.6,247.01 1589.8,229 1534.3,222.33 1472.2,205.35 1431.8,193.02", style=solid]; name [color=blue, height=0.5, @@ -52,7 +52,7 @@ digraph { "cell line as a model of disease association" -> name [color=blue, label=name, lp="1693.8,221.5", - pos="e,1542.1,192.37 3400.9,263.47 2939.8,261.8 1840.5,255.11 1673.8,229 1631.5,222.37 1584.9,207.67 1551.9,195.91", + pos="e,1542.1,192.34 3136.6,262.82 2724.6,259.98 1814.4,251.23 1673.8,229 1631.5,222.31 1584.9,207.61 1551.9,195.87", style=solid]; description [color=blue, height=0.5, @@ -62,7 +62,7 @@ digraph { "cell line as a model of disease association" -> description [color=blue, label=description, lp="1797.3,221.5", - pos="e,1682.2,195.26 3402,262.59 2939.2,259.02 1835.3,248.5 1756.8,229 1733.5,223.22 1709.4,211.22 1690.8,200.42", + pos="e,1682.2,195.23 3135.4,264.52 2738.2,264.79 1886.8,261.5 1756.8,229 1733.5,223.18 1709.4,211.18 1690.8,200.4", style=solid]; "has attribute" [color=blue, height=0.5, @@ -72,7 +72,7 @@ digraph { "cell line as a model of disease association" -> "has attribute" [color=blue, label="has attribute", lp="1916.8,221.5", - pos="e,1818.4,195.2 3401,263.21 2958.6,261.05 1941,253.43 1869.8,229 1853.6,223.45 1838.1,212.42 1826.1,202.13", + pos="e,1818.4,195.17 3137.2,262.43 2748.5,258.96 1928.5,249.28 1869.8,229 1853.6,223.42 1838.1,212.39 1826.1,202.1", style=solid]; predicate [color=blue, height=0.5, @@ -82,18 +82,18 @@ digraph { "cell line as a model of disease association" -> predicate [color=blue, label=predicate, lp="2016.8,221.5", - pos="e,1956.8,196.14 3400,264.68 2978.2,265.39 2043.5,263.07 1982.8,229 1973.3,223.7 1966.3,214.34 1961.2,205.14", + pos="e,1956.8,196.13 3135.8,263.74 2769.7,262.57 2032,256.76 1982.8,229 1973.4,223.68 1966.3,214.32 1961.2,205.12", style=solid]; object [color=blue, height=0.5, label="named thing", - pos="5742.8,91", + pos="5477.8,91", width=1.9318]; "cell line as a model of disease association" -> object [color=blue, label=object, lp="2095.8,178", - pos="e,5673.3,91.949 3403.7,261.67 3091.4,257.52 2502.1,247.5 2292.8,229 2191.1,220.02 2002.3,232.83 2073.8,160 2138.9,93.7 5133.2,91.768 \ -5663.1,91.946", + pos="e,5408,92.052 3138.1,262.04 2866.7,258.63 2397.1,249.87 2226.8,229 2152.7,219.93 2021.6,213.27 2073.8,160 2133.9,98.687 4890.2,92.655 \ +5397.9,92.064", style=solid]; negated [color=blue, height=0.5, @@ -102,8 +102,8 @@ digraph { width=1.2999]; "cell line as a model of disease association" -> negated [color=blue, label=negated, - lp="2403.8,221.5", - pos="e,2208.5,190.32 3401.5,262.99 3105.1,260.7 2567.1,253.24 2374.8,229 2320,222.1 2258.7,205.5 2218.3,193.31", + lp="2296.8,221.5", + pos="e,2195.4,194.18 3137.5,262.33 2850.5,259.21 2349.1,250.7 2267.8,229 2245.1,222.95 2221.8,210.62 2204.1,199.71", style=solid]; qualifiers [color=blue, height=0.5, @@ -112,8 +112,8 @@ digraph { width=2.1304]; "cell line as a model of disease association" -> qualifiers [color=blue, label=qualifiers, - lp="2538.3,221.5", - pos="e,2357.2,193.12 3401.6,263.01 3132.7,260.74 2671.8,253.32 2504.8,229 2457.4,222.1 2404.8,207.72 2367,196.15", + lp="2377.3,221.5", + pos="e,2319.8,196.04 3138.3,261.89 2857.5,258.22 2377.2,249.04 2343.8,229 2334.8,223.64 2328.4,214.39 2323.9,205.3", style=solid]; publications [color=blue, height=0.5, @@ -122,8 +122,8 @@ digraph { width=1.7332]; "cell line as a model of disease association" -> publications [color=blue, label=publications, - lp="2677.8,221.5", - pos="e,2507.2,192.88 3401.5,262.95 3161.5,260.6 2775.9,253.07 2633.8,229 2593.3,222.14 2548.8,207.9 2516.7,196.37", + lp="2462.8,221.5", + pos="e,2439.9,193.49 3136.2,263.33 2872.8,261.44 2443.3,254.45 2418.8,229 2408.9,218.74 2418,207.83 2431.2,198.82", style=solid]; "has evidence" [color=blue, height=0.5, @@ -132,282 +132,285 @@ digraph { width=2.0943]; "cell line as a model of disease association" -> "has evidence" [color=blue, label="has evidence", - lp="2827.3,221.5", - pos="e,2663.8,193.89 3403.7,261.75 3199.2,258.32 2895.7,249.82 2780.8,229 2743.7,222.28 2703.2,208.76 2673.2,197.47", + lp="2560.3,221.5", + pos="e,2570.8,189.91 3137.5,262.36 2900.2,259.4 2535.1,251.25 2513.8,229 2509.2,224.19 2509.8,219.36 2513.8,214 2520.1,205.45 2539.7,\ +198.12 2560.9,192.41", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2829.8,178", - width=3.015]; + label=string, + pos="2759.8,178", + width=1.0652]; "cell line as a model of disease association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2971.3,221.5", - pos="e,2849.2,195.77 3410.2,259.43 3220.6,254.13 2953.5,244.12 2906.8,229 2888.9,223.23 2871.2,212.21 2857.3,201.98", + lp="2691.3,221.5", + pos="e,2730.8,189.96 3140.4,260.9 2936,256.71 2644.4,247.52 2626.8,229 2581.7,181.64 2570.5,235.8 2711.8,196 2714.9,195.13 2718.1,194.15 \ +2721.3,193.13", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="3064.8,178", - width=3.015]; + label=string, + pos="2854.8,178", + width=1.0652]; "cell line as a model of disease association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="3138.8,221.5", - pos="e,3049.1,195.98 3414.8,258.3 3257.3,252.59 3056.6,242.69 3043.8,229 3037.4,222.18 3039.1,213.11 3043.6,204.57", + lp="2857.8,221.5", + pos="e,2825.3,189.76 3148.3,258.61 2985.8,253.05 2776.1,243.18 2762.8,229 2758.2,224.15 2759,219.49 2762.8,214 2763.6,212.77 2791,202.43 \ +2815.7,193.3", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="3299.8,178", - width=3.015]; + label=string, + pos="2949.8,178", + width=1.0652]; "cell line as a model of disease association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="3348.3,221.5", - pos="e,3261.4,194.99 3421.2,257.02 3337.9,251.91 3254.7,243.29 3241.8,229 3232.5,218.83 3240.2,208.72 3252.7,200.28", + lp="3073.3,221.5", + pos="e,2951,196.08 3162.4,255.99 3074.3,250.44 2982.9,241.74 2966.8,229 2959.6,223.36 2955.5,214.59 2953.1,205.95", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="3481.8,178", + pos="3169.8,178", width=1.5346]; "cell line as a model of disease association" -> timepoint [color=blue, label=timepoint, - lp="3496.8,221.5", - pos="e,3467.2,195.52 3506.1,249.11 3485.7,243.97 3468.3,237.34 3461.8,229 3456.1,221.76 3457.7,212.7 3461.9,204.28", + lp="3230.8,221.5", + pos="e,3174.7,196.24 3233.9,249.48 3220.2,244.49 3207,237.84 3195.8,229 3188.2,223.03 3182.6,214.22 3178.5,205.65", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="3593.8,178", + pos="3281.8,178", width=1.0652]; "cell line as a model of disease association" -> "original subject" [color=blue, label="original subject", - lp="3593.8,221.5", - pos="e,3565.1,190.29 3556.6,247.32 3549.1,242.57 3542.3,236.56 3537.8,229 3529.7,215.65 3541.4,203.87 3556.2,195.09", + lp="3328.8,221.5", + pos="e,3273.3,195.81 3291.6,247.32 3284.1,242.57 3277.3,236.56 3272.8,229 3268.6,221.99 3268.6,213.49 3270.3,205.5", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3707.8,178", + pos="3406.8,178", width=1.5887]; "cell line as a model of disease association" -> "original predicate" [color=blue, label="original predicate", - lp="3731.3,221.5", - pos="e,3689.5,195.28 3626.9,246.83 3634.3,241.23 3642.4,234.94 3649.8,229 3660.5,220.35 3672,210.53 3681.9,201.9", + lp="3457.3,221.5", + pos="e,3401.6,196.38 3366.1,246.8 3372.8,241.66 3379.6,235.62 3384.8,229 3390.2,222.12 3394.6,213.69 3398,205.72", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3821.8,178", + pos="3535.8,178", width=1.0652]; "cell line as a model of disease association" -> "original object" [color=blue, label="original object", - lp="3863.3,221.5", - pos="e,3818.3,195.93 3728.7,250.75 3759.3,245.49 3786.6,238.39 3798.8,229 3806.4,223.14 3811.5,214.2 3815,205.49", + lp="3585.3,221.5", + pos="e,3536.5,196.11 3464.9,250.75 3491.7,245.6 3514.9,238.55 3524.8,229 3530.9,223.08 3534,214.61 3535.4,206.32", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3954.8,178", + pos="3668.8,178", width=2.1304]; "cell line as a model of disease association" -> "subject category" [color=blue, label="subject category", - lp="3995.3,221.5", - pos="e,3947,196.33 3753.8,252.81 3827.6,246.32 3903.8,237.73 3918.8,229 3928.3,223.42 3936.1,214.17 3941.8,205.14", + lp="3714.3,221.5", + pos="e,3663.7,196.22 3488.1,252.72 3557.3,246.4 3627.3,237.98 3640.8,229 3649.2,223.41 3655.3,214.41 3659.7,205.57", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="4125.8,178", + pos="3839.8,178", width=2.1304]; "cell line as a model of disease association" -> "object category" [color=blue, label="object category", - lp="4141.3,221.5", - pos="e,4109.2,195.62 3748.7,252.33 3771.5,250.52 3794.8,248.7 3816.8,247 3870.5,242.85 4008.3,247.88 4058.8,229 4074.5,223.14 4089.6,\ -212.4 4101.5,202.38", + lp="3858.3,221.5", + pos="e,3824.2,196.08 3484.3,252.38 3506.9,250.58 3530,248.74 3551.8,247 3602,243 3731,247.64 3777.8,229 3792.2,223.24 3806,212.86 3816.8,\ +203.05", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="4258.8,178", + pos="3972.8,178", width=1.0652]; "cell line as a model of disease association" -> "subject closure" [color=blue, label="subject closure", - lp="4277.3,221.5", - pos="e,4243,194.68 3745.2,252.06 3769.1,250.23 3793.6,248.47 3816.8,247 3859.4,244.3 4161.1,244.81 4200.8,229 4208.7,225.86 4223.1,213.44 \ -4235.6,201.77", + lp="3995.3,221.5", + pos="e,3960.3,195.25 3480.5,252.08 3504.3,250.25 3528.7,248.49 3551.8,247 3592.4,244.38 3880.2,244.61 3917.8,229 3931.5,223.32 3943.9,\ +212.69 3953.5,202.68", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="4354.8,178", + pos="4085.8,178", width=1.0652]; "cell line as a model of disease association" -> "object closure" [color=blue, label="object closure", - lp="4395.8,221.5", - pos="e,4352.3,196.37 3743.8,251.93 3768.1,250.09 3793.2,248.35 3816.8,247 3845.5,245.36 4310.1,245.32 4333.8,229 4341.5,223.64 4346.5,\ -214.81 4349.5,206.05", + lp="4119.8,221.5", + pos="e,4079.7,196.09 3479.1,251.93 3503.3,250.09 3528.3,248.36 3551.8,247 3579.6,245.39 4029.5,242.83 4053.8,229 4063.2,223.64 4070.2,\ +214.26 4075.3,205.07", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="4487.8,178", + pos="4218.8,178", width=2.1304]; "cell line as a model of disease association" -> "subject category closure" [color=blue, label="subject category closure", - lp="4554.3,221.5", - pos="e,4479.8,196.2 3742.9,251.86 3767.5,250.01 3792.9,248.29 3816.8,247 3851.9,245.1 4418.5,245.08 4449.8,229 4460.1,223.71 4468.4,214.22 \ -4474.5,204.92", + lp="4281.3,221.5", + pos="e,4208.6,196.26 3478.2,251.85 3502.7,250.01 3528,248.29 3551.8,247 3586.3,245.12 4142.4,243.52 4173.8,229 4185.3,223.69 4195.1,213.93 \ +4202.6,204.43", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="4676.8,178", + pos="4411.8,178", width=2.1304]; "cell line as a model of disease association" -> "object category closure" [color=blue, label="object category closure", - lp="4744.3,221.5", - pos="e,4671.1,196.13 3742.1,251.79 3766.9,249.93 3792.6,248.23 3816.8,247 3862.8,244.67 4605.8,251.84 4645.8,229 4655,223.74 4661.8,214.51 \ -4666.7,205.4", + lp="4474.3,221.5", + pos="e,4403.5,196.24 3477.1,251.8 3501.9,249.94 3527.6,248.23 3551.8,247 3597.3,244.68 4332,249.46 4372.8,229 4383.2,223.76 4391.7,214.28 \ +4398.1,204.97", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4866.8,178", + pos="4601.8,178", width=1.0652]; "cell line as a model of disease association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4916.8,221.5", - pos="e,4859.8,196.2 3741.8,251.73 3766.7,249.87 3792.5,248.18 3816.8,247 3844.9,245.63 4806.9,242.24 4831.8,229 4841.6,223.77 4849.3,\ -214.42 4854.9,205.21", + lp="4647.8,221.5", + pos="e,4593.5,195.77 3476.8,251.74 3501.7,249.87 3527.5,248.18 3551.8,247 3607.8,244.27 4511.4,253.76 4561.8,229 4572.6,223.67 4581.5,\ +213.85 4588.1,204.31", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="5025.8,178", + pos="4760.8,178", width=1.0652]; "cell line as a model of disease association" -> "object namespace" [color=blue, label="object namespace", - lp="5069.8,221.5", - pos="e,5018.4,195.75 3741.5,251.71 3766.5,249.84 3792.4,248.16 3816.8,247 3849.3,245.45 4959.8,243.88 4988.8,229 4999.1,223.69 5007.3,\ -214.01 5013.3,204.57", + lp="4801.8,221.5", + pos="e,4752.2,195.79 3476.5,251.71 3501.5,249.84 3527.4,248.16 3551.8,247 3584.2,245.46 4690.6,243.1 4719.8,229 4730.8,223.69 4739.8,\ +213.88 4746.6,204.34", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="5176.8,178", + pos="4911.8,178", width=1.0652]; "cell line as a model of disease association" -> "subject label closure" [color=blue, label="subject label closure", - lp="5229.8,221.5", - pos="e,5168.8,195.78 3741.2,251.69 3766.3,249.82 3792.3,248.14 3816.8,247 3853.4,245.29 5104.9,245.32 5137.8,229 5148.5,223.68 5157.1,\ -213.86 5163.5,204.32", + lp="4963.8,221.5", + pos="e,4902.9,195.81 3476.2,251.69 3501.3,249.82 3527.3,248.14 3551.8,247 3588.4,245.29 4836.7,244.69 4869.8,229 4880.9,223.72 4890.2,\ +213.9 4897.1,204.36", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="5347.8,178", + pos="5082.8,178", width=1.0652]; "cell line as a model of disease association" -> "object label closure" [color=blue, label="object label closure", - lp="5395.3,221.5", - pos="e,5339.5,195.8 3740.9,251.68 3766.1,249.81 3792.2,248.13 3816.8,247 3858.2,245.1 5270.6,247.17 5307.8,229 5318.6,223.7 5327.5,213.88 \ -5334.1,204.34", + lp="5131.3,221.5", + pos="e,5074.2,195.81 3475.9,251.68 3501.1,249.81 3527.2,248.13 3551.8,247 3593.1,245.1 5004.5,246.93 5041.8,229 5052.8,223.71 5061.8,\ +213.9 5068.6,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="5491.8,178", + pos="5226.8,178", width=2.347]; "cell line as a model of disease association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="5551.3,221.5", - pos="e,5488.8,196.01 3740.6,251.68 3765.9,249.8 3792.1,248.12 3816.8,247 3862.6,244.92 5430.3,253.97 5468.8,229 5476.9,223.71 5482.2,\ -214.73 5485.7,205.83", + lp="5287.3,221.5", + pos="e,5224,196.48 3475.6,251.68 3500.9,249.8 3527.1,248.12 3551.8,247 3574.7,245.96 5185.6,241.65 5204.8,229 5212.7,223.76 5217.8,214.96 \ +5221.1,206.18", style=solid]; type [height=0.5, - pos="5625.8,178", + pos="5360.8,178", width=0.86659]; "cell line as a model of disease association" -> type [color=blue, label=type, - lp="5647.8,221.5", - pos="e,5630.9,196.18 3740.6,251.66 3765.9,249.78 3792.1,248.1 3816.8,247 3841.9,245.88 5606.9,246.67 5624.8,229 5630.7,223.09 5632.3,\ -214.52 5632,206.13", + lp="5383.8,221.5", + pos="e,5366.3,196.13 3475.6,251.66 3500.9,249.78 3527.1,248.1 3551.8,247 3576.9,245.87 5343.1,246.86 5360.8,229 5366.7,223.04 5368.1,\ +214.44 5367.6,206.06", style=solid]; category [height=0.5, - pos="5726.8,178", + pos="5461.8,178", width=1.4263]; "cell line as a model of disease association" -> category [color=blue, label=category, - lp="5725.3,221.5", - pos="e,5713.2,195.46 3740.6,251.66 3765.9,249.78 3792.1,248.1 3816.8,247 3868.1,244.7 5619.6,246.94 5667.8,229 5682.4,223.57 5695.8,212.81 \ -5706.2,202.66", + lp="5460.3,221.5", + pos="e,5448.5,195.46 3475.6,251.66 3500.9,249.78 3527.1,248.1 3551.8,247 3603.2,244.7 5355.6,247.15 5403.8,229 5418.1,223.62 5431.2,213.01 \ +5441.3,202.95", style=solid]; subject [height=0.5, - pos="5840.8,178", + pos="5575.8,178", width=1.2277]; "cell line as a model of disease association" -> subject [color=blue, label=subject, - lp="5819.8,221.5", - pos="e,5822.5,194.56 3740.6,251.65 3765.9,249.77 3792.1,248.1 3816.8,247 3870.7,244.6 5708.9,244.13 5760.8,229 5780.2,223.32 5799.6,211.46 \ -5814.4,200.71", + lp="5554.8,221.5", + pos="e,5557.5,194.56 3475.6,251.65 3500.9,249.77 3527.1,248.1 3551.8,247 3605.7,244.6 5443.9,244.13 5495.8,229 5515.2,223.32 5534.6,211.46 \ +5549.4,200.71", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="5987.8,178", + pos="5722.8,178", width=2.3651]; "cell line as a model of disease association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="5972.8,221.5", - pos="e,5954.6,194.62 3740.6,251.64 3765.9,249.76 3792.1,248.09 3816.8,247 3929.6,242 5738.6,249.02 5849.8,229 5882.8,223.05 5918.4,209.97 \ -5945.2,198.68", + lp="5707.8,221.5", + pos="e,5689.6,194.62 3475.6,251.64 3500.9,249.76 3527.1,248.09 3551.8,247 3664.6,242 5473.6,249.02 5584.8,229 5617.8,223.05 5653.4,209.97 \ +5680.2,198.68", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="6166.8,178", + pos="5901.8,178", width=2.1123]; "cell line as a model of disease association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="6154.8,221.5", - pos="e,6137.2,194.87 3740.3,251.64 3765.7,249.76 3792,248.09 3816.8,247 3940.4,241.57 5923.4,253.41 6044.8,229 6073.8,223.17 6104.6,210.49 \ -6128,199.36", + lp="5889.8,221.5", + pos="e,5872.2,194.87 3475.3,251.64 3500.7,249.76 3527,248.09 3551.8,247 3675.4,241.57 5658.4,253.41 5779.8,229 5808.8,223.17 5839.6,210.49 \ +5863,199.36", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="6303.8,178", + pos="6038.8,178", width=1.011]; "cell line as a model of disease association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="6305.3,221.5", - pos="e,6285.4,193.86 3740.3,251.63 3765.7,249.75 3792,248.08 3816.8,247 3883.5,244.09 6155.5,246.95 6219.8,229 6240.6,223.19 6261.5,210.78 \ -6277.3,199.77", + lp="6040.3,221.5", + pos="e,6020.4,193.86 3475.3,251.63 3500.7,249.75 3527,248.08 3551.8,247 3618.5,244.09 5890.5,246.95 5954.8,229 5975.6,223.19 5996.5,210.78 \ +6012.3,199.77", style=solid]; relation [height=0.5, - pos="5791.8,18", + pos="5526.8,18", width=1.2999]; - object -> relation [pos="e,5780.2,35.705 5754.4,73.174 5760.4,64.509 5767.8,53.768 5774.4,44.141", + object -> relation [pos="e,5515.2,35.705 5489.4,73.174 5495.4,64.509 5502.8,53.768 5509.4,44.141", style=dotted]; association_type [color=blue, height=0.5, label=string, - pos="3863.8,265", + pos="3598.8,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3994.8,265", + pos="3729.8,265", width=2.0762]; subject -> object [label=relation, - lp="5798.8,134.5", - pos="e,5749.2,108.97 5808.3,165.59 5795.5,159.94 5781.4,152.13 5770.8,142 5763.8,135.31 5758,126.48 5753.6,118.1"]; - subject -> relation [pos="e,5803,35.828 5839.4,159.99 5837.3,139.02 5832.4,102.55 5821.8,73 5818.3,63.258 5813.2,53.189 5808.1,44.423", + lp="5533.8,134.5", + pos="e,5484.2,108.97 5543.3,165.59 5530.5,159.94 5516.4,152.13 5505.8,142 5498.8,135.31 5493,126.48 5488.6,118.1"]; + subject -> relation [pos="e,5538,35.828 5574.4,159.99 5572.3,139.02 5567.4,102.55 5556.8,73 5553.3,63.258 5548.2,53.189 5543.1,44.423", style=dotted]; "cell line as a model of disease association_subject" [color=blue, height=0.5, label="cell line", - pos="4134.8,265", + pos="3869.8,265", width=1.2999]; } diff --git a/graphviz/cell_line_as_a_model_of_disease_association.svg b/graphviz/cell_line_as_a_model_of_disease_association.svg index 916e1aa193..58462d5eae 100644 --- a/graphviz/cell_line_as_a_model_of_disease_association.svg +++ b/graphviz/cell_line_as_a_model_of_disease_association.svg @@ -4,16 +4,16 @@ - + %3 - + cell line as a model of disease association - -cell line as a model of disease association + +cell line as a model of disease association @@ -24,8 +24,8 @@ cell line as a model of disease association->cell line to disease or phenotypic feature association - - + + is_a @@ -37,8 +37,8 @@ cell line as a model of disease association->model to disease association mixin - - + + uses @@ -50,8 +50,8 @@ cell line as a model of disease association->entity to disease association mixin - - + + uses @@ -63,7 +63,7 @@ cell line as a model of disease association->id - + id @@ -76,8 +76,8 @@ cell line as a model of disease association->iri - - + + iri @@ -89,8 +89,8 @@ cell line as a model of disease association->name - - + + name @@ -102,8 +102,8 @@ cell line as a model of disease association->description - - + + description @@ -115,8 +115,8 @@ cell line as a model of disease association->has attribute - - + + has attribute @@ -128,21 +128,21 @@ cell line as a model of disease association->predicate - - + + predicate object - -named thing + +named thing cell line as a model of disease association->object - - + + object @@ -154,9 +154,9 @@ cell line as a model of disease association->negated - - -negated + + +negated @@ -167,9 +167,9 @@ cell line as a model of disease association->qualifiers - - -qualifiers + + +qualifiers @@ -180,9 +180,9 @@ cell line as a model of disease association->publications - - -publications + + +publications @@ -193,364 +193,364 @@ cell line as a model of disease association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string cell line as a model of disease association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string cell line as a model of disease association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string cell line as a model of disease association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type cell line as a model of disease association->timepoint - - -timepoint + + +timepoint original subject - -string + +string cell line as a model of disease association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie cell line as a model of disease association->original predicate - - -original predicate + + +original predicate original object - -string + +string cell line as a model of disease association->original object - - -original object + + +original object subject category - -ontology class + +ontology class cell line as a model of disease association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class cell line as a model of disease association->object category - - -object category + + +object category subject closure - -string + +string cell line as a model of disease association->subject closure - - -subject closure + + +subject closure object closure - -string + +string cell line as a model of disease association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class cell line as a model of disease association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class cell line as a model of disease association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string cell line as a model of disease association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string cell line as a model of disease association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string cell line as a model of disease association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string cell line as a model of disease association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source cell line as a model of disease association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type cell line as a model of disease association->type - - -type + + +type category - -category + +category cell line as a model of disease association->category - - -category + + +category subject - -subject + +subject cell line as a model of disease association->subject - - -subject + + +subject frequency qualifier - -frequency value + +frequency value cell line as a model of disease association->frequency qualifier - - -frequency qualifier + + +frequency qualifier severity qualifier - -severity value + +severity value cell line as a model of disease association->severity qualifier - - -severity qualifier + + +severity qualifier onset qualifier - -onset + +onset cell line as a model of disease association->onset qualifier - - -onset qualifier + + +onset qualifier relation - -relation + +relation object->relation - - + + association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation subject->relation - - + + cell line as a model of disease association_subject - -cell line + +cell line diff --git a/graphviz/cell_line_to_disease_or_phenotypic_feature_association.gv b/graphviz/cell_line_to_disease_or_phenotypic_feature_association.gv index 79787e2840..8b28b99370 100644 --- a/graphviz/cell_line_to_disease_or_phenotypic_feature_association.gv +++ b/graphviz/cell_line_to_disease_or_phenotypic_feature_association.gv @@ -1,30 +1,30 @@ digraph { - graph [bb="0,0,5726.6,283"]; + graph [bb="0,0,5461.6,283"]; node [label="\N"]; "cell line to disease or phenotypic feature association" [height=0.5, label="cell line to disease or phenotypic feature association", - pos="3267.4,265", + pos="3002.4,265", width=7.0771]; association [height=0.5, pos="62.394,178", width=1.7332]; "cell line to disease or phenotypic feature association" -> association [label=is_a, - lp="717.39,221.5", - pos="e,106.47,190.83 3012.6,264.25 2551.6,263.86 1548.7,259.22 703.39,229 449.8,219.93 384.44,233.02 133.39,196 127.91,195.19 122.22,\ -194.16 116.57,193.01"]; + lp="716.39,221.5", + pos="e,106.47,190.83 2747.9,263.68 2323.7,262.34 1445.2,256.18 702.39,229 449.25,219.74 384,232.97 133.39,196 127.91,195.19 122.22,194.16 \ +116.57,193.01"]; "cell line to entity association mixin" [height=0.5, pos="315.39,178", width=4.8024]; "cell line to disease or phenotypic feature association" -> "cell line to entity association mixin" [label=uses, - lp="1023.9,221.5", - pos="e,436.75,190.82 3012.7,264.13 2594,263.43 1734.5,258.14 1007.4,229 780.44,219.91 723.83,213.9 497.39,196 481,194.7 463.78,193.24 \ -446.75,191.72"]; + lp="1021.9,221.5", + pos="e,437.24,190.86 2748.5,263.4 2369.1,261.62 1631.6,254.81 1005.4,229 779.33,219.68 722.94,213.86 497.39,196 481.28,194.72 464.38,\ +193.28 447.63,191.79"]; "entity to disease or phenotypic feature association mixin" [height=0.5, pos="780.39,178", width=7.6188]; "cell line to disease or phenotypic feature association" -> "entity to disease or phenotypic feature association mixin" [label=uses, - lp="1206.9,221.5", - pos="e,884.16,194.7 3014.1,263.05 2540.5,260.71 1537.4,253.01 1190.4,229 1090,222.05 976.37,207.68 894.27,196.13"]; + lp="1204.9,221.5", + pos="e,884.08,194.69 2750.2,262.34 2325.3,258.99 1484,249.91 1188.4,229 1088.7,221.95 976.04,207.66 894.38,196.15"]; id [color=blue, height=0.5, label=string, @@ -32,9 +32,9 @@ digraph { width=1.0652]; "cell line to disease or phenotypic feature association" -> id [color=blue, label=id, - lp="1324.4,221.5", - pos="e,1140.4,189.97 3015.5,262.12 2526.3,258.09 1481.4,247.43 1317.4,229 1246.1,220.99 1228.5,215.35 1159.4,196 1156.3,195.13 1153.1,\ -194.16 1149.9,193.14", + lp="1320.4,221.5", + pos="e,1140.4,189.95 2747.3,264.66 2345.4,264.68 1583,260.39 1313.4,229 1243.9,220.9 1226.7,215.06 1159.4,196 1156.3,195.12 1153.1,194.15 \ +1149.9,193.12", style=solid]; iri [color=blue, height=0.5, @@ -44,7 +44,8 @@ digraph { "cell line to disease or phenotypic feature association" -> iri [color=blue, label=iri, lp="1421.4,221.5", - pos="e,1245.7,190.01 3015.7,262.05 2545.6,258.01 1567.8,247.48 1413.4,229 1357.9,222.36 1295.8,205.37 1255.5,193.03", + pos="e,1245.3,190.08 2747.6,264.5 2365.9,264.21 1663.6,259.35 1413.4,229 1346.5,220.89 1330.4,213.64 1265.4,196 1262,195.09 1258.6,194.09 \ +1255.1,193.06", style=solid]; name [color=blue, height=0.5, @@ -54,7 +55,7 @@ digraph { "cell line to disease or phenotypic feature association" -> name [color=blue, label=name, lp="1517.4,221.5", - pos="e,1365.7,192.35 3014.2,262.81 2560.5,260.11 1642.7,251.88 1497.4,229 1455.1,222.34 1408.5,207.64 1375.5,195.89", + pos="e,1365.7,192.32 2751.3,261.85 2355,257.89 1617.2,248.08 1497.4,229 1455.1,222.27 1408.5,207.57 1375.5,195.85", style=solid]; description [color=blue, height=0.5, @@ -64,7 +65,7 @@ digraph { "cell line to disease or phenotypic feature association" -> description [color=blue, label=description, lp="1620.9,221.5", - pos="e,1505.8,195.24 3016.6,261.72 2563.4,257.19 1648.6,246 1580.4,229 1557.1,223.2 1533,211.2 1514.5,200.41", + pos="e,1505.8,195.21 2748.2,263.8 2369.5,262.59 1690,256.53 1580.4,229 1557.1,223.15 1533.1,211.15 1514.5,200.37", style=solid]; "has attribute" [color=blue, height=0.5, @@ -74,7 +75,7 @@ digraph { "cell line to disease or phenotypic feature association" -> "has attribute" [color=blue, label="has attribute", lp="1740.4,221.5", - pos="e,1642,195.18 3015.1,262.4 2586,259.11 1754.6,250.06 1693.4,229 1677.2,223.43 1661.8,212.4 1649.8,202.11", + pos="e,1642.3,195.4 2753.1,261.21 2387.2,256.56 1742.4,246 1693.4,229 1677.4,223.43 1662,212.51 1650,202.29", style=solid]; predicate [color=blue, height=0.5, @@ -84,18 +85,18 @@ digraph { "cell line to disease or phenotypic feature association" -> predicate [color=blue, label=predicate, lp="1840.4,221.5", - pos="e,1780.4,196.13 3012.6,264.07 2607.8,263.32 1857.9,257.98 1806.4,229 1797,223.69 1789.9,214.33 1784.8,205.13", + pos="e,1780.4,196.11 2749.6,262.59 2410.7,259.82 1846.7,251.81 1806.4,229 1797,223.67 1789.9,214.3 1784.8,205.1", style=solid]; object [color=blue, height=0.5, label="named thing", - pos="5584.4,91", + pos="5319.4,91", width=1.9318]; "cell line to disease or phenotypic feature association" -> object [color=blue, label=object, lp="1919.4,178", - pos="e,5514.6,91.943 3022.5,260.03 2737.4,254.8 2284,244.42 2114.4,229 2013.6,219.84 1826.5,232.22 1897.4,160 1962.8,93.377 4971.8,91.711 \ -5504.3,91.938", + pos="e,5249.7,92.045 2757.4,260.03 2520.8,255.28 2179.4,245.8 2047.4,229 1974.6,219.74 1846,212.4 1897.4,160 1957.8,98.35 4730.2,92.593 \ +5239.5,92.055", style=solid]; negated [color=blue, height=0.5, @@ -104,8 +105,8 @@ digraph { width=1.2999]; "cell line to disease or phenotypic feature association" -> negated [color=blue, label=negated, - lp="2224.4,221.5", - pos="e,2032,190.37 3017.5,261.44 2751.5,257.72 2348.2,248.93 2195.4,229 2141.6,221.98 2081.4,205.49 2041.6,193.35", + lp="2116.4,221.5", + pos="e,2018.3,194.38 2755.7,260.46 2506.7,255.94 2150,246.52 2087.4,229 2065.9,222.99 2044,210.95 2027.1,200.18", style=solid]; qualifiers [color=blue, height=0.5, @@ -114,8 +115,8 @@ digraph { width=2.1304]; "cell line to disease or phenotypic feature association" -> qualifiers [color=blue, label=qualifiers, - lp="2356.9,221.5", - pos="e,2180.1,193.18 3018.5,261.14 2784.7,257.3 2452.2,248.53 2323.4,229 2277.5,222.05 2226.8,207.84 2190,196.34", + lp="2194.9,221.5", + pos="e,2141.6,196.4 2757.4,260.01 2518,255.17 2186,245.52 2161.4,229 2153.4,223.66 2148.2,214.84 2144.7,206.08", style=solid]; publications [color=blue, height=0.5, @@ -124,8 +125,8 @@ digraph { width=1.7332]; "cell line to disease or phenotypic feature association" -> publications [color=blue, label=publications, - lp="2494.4,221.5", - pos="e,2329.8,193.06 3019.6,260.68 2819.9,256.65 2555.6,247.87 2450.4,229 2412,222.11 2369.9,208.11 2339.3,196.67", + lp="2280.4,221.5", + pos="e,2260.3,192.96 2754.4,260.8 2537.6,256.75 2254.4,247.86 2236.4,229 2225.9,217.96 2236.3,206.87 2251.2,197.94", style=solid]; "has evidence" [color=blue, height=0.5, @@ -134,250 +135,252 @@ digraph { width=2.0943]; "cell line to disease or phenotypic feature association" -> "has evidence" [color=blue, label="has evidence", - lp="2639.9,221.5", - pos="e,2485.6,194.18 3028.1,258.78 2868.6,253.92 2674,244.94 2593.4,229 2559.4,222.29 2522.6,209.15 2495,198.02", + lp="2377.9,221.5", + pos="e,2392.4,189.32 2761.2,259.15 2575,254.18 2346.5,244.89 2331.4,229 2326.8,224.16 2327.4,219.33 2331.4,214 2338.2,204.89 2359.6,197.36 \ +2382.5,191.65", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2653.4,178", - width=3.015]; + label=string, + pos="2583.4,178", + width=1.0652]; "cell line to disease or phenotypic feature association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2778.9,221.5", - pos="e,2668.6,196.17 3014.2,262.87 2895.6,259.33 2768.7,250.36 2714.4,229 2700,223.35 2686.5,212.99 2675.9,203.16", + lp="2507.9,221.5", + pos="e,2554.7,189.94 2775.2,256.83 2625.6,250.96 2455.2,241.57 2443.4,229 2396.1,178.66 2369.1,241.46 2535.4,196 2538.5,195.14 2541.8,\ +194.17 2545,193.14", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2888.4,178", - width=3.015]; + label=string, + pos="2678.4,178", + width=1.0652]; "cell line to disease or phenotypic feature association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2945.4,221.5", - pos="e,2863.1,195.6 3035.1,257.56 2947,252.68 2864.3,244.09 2850.4,229 2842.8,220.79 2847.4,211.15 2855.6,202.54", + lp="2674.4,221.5", + pos="e,2648.7,189.52 2768.3,257.84 2678.3,253 2593.6,244.38 2579.4,229 2574.9,224.1 2575.5,219.44 2579.4,214 2593.3,194.38 2607.7,204.01 \ +2630.4,196 2633.3,194.99 2636.2,193.94 2639.2,192.88", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="3123.4,178", - width=3.015]; + label=string, + pos="2773.4,178", + width=1.0652]; "cell line to disease or phenotypic feature association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="3154.9,221.5", - pos="e,3072.6,194.03 3100.8,251.32 3076.6,246.2 3057,239.03 3048.4,229 3038,216.84 3047.9,206.43 3063.4,198.31", + lp="2886.9,221.5", + pos="e,2771.1,196.06 2838.2,251.22 2812,246.12 2790.2,238.98 2780.4,229 2774.5,223.02 2772.1,214.53 2771.3,206.24", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="3305.4,178", + pos="2992.4,178", width=1.5346]; "cell line to disease or phenotypic feature association" -> timepoint [color=blue, label=timepoint, - lp="3303.4,221.5", - pos="e,3283.3,194.53 3264.5,246.62 3263.6,236.66 3263.9,224.16 3268.4,214 3270.3,209.58 3273.2,205.46 3276.4,201.7", + lp="3033.4,221.5", + pos="e,2994.4,196.18 3000.4,246.8 2999,235.16 2997.2,219.55 2995.6,206.24", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="3417.4,178", + pos="3104.4,178", width=1.0652]; "cell line to disease or phenotypic feature association" -> "original subject" [color=blue, label="original subject", - lp="3417.4,221.5", - pos="e,3395.3,192.7 3304,247.02 3315.2,241.54 3327.4,235.26 3338.4,229 3349,222.96 3351.1,220.57 3361.4,214 3369.6,208.79 3378.4,203.21 \ -3386.7,198.07", + lp="3141.4,221.5", + pos="e,3096.5,195.95 3045.1,247.24 3054.7,242.26 3064.4,236.18 3072.4,229 3079.9,222.22 3086.4,213.26 3091.5,204.8", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3531.4,178", + pos="3230.4,178", width=1.5887]; "cell line to disease or phenotypic feature association" -> "original predicate" [color=blue, label="original predicate", - lp="3556.9,221.5", - pos="e,3514.4,195.43 3410.4,250.1 3432.1,245.06 3453.8,238.23 3473.4,229 3480.9,225.48 3494.7,213.61 3507,202.31", + lp="3278.9,221.5", + pos="e,3224.8,196.02 3133.3,249.53 3162.8,244.34 3189.1,237.59 3201.4,229 3209.7,223.18 3216,214.13 3220.6,205.32", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3645.4,178", + pos="3364.4,178", width=1.0652]; "cell line to disease or phenotypic feature association" -> "original object" [color=blue, label="original object", - lp="3687.9,221.5", - pos="e,3642.4,196.18 3460.8,253.27 3536.6,247.5 3609,239.41 3623.4,229 3631.1,223.42 3636.1,214.54 3639.4,205.8", + lp="3408.9,221.5", + pos="e,3362.8,196.08 3193.9,253.06 3265.7,247.34 3333.2,239.35 3346.4,229 3353.6,223.37 3357.9,214.59 3360.5,205.96", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3778.4,178", + pos="3497.4,178", width=2.1304]; "cell line to disease or phenotypic feature association" -> "subject category" [color=blue, label="subject category", - lp="3818.9,221.5", - pos="e,3771.3,195.98 3449.5,252.39 3581.1,243.72 3736.8,232.76 3743.4,229 3753.1,223.5 3760.7,214.1 3766.3,204.93", + lp="3539.9,221.5", + pos="e,3490.9,195.95 3181.8,252.21 3308.9,243.56 3458.1,232.72 3464.4,229 3473.8,223.46 3481.1,214.06 3486.3,204.89", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3949.4,178", + pos="3668.4,178", width=2.1304]; "cell line to disease or phenotypic feature association" -> "object category" [color=blue, label="object category", - lp="3964.9,221.5", - pos="e,3932.9,195.75 3446.3,252.16 3474.8,250.37 3503.9,248.59 3531.4,247 3609.4,242.49 3808.9,255.5 3882.4,229 3898.1,223.32 3913.3,\ -212.6 3925.2,202.54", + lp="3684.9,221.5", + pos="e,3652.5,195.74 3181.7,252.19 3210,250.4 3239,248.61 3266.4,247 3341.3,242.59 3533.1,255.03 3603.4,229 3618.8,223.3 3633.5,212.58 \ +3645,202.52", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="4082.4,178", + pos="3801.4,178", width=1.0652]; "cell line to disease or phenotypic feature association" -> "subject closure" [color=blue, label="subject closure", - lp="4100.9,221.5", - pos="e,4066.6,194.71 3443.4,251.98 3472.8,250.17 3503,248.43 3531.4,247 3586.1,244.24 3973.4,249.02 4024.4,229 4032.3,225.9 4046.7,213.48 \ -4059.2,201.8", + lp="3823.9,221.5", + pos="e,3788.3,195.31 3178.8,251.99 3208.1,250.18 3238.1,248.44 3266.4,247 3319.5,244.29 3695,248.66 3744.4,229 3758.4,223.41 3771.3,212.79 \ +3781.3,202.77", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="4178.4,178", + pos="3909.4,178", width=1.0652]; "cell line to disease or phenotypic feature association" -> "object closure" [color=blue, label="object closure", - lp="4220.4,221.5", - pos="e,4176,196.39 3442,251.88 3471.8,250.06 3502.5,248.35 3531.4,247 3566.1,245.38 4128.7,248.67 4157.4,229 4165.2,223.66 4170.1,214.84 \ -4173.2,206.07", + lp="3946.4,221.5", + pos="e,3905,196.03 3177,251.89 3206.8,250.07 3237.5,248.35 3266.4,247 3300.6,245.4 3853.3,246.97 3882.4,229 3891,223.68 3897.1,214.57 \ +3901.2,205.57", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="4311.4,178", + pos="4042.4,178", width=2.1304]; "cell line to disease or phenotypic feature association" -> "subject category closure" [color=blue, label="subject category closure", - lp="4378.9,221.5", - pos="e,4303.8,196.2 3441.3,251.81 3471.3,249.99 3502.3,248.29 3531.4,247 3572.6,245.17 4237.8,248.03 4274.4,229 4284.6,223.72 4292.7,\ -214.23 4298.7,204.92", + lp="4106.9,221.5", + pos="e,4033.1,196.26 3176.3,251.82 3206.3,249.99 3237.3,248.29 3266.4,247 3307.1,245.19 3963.6,246.68 4000.4,229 4011.3,223.73 4020.5,\ +214.11 4027.4,204.7", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="4500.4,178", + pos="4235.4,178", width=2.1304]; "cell line to disease or phenotypic feature association" -> "object category closure" [color=blue, label="object category closure", - lp="4568.9,221.5", - pos="e,4495.1,196.12 3440.2,251.75 3470.6,249.92 3501.9,248.23 3531.4,247 3557.5,245.91 4447.8,242.07 4470.4,229 4479.5,223.73 4486.2,\ -214.5 4490.8,205.39", + lp="4298.9,221.5", + pos="e,4227.8,196.22 3175.2,251.75 3205.6,249.92 3236.9,248.23 3266.4,247 3318.1,244.84 4152.4,252.75 4198.4,229 4208.6,223.74 4216.7,\ +214.26 4222.7,204.95", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4690.4,178", + pos="4425.4,178", width=1.0652]; "cell line to disease or phenotypic feature association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4740.4,221.5", - pos="e,4683.7,196.2 3439.5,251.71 3470.1,249.87 3501.7,248.19 3531.4,247 3562.6,245.75 4628.9,243.84 4656.4,229 4666.1,223.77 4673.6,\ -214.41 4679,205.2", + lp="4472.4,221.5", + pos="e,4417.4,195.77 3174.5,251.71 3205.1,249.87 3236.7,248.19 3266.4,247 3297.5,245.75 4358.5,242.88 4386.4,229 4397.1,223.66 4405.8,\ +213.84 4412.2,204.31", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4849.4,178", + pos="4584.4,178", width=1.0652]; "cell line to disease or phenotypic feature association" -> "object namespace" [color=blue, label="object namespace", - lp="4893.4,221.5", - pos="e,4842,195.75 3439.2,251.68 3469.9,249.84 3501.6,248.17 3531.4,247 3567,245.61 4780.7,245.24 4812.4,229 4822.7,223.7 4830.9,214.02 \ -4836.9,204.58", + lp="4626.4,221.5", + pos="e,4576.1,195.79 3174.2,251.68 3204.9,249.84 3236.6,248.17 3266.4,247 3301.9,245.61 4512.5,244.6 4544.4,229 4555.3,223.69 4564.1,\ +213.87 4570.7,204.33", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="5000.4,178", + pos="4735.4,178", width=1.0652]; "cell line to disease or phenotypic feature association" -> "subject label closure" [color=blue, label="subject label closure", - lp="5053.4,221.5", - pos="e,4992.4,195.78 3438.8,251.67 3469.6,249.82 3501.4,248.15 3531.4,247 3571.1,245.47 4925.8,246.65 4961.4,229 4972.1,223.68 4980.8,\ -213.86 4987.2,204.32", + lp="4788.4,221.5", + pos="e,4726.8,195.8 3173.8,251.67 3204.6,249.82 3236.4,248.15 3266.4,247 3306,245.47 4658.6,246.19 4694.4,229 4705.4,223.71 4714.4,213.9 \ +4721.2,204.35", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="5171.4,178", + pos="4906.4,178", width=1.0652]; "cell line to disease or phenotypic feature association" -> "object label closure" [color=blue, label="object label closure", - lp="5219.9,221.5", - pos="e,5163.1,195.8 3438.5,251.66 3469.4,249.8 3501.3,248.14 3531.4,247 3575.8,245.32 5091.4,248.48 5131.4,229 5142.3,223.7 5151.1,213.89 \ -5157.7,204.35", + lp="4954.9,221.5", + pos="e,4898.1,195.8 3173.5,251.66 3204.4,249.8 3236.3,248.14 3266.4,247 3310.8,245.32 4826.4,248.48 4866.4,229 4877.3,223.7 4886.1,213.89 \ +4892.7,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="5333.4,178", + pos="5068.4,178", width=2.347]; "cell line to disease or phenotypic feature association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="5381.9,221.5", - pos="e,5324.8,196.3 3438.5,251.63 3469.4,249.78 3501.3,248.12 3531.4,247 3580.3,245.18 5249.4,250.43 5293.4,229 5304.1,223.78 5312.9,\ -214.17 5319.4,204.76", + lp="5116.9,221.5", + pos="e,5059.8,196.3 3173.5,251.63 3204.4,249.78 3236.3,248.12 3266.4,247 3315.3,245.18 4984.4,250.43 5028.4,229 5039.1,223.78 5047.9,\ +214.17 5054.4,204.76", style=solid]; type [height=0.5, - pos="5467.4,178", + pos="5202.4,178", width=0.86659]; "cell line to disease or phenotypic feature association" -> type [color=blue, label=type, - lp="5481.4,221.5", - pos="e,5468.2,196.19 3438.1,251.63 3469.1,249.77 3501.2,248.11 3531.4,247 3558.1,246.02 5434.5,245.64 5455.4,229 5462.2,223.55 5465.6,\ -214.93 5467.2,206.37", + lp="5216.4,221.5", + pos="e,5203.2,196.19 3173.1,251.63 3204.1,249.77 3236.2,248.11 3266.4,247 3293.1,246.02 5169.5,245.64 5190.4,229 5197.2,223.55 5200.6,\ +214.93 5202.2,206.37", style=solid]; category [height=0.5, - pos="5568.4,178", + pos="5303.4,178", width=1.4263]; "cell line to disease or phenotypic feature association" -> category [color=blue, label=category, - lp="5560.9,221.5", - pos="e,5552.8,195.26 3438.1,251.63 3469.1,249.77 3501.2,248.11 3531.4,247 3586.1,244.99 5449.5,246.48 5501.4,229 5517.6,223.54 5533.1,\ -212.51 5545.1,202.2", + lp="5295.9,221.5", + pos="e,5287.8,195.26 3173.1,251.63 3204.1,249.77 3236.2,248.11 3266.4,247 3321.1,244.99 5184.5,246.48 5236.4,229 5252.6,223.54 5268.1,\ +212.51 5280.1,202.2", style=solid]; subject [height=0.5, - pos="5682.4,178", + pos="5417.4,178", width=1.2277]; "cell line to disease or phenotypic feature association" -> subject [color=blue, label=subject, - lp="5657.4,221.5", - pos="e,5662.9,194.34 3438.1,251.61 3469.1,249.76 3501.2,248.1 3531.4,247 3588.7,244.91 5541.1,244.17 5596.4,229 5617.3,223.26 5638.4,\ -211.1 5654.5,200.21", + lp="5392.4,221.5", + pos="e,5397.9,194.34 3173.1,251.61 3204.1,249.76 3236.2,248.1 3266.4,247 3323.7,244.91 5276.1,244.17 5331.4,229 5352.3,223.26 5373.4,\ +211.1 5389.5,200.21", style=solid]; relation [height=0.5, - pos="5633.4,18", + pos="5368.4,18", width=1.2999]; - object -> relation [pos="e,5621.9,35.705 5596,73.174 5602,64.509 5609.4,53.768 5616,44.141", + object -> relation [pos="e,5356.9,35.705 5331,73.174 5337,64.509 5344.4,53.768 5351,44.141", style=dotted]; association_type [color=blue, height=0.5, label=string, - pos="3578.4,265", + pos="3313.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3709.4,265", + pos="3444.4,265", width=2.0762]; subject -> object [label=relation, - lp="5640.4,134.5", - pos="e,5590.8,108.97 5649.9,165.59 5637.1,159.94 5623,152.13 5612.4,142 5605.4,135.31 5599.7,126.48 5595.3,118.1"]; - subject -> relation [pos="e,5644.6,35.828 5681,159.99 5678.9,139.02 5674,102.55 5663.4,73 5659.9,63.258 5654.8,53.189 5649.8,44.423", + lp="5375.4,134.5", + pos="e,5325.8,108.97 5384.9,165.59 5372.1,159.94 5358,152.13 5347.4,142 5340.4,135.31 5334.7,126.48 5330.3,118.1"]; + subject -> relation [pos="e,5379.6,35.828 5416,159.99 5413.9,139.02 5409,102.55 5398.4,73 5394.9,63.258 5389.8,53.189 5384.8,44.423", style=dotted]; "cell line to disease or phenotypic feature association_subject" [color=blue, height=0.5, label="disease or phenotypic feature", - pos="3951.4,265", + pos="3686.4,265", width=4.1344]; } diff --git a/graphviz/cell_line_to_disease_or_phenotypic_feature_association.svg b/graphviz/cell_line_to_disease_or_phenotypic_feature_association.svg index 7263c591ec..d82f32324d 100644 --- a/graphviz/cell_line_to_disease_or_phenotypic_feature_association.svg +++ b/graphviz/cell_line_to_disease_or_phenotypic_feature_association.svg @@ -4,16 +4,16 @@ - + %3 - + cell line to disease or phenotypic feature association - -cell line to disease or phenotypic feature association + +cell line to disease or phenotypic feature association @@ -24,9 +24,9 @@ cell line to disease or phenotypic feature association->association - + -is_a +is_a @@ -37,9 +37,9 @@ cell line to disease or phenotypic feature association->cell line to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ cell line to disease or phenotypic feature association->entity to disease or phenotypic feature association mixin - - -uses + + +uses @@ -63,9 +63,9 @@ cell line to disease or phenotypic feature association->id - - -id + + +id @@ -76,8 +76,8 @@ cell line to disease or phenotypic feature association->iri - - + + iri @@ -89,8 +89,8 @@ cell line to disease or phenotypic feature association->name - - + + name @@ -102,8 +102,8 @@ cell line to disease or phenotypic feature association->description - - + + description @@ -115,8 +115,8 @@ cell line to disease or phenotypic feature association->has attribute - - + + has attribute @@ -128,21 +128,21 @@ cell line to disease or phenotypic feature association->predicate - - + + predicate object - -named thing + +named thing cell line to disease or phenotypic feature association->object - - + + object @@ -154,9 +154,9 @@ cell line to disease or phenotypic feature association->negated - - -negated + + +negated @@ -167,9 +167,9 @@ cell line to disease or phenotypic feature association->qualifiers - - -qualifiers + + +qualifiers @@ -180,9 +180,9 @@ cell line to disease or phenotypic feature association->publications - - -publications + + +publications @@ -193,325 +193,325 @@ cell line to disease or phenotypic feature association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string cell line to disease or phenotypic feature association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string cell line to disease or phenotypic feature association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string cell line to disease or phenotypic feature association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type cell line to disease or phenotypic feature association->timepoint - - -timepoint + + +timepoint original subject - -string + +string cell line to disease or phenotypic feature association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie cell line to disease or phenotypic feature association->original predicate - - -original predicate + + +original predicate original object - -string + +string cell line to disease or phenotypic feature association->original object - - -original object + + +original object subject category - -ontology class + +ontology class cell line to disease or phenotypic feature association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class cell line to disease or phenotypic feature association->object category - - -object category + + +object category subject closure - -string + +string cell line to disease or phenotypic feature association->subject closure - - -subject closure + + +subject closure object closure - -string + +string cell line to disease or phenotypic feature association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class cell line to disease or phenotypic feature association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class cell line to disease or phenotypic feature association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string cell line to disease or phenotypic feature association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string cell line to disease or phenotypic feature association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string cell line to disease or phenotypic feature association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string cell line to disease or phenotypic feature association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source cell line to disease or phenotypic feature association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type cell line to disease or phenotypic feature association->type - - -type + + +type category - -category + +category cell line to disease or phenotypic feature association->category - - -category + + +category subject - -subject + +subject cell line to disease or phenotypic feature association->subject - - -subject + + +subject relation - -relation + +relation object->relation - - + + association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation subject->relation - - + + cell line to disease or phenotypic feature association_subject - -disease or phenotypic feature + +disease or phenotypic feature diff --git a/graphviz/chemical_affects_gene_association.gv b/graphviz/chemical_affects_gene_association.gv index ffb6f73a80..747d9b9b03 100644 --- a/graphviz/chemical_affects_gene_association.gv +++ b/graphviz/chemical_affects_gene_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,9821.6,283"]; + graph [bb="0,0,9636.6,283"]; node [label="\N"]; "chemical affects gene association" [height=0.5, label="chemical affects gene association", - pos="3592.4,265", + pos="3407.4,265", width=4.5857]; association [height=0.5, pos="62.394,178", width=1.7332]; "chemical affects gene association" -> association [label=is_a, lp="280.39,221.5", - pos="e,102.9,191.86 3427.9,263.32 2779,260.5 424.35,248.92 266.39,229 213.09,222.28 153.56,206.73 112.63,194.74"]; + pos="e,102.9,191.85 3242.2,264.38 2637,265.44 561.64,266.32 266.39,229 213.09,222.26 153.56,206.71 112.63,194.73"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "chemical affects gene association" -> id [color=blue, label=id, - lp="396.39,221.5", - pos="e,210.38,189.98 3427.4,264.06 2814.9,264.02 691.69,261.52 389.39,229 317.2,221.23 299.34,215.5 229.39,196 226.29,195.13 223.09,194.17 \ -219.89,193.15", + lp="395.39,221.5", + pos="e,210.38,189.98 3242.6,263.95 2653.4,263.52 671.79,259.76 388.39,229 316.64,221.21 298.9,215.43 229.39,196 226.29,195.13 223.09,\ +194.17 219.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "chemical affects gene association" -> iri [color=blue, label=iri, - lp="509.39,221.5", - pos="e,315.3,190.2 3427.5,263.92 2829.2,263.38 792.3,259.3 501.39,229 426.58,221.21 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ -325.06,193.15", + lp="501.39,221.5", + pos="e,315.32,190.15 3242.6,263.89 2667,263.23 766,258.82 493.39,229 422.08,221.2 404.75,214.31 335.39,196 332.02,195.11 328.55,194.13 \ +325.07,193.11", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "chemical affects gene association" -> name [color=blue, label=name, - lp="616.39,221.5", - pos="e,438.98,191.51 3427.3,264.37 2840.5,265.38 876.61,265.94 596.39,229 545.08,222.24 487.87,206.56 448.76,194.55", + lp="604.39,221.5", + pos="e,437.62,191.84 3242.3,264.4 2678.2,265.42 846.65,265.84 584.39,229 536.84,222.32 484.1,207.03 447.5,195.11", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "chemical affects gene association" -> description [color=blue, label=description, - lp="736.89,221.5", - pos="e,585.15,194.1 3427.8,263.46 2834.2,261.34 831.31,252.45 696.39,229 661.19,222.88 623.06,209.44 594.73,198.03", + lp="717.89,221.5", + pos="e,581.51,194.58 3242.4,263.54 2670.9,261.72 803.3,253.91 677.39,229 647.23,223.03 615.03,210.13 590.74,198.93", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "chemical affects gene association" -> "has attribute" [color=blue, label="has attribute", - lp="882.39,221.5", - pos="e,725.96,192.9 3427.8,263.42 2853.1,261.18 963.09,252.1 835.39,229 800.4,222.67 762.54,208.53 735.18,196.9", + lp="852.39,221.5", + pos="e,721.31,194.09 3242.5,263.66 2688.8,262.28 924.18,255.78 805.39,229 778.86,223.02 751.01,210.12 730.11,198.92", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "chemical affects gene association" -> negated [color=blue, label=negated, - lp="1037.4,221.5", - pos="e,847.4,190.57 3427.2,263.85 2895.1,263.09 1246.8,258.36 1008.4,229 955.42,222.48 896.26,205.95 857.14,193.67", + lp="990.39,221.5", + pos="e,843.01,192.07 3242.9,263.05 2712.2,259.8 1073.5,248.25 961.39,229 923.33,222.46 881.82,207.73 852.47,195.94", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "chemical affects gene association" -> qualifiers [color=blue, label=qualifiers, - lp="1177.9,221.5", - pos="e,996.43,193.22 3427.4,263.96 2914.4,263.52 1368.6,259.64 1144.4,229 1096.8,222.49 1044,208 1006.2,196.29", + lp="1101.9,221.5", + pos="e,981.91,194.8 3242.8,263.32 2727.7,260.98 1174.2,252.01 1068.4,229 1041.2,223.09 1012.6,210.5 990.8,199.43", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "chemical affects gene association" -> publications [color=blue, label=publications, - lp="1325.4,221.5", - pos="e,1147.6,192.75 3427.5,264.08 2934.3,263.96 1491.3,260.86 1281.4,229 1238.3,222.47 1190.9,207.88 1157.1,196.13", + lp="1204.4,221.5", + pos="e,1122.5,195.86 3243,263.11 2732.9,260.12 1208.1,249.5 1160.4,229 1148,223.68 1137.2,213.58 1128.8,203.85", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,480 +100,480 @@ digraph { width=2.0943]; "chemical affects gene association" -> "has evidence" [color=blue, label="has evidence", - lp="1486.9,221.5", - pos="e,1306.2,193.44 3427.3,263.83 2957.4,263 1634.3,258.08 1440.4,229 1397.5,222.57 1350.2,208.41 1316,196.8", + lp="1303.9,221.5", + pos="e,1257.3,196 3242.2,264.38 2744.6,265.12 1292.1,264.27 1257.4,229 1251.3,222.83 1251.3,214.08 1253.7,205.63", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1469.4,178", - width=3.015]; + label=string, + pos="1399.4,178", + width=1.0652]; "chemical affects gene association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1645.9,221.5", - pos="e,1497.8,195.52 3428.4,262.93 2964.5,259.68 1670.8,248.86 1581.4,229 1555.3,223.21 1527.9,211.09 1506.7,200.23", + lp="1422.9,221.5", + pos="e,1376.5,192.5 3242.3,264.24 2761.1,264.54 1391.3,262.45 1358.4,229 1349.1,219.57 1357.1,208.23 1368.3,198.73", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1704.4,178", - width=3.015]; + label=string, + pos="1494.4,178", + width=1.0652]; "chemical affects gene association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1821.4,221.5", - pos="e,1707.2,196.45 3427.9,263.25 2978.7,260.91 1761.6,252.42 1726.4,229 1718.5,223.73 1713.4,214.92 1710.1,206.15", + lp="1593.4,221.5", + pos="e,1490.5,196.31 3242.4,263.9 2784.6,263.23 1530,258.69 1498.4,229 1492.3,223.3 1490.2,214.88 1490,206.57", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1939.4,178", - width=3.015]; + label=string, + pos="1669.4,178", + width=1.0652]; "chemical affects gene association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2030.9,221.5", - pos="e,1926.6,196.33 3427.8,263.56 3012.1,262.06 1950.5,255.61 1924.4,229 1918.2,222.7 1918.9,213.95 1922.1,205.54", + lp="1815.9,221.5", + pos="e,1677.7,195.76 3242,264.36 2828.4,264.77 1777.3,262.48 1709.4,229 1698.6,223.65 1689.7,213.83 1683.1,204.3", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2121.4,178", + pos="1896.4,178", width=1.5346]; "chemical affects gene association" -> timepoint [color=blue, label=timepoint, - lp="2192.4,221.5", - pos="e,2128.7,196.19 3427.4,263.89 3062.1,263.11 2212.6,258.16 2157.4,229 2147.4,223.7 2139.5,214.21 2133.6,204.91", + lp="1983.4,221.5", + pos="e,1908.4,195.84 3242.8,263.24 2873.6,261.1 2007.2,253.5 1948.4,229 1935.4,223.6 1923.9,213.35 1914.9,203.53", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2233.4,178", + pos="2008.4,178", width=1.0652]; "chemical affects gene association" -> "original subject" [color=blue, label="original subject", - lp="2294.4,221.5", - pos="e,2229.9,196.34 3428.8,262.57 3073.2,259.1 2259.9,248.99 2238.4,229 2232.3,223.32 2230,214.91 2229.6,206.6", + lp="2092.4,221.5", + pos="e,2013.1,196.06 3242.3,264.12 2888.9,263.78 2087.2,259.63 2036.4,229 2027.5,223.66 2021.3,214.42 2016.9,205.32", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2347.4,178", + pos="2133.4,178", width=1.5887]; "chemical affects gene association" -> "original predicate" [color=blue, label="original predicate", - lp="2427.9,221.5", - pos="e,2348.4,196.29 3427.3,264.25 3102.2,264.05 2406.4,259.99 2364.4,229 2357.1,223.6 2352.9,214.88 2350.5,206.22", + lp="2230.9,221.5", + pos="e,2140.1,196.15 3242.9,263.31 2916.4,261.4 2213.7,254.35 2167.4,229 2157.7,223.71 2150.3,214.34 2144.8,205.14", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2461.4,178", + pos="2262.4,178", width=1.0652]; "chemical affects gene association" -> "original object" [color=blue, label="original object", - lp="2571.9,221.5", - pos="e,2475,195.34 3427.1,264.56 3147.3,264.64 2602.5,260.63 2520.4,229 2505.9,223.41 2492.4,212.63 2482,202.51", + lp="2375.9,221.5", + pos="e,2276.4,194.87 3242.2,264.42 2960.1,264.28 2407.9,259.99 2324.4,229 2309.2,223.35 2294.9,212.35 2283.8,202.11", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2594.4,178", + pos="2395.4,178", width=2.1304]; "chemical affects gene association" -> "subject category" [color=blue, label="subject category", - lp="2708.9,221.5", - pos="e,2607.3,195.8 3427.4,264.01 3176.1,263.1 2719.2,257.48 2649.4,229 2636,223.54 2623.8,213.28 2614.3,203.47", + lp="2516.9,221.5", + pos="e,2410.4,195.82 3242.6,263.57 2990,262.06 2528.7,255.64 2457.4,229 2442.6,223.47 2428.7,212.91 2417.8,202.92", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2765.4,178", + pos="2566.4,178", width=2.1304]; "chemical affects gene association" -> "object category" [color=blue, label="object category", - lp="2837.9,221.5", - pos="e,2766.4,196.24 3430.2,261.65 3201.2,257.66 2807.8,248.07 2782.4,229 2775.1,223.55 2770.9,214.81 2768.5,206.16", + lp="2648.9,221.5", + pos="e,2570.8,195.98 3245.7,261.12 3016.2,256.45 2620.5,245.98 2593.4,229 2584.8,223.62 2578.8,214.49 2574.6,205.5", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="2898.4,178", + pos="2699.4,178", width=1.0652]; "chemical affects gene association" -> "subject closure" [color=blue, label="subject closure", - lp="2958.9,221.5", - pos="e,2895.4,196.31 3431.3,260.98 3234,256.53 2923.4,246.74 2904.4,229 2898.3,223.29 2895.9,214.88 2895.3,206.57", + lp="2773.9,221.5", + pos="e,2701.5,196.29 3242.3,264.82 3052.3,264.33 2760.9,258.64 2719.4,229 2711.9,223.61 2707.1,214.89 2704.2,206.23", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="2997.4,178", + pos="2812.4,178", width=1.0652]; "chemical affects gene association" -> "object closure" [color=blue, label="object closure", - lp="3083.4,221.5", - pos="e,3004.8,196.03 3431.3,260.9 3278.6,256.83 3067.5,247.86 3033.4,229 3023.6,223.57 3015.7,214.18 3009.9,205", + lp="2898.4,221.5", + pos="e,2819.8,196.03 3246.3,260.9 3093.6,256.83 2882.5,247.86 2848.4,229 2838.6,223.57 2830.7,214.18 2824.9,205", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3130.4,178", + pos="2945.4,178", width=2.1304]; "chemical affects gene association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3234.9,221.5", - pos="e,3131.5,196.13 3433.7,259.96 3315.2,255.55 3170,246.6 3147.4,229 3140.2,223.42 3136,214.66 3133.6,206.02", + lp="3049.9,221.5", + pos="e,2946.5,196.13 3248.7,259.96 3130.2,255.55 2985,246.6 2962.4,229 2955.2,223.42 2951,214.66 2948.6,206.02", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3323.4,178", + pos="3138.4,178", width=2.1304]; "chemical affects gene association" -> "object category closure" [color=blue, label="object category closure", - lp="3418.9,221.5", - pos="e,3322.9,196.29 3441.3,257.71 3395.2,252.79 3352.1,244.14 3335.4,229 3329,223.21 3325.7,214.66 3324.1,206.26", + lp="3233.9,221.5", + pos="e,3137.9,196.29 3256.3,257.71 3210.2,252.79 3167.1,244.14 3150.4,229 3144,223.21 3140.7,214.66 3139.1,206.26", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3513.4,178", + pos="3328.4,178", width=1.0652]; "chemical affects gene association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3578.4,221.5", - pos="e,3507.5,196.09 3532,248.19 3523.5,243.39 3515.8,237.14 3510.4,229 3506,222.34 3505.1,214.03 3505.8,206.11", + lp="3393.4,221.5", + pos="e,3322.5,196.09 3347,248.19 3338.5,243.39 3330.8,237.14 3325.4,229 3321,222.34 3320.1,214.03 3320.8,206.11", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3619.4,178", + pos="3434.4,178", width=1.0652]; "chemical affects gene association" -> "object namespace" [color=blue, label="object namespace", - lp="3717.4,221.5", - pos="e,3638.4,194.12 3632.5,247.38 3639.6,242.53 3646.2,236.48 3650.4,229 3655.5,219.97 3651.7,210.23 3645.2,201.78", + lp="3532.4,221.5", + pos="e,3453.4,194.12 3447.5,247.38 3454.6,242.53 3461.2,236.48 3465.4,229 3470.5,219.97 3466.7,210.23 3460.2,201.78", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3714.4,178", + pos="3529.4,178", width=1.0652]; "chemical affects gene association" -> "subject label closure" [color=blue, label="subject label closure", - lp="3862.4,221.5", - pos="e,3743.7,189.79 3719.7,253.51 3749.7,248.32 3775.7,240.57 3785.4,229 3789.7,223.88 3788.9,219.66 3785.4,214 3781.4,207.54 3767.5,\ -200.12 3753.1,193.78", + lp="3677.4,221.5", + pos="e,3558.7,189.79 3534.7,253.51 3564.7,248.32 3590.7,240.57 3600.4,229 3604.7,223.88 3603.9,219.66 3600.4,214 3596.4,207.54 3582.5,\ +200.12 3568.1,193.78", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="3809.4,178", + pos="3624.4,178", width=1.0652]; "chemical affects gene association" -> "object label closure" [color=blue, label="object label closure", - lp="4025.9,221.5", - pos="e,3838.4,189.94 3710.5,252.35 3811.2,242.38 3939.9,229.55 3940.4,229 3982.9,181.95 3981.1,231.18 3857.4,196 3854.3,195.12 3851.1,\ -194.14 3847.9,193.12", + lp="3840.9,221.5", + pos="e,3653.4,189.94 3525.5,252.35 3626.2,242.38 3754.9,229.55 3755.4,229 3797.9,181.95 3796.1,231.18 3672.4,196 3669.3,195.12 3666.1,\ +194.14 3662.9,193.12", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="3950.4,178", + pos="3765.4,178", width=2.347]; "chemical affects gene association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4172.9,221.5", - pos="e,4013.4,190.03 3707.5,252.05 3727.1,250.21 3747.3,248.45 3766.4,247 3784.9,245.6 4086.7,242.45 4099.4,229 4104,224.16 4103.5,219.23 \ -4099.4,214 4094.2,207.48 4058.5,198.96 4023.3,191.96", + lp="3987.9,221.5", + pos="e,3828.4,190.03 3522.5,252.05 3542.1,250.21 3562.3,248.45 3581.4,247 3599.9,245.6 3901.7,242.45 3914.4,229 3919,224.16 3918.5,219.23 \ +3914.4,214 3909.2,207.48 3873.5,198.96 3838.3,191.96", style=solid]; type [height=0.5, - pos="4084.4,178", + pos="3899.4,178", width=0.86659]; "chemical affects gene association" -> type [color=blue, label=type, - lp="4266.4,221.5", - pos="e,4107.9,189.9 3706,251.91 3726.1,250.05 3746.9,248.32 3766.4,247 3793,245.2 4227.9,248.22 4246.4,229 4251,224.2 4250.7,219.05 4246.4,\ -214 4228.6,193.41 4151.6,203.26 4125.4,196 4122.8,195.27 4120.1,194.42 4117.4,193.5", + lp="4081.4,221.5", + pos="e,3922.9,189.9 3521,251.91 3541.1,250.05 3561.9,248.32 3581.4,247 3608,245.2 4042.9,248.22 4061.4,229 4066,224.2 4065.7,219.05 4061.4,\ +214 4043.6,193.41 3966.6,203.26 3940.4,196 3937.8,195.27 3935.1,194.42 3932.4,193.5", style=solid]; category [height=0.5, - pos="4185.4,178", + pos="4000.4,178", width=1.4263]; "chemical affects gene association" -> category [color=blue, label=category, - lp="4321.9,221.5", - pos="e,4224,190.03 3706,251.86 3726.1,250.01 3746.9,248.29 3766.4,247 3795.2,245.09 4266.3,249.79 4286.4,229 4291,224.21 4290.3,219.43 \ -4286.4,214 4283,209.18 4257.9,200.47 4233.6,192.95", + lp="4136.9,221.5", + pos="e,4039,190.03 3521,251.86 3541.1,250.01 3561.9,248.29 3581.4,247 3610.2,245.09 4081.3,249.79 4101.4,229 4106,224.21 4105.3,219.43 \ +4101.4,214 4098,209.18 4072.9,200.47 4048.6,192.95", style=solid]; "subject form or variant qualifier" [height=0.5, - pos="4414.4,178", + pos="4229.4,178", width=4.4232]; "chemical affects gene association" -> "subject form or variant qualifier" [color=blue, label="subject form or variant qualifier", - lp="4496.9,221.5", - pos="e,4400.5,196.33 3705.6,251.84 3725.8,249.98 3746.7,248.26 3766.4,247 3832,242.8 4296.3,253.08 4357.4,229 4371.1,223.62 4383.6,213.43 \ -4393.5,203.65", + lp="4311.9,221.5", + pos="e,4215.5,196.33 3520.6,251.84 3540.8,249.98 3561.7,248.26 3581.4,247 3647,242.8 4111.3,253.08 4172.4,229 4186.1,223.62 4198.6,213.43 \ +4208.5,203.65", style=solid]; "subject part qualifier" [height=0.5, - pos="4700.4,178", + pos="4515.4,178", width=3.015]; "chemical affects gene association" -> "subject part qualifier" [color=blue, label="subject part qualifier", - lp="4725.9,221.5", - pos="e,4679.1,195.72 3704.6,251.77 3725.1,249.89 3746.4,248.19 3766.4,247 3860.6,241.41 4524.6,254.75 4615.4,229 4635.1,223.41 4654.9,\ -212.14 4670.5,201.71", + lp="4540.9,221.5", + pos="e,4494.1,195.72 3519.6,251.77 3540.1,249.89 3561.4,248.19 3581.4,247 3675.6,241.41 4339.6,254.75 4430.4,229 4450.1,223.41 4469.9,\ +212.14 4485.5,201.71", style=solid]; "subject derivative qualifier" [height=0.5, - pos="4962.4,178", + pos="4777.4,178", width=3.7733]; "chemical affects gene association" -> "subject derivative qualifier" [color=blue, label="subject derivative qualifier", - lp="4963.9,221.5", - pos="e,4922.5,195.26 3704.1,251.75 3724.8,249.86 3746.2,248.16 3766.4,247 3881.7,240.38 4691.5,247.72 4805.4,229 4842.3,222.93 4882.5,\ -210.01 4913,198.82", + lp="4778.9,221.5", + pos="e,4737.5,195.26 3519.1,251.75 3539.8,249.86 3561.2,248.16 3581.4,247 3696.7,240.38 4506.5,247.72 4620.4,229 4657.3,222.93 4697.5,\ +210.01 4728,198.82", style=solid]; "subject aspect qualifier" [height=0.5, - pos="5235.4,178", + pos="5050.4,178", width=3.3039]; "chemical affects gene association" -> "subject aspect qualifier" [color=blue, label="subject aspect qualifier", - lp="5214.9,221.5", - pos="e,5192.9,194.92 3704.1,251.69 3724.8,249.81 3746.2,248.12 3766.4,247 3910.4,238.98 4921.8,250.44 5064.4,229 5105.2,222.87 5149.9,\ -209.56 5183.3,198.22", + lp="5029.9,221.5", + pos="e,5007.9,194.92 3519.1,251.69 3539.8,249.81 3561.2,248.12 3581.4,247 3725.4,238.98 4736.8,250.44 4879.4,229 4920.2,222.87 4964.9,\ +209.56 4998.3,198.22", style=solid]; "subject context qualifier" [height=0.5, - pos="5495.4,178", + pos="5310.4,178", width=3.4303]; "chemical affects gene association" -> "subject context qualifier" [color=blue, label="subject context qualifier", - lp="5465.4,221.5", - pos="e,5448,194.69 3703.7,251.7 3724.5,249.8 3746.1,248.11 3766.4,247 3936.8,237.69 5133.2,251.57 5302.4,229 5348.8,222.8 5400.2,209.17 \ -5438.2,197.71", + lp="5280.4,221.5", + pos="e,5263,194.69 3518.7,251.7 3539.5,249.8 3561.1,248.11 3581.4,247 3751.8,237.69 4948.2,251.57 5117.4,229 5163.8,222.8 5215.2,209.17 \ +5253.2,197.71", style=solid]; "subject direction qualifier" [height=0.5, - pos="5766.4,178", + pos="5581.4,178", width=3.6108]; "chemical affects gene association" -> "subject direction qualifier" [color=blue, label="subject direction qualifier", - lp="5730.4,221.5", - pos="e,5715.2,194.59 3703.7,251.67 3724.5,249.78 3746.1,248.09 3766.4,247 3965,236.32 5359,253.19 5556.4,229 5607.4,222.76 5663.9,208.87 \ -5705.5,197.32", + lp="5545.4,221.5", + pos="e,5530.2,194.59 3518.7,251.67 3539.5,249.78 3561.1,248.09 3581.4,247 3780,236.32 5174,253.19 5371.4,229 5422.4,222.76 5478.9,208.87 \ +5520.5,197.32", style=solid]; "object form or variant qualifier" [height=0.5, - pos="6068.4,178", + pos="5883.4,178", width=4.2788]; "chemical affects gene association" -> "object form or variant qualifier" [color=blue, label="object form or variant qualifier", - lp="6030.9,221.5", - pos="e,6008.7,194.72 3703.7,251.65 3724.5,249.76 3746.1,248.08 3766.4,247 3995,234.86 5598.8,253.27 5826.4,229 5885.1,222.74 5950.7,208.74 \ -5998.8,197.15", + lp="5845.9,221.5", + pos="e,5823.7,194.72 3518.7,251.65 3539.5,249.76 3561.1,248.08 3581.4,247 3810,234.86 5413.8,253.27 5641.4,229 5700.1,222.74 5765.7,208.74 \ +5813.8,197.15", style=solid]; "object part qualifier" [height=0.5, - pos="6343.4,178", + pos="6158.4,178", width=2.8525]; "chemical affects gene association" -> "object part qualifier" [color=blue, label="object part qualifier", - lp="6294.4,221.5", - pos="e,6296.8,194.14 3703.7,251.63 3724.5,249.74 3746.1,248.07 3766.4,247 4030.4,233.13 5883.2,262.6 6145.4,229 6194,222.77 6247.9,208.68 \ -6287.1,197.04", + lp="6109.4,221.5", + pos="e,6111.8,194.14 3518.7,251.63 3539.5,249.74 3561.1,248.07 3581.4,247 3845.4,233.13 5698.2,262.6 5960.4,229 6009,222.77 6062.9,208.68 \ +6102.1,197.04", style=solid]; "object aspect qualifier" [height=0.5, - pos="6577.4,178", + pos="6392.4,178", width=3.1594]; "chemical affects gene association" -> "object aspect qualifier" [color=blue, label="object aspect qualifier", - lp="6529.9,221.5", - pos="e,6528,194.27 3703.7,251.62 3724.5,249.73 3746.1,248.06 3766.4,247 4055.2,231.92 6082.3,264.03 6369.4,229 6420.4,222.77 6477.1,208.67 \ -6518.3,197.02", + lp="6344.9,221.5", + pos="e,6343,194.27 3518.7,251.62 3539.5,249.73 3561.1,248.06 3581.4,247 3870.2,231.92 5897.3,264.03 6184.4,229 6235.4,222.77 6292.1,208.67 \ +6333.3,197.02", style=solid]; "object context qualifier" [height=0.5, - pos="6827.4,178", + pos="6642.4,178", width=3.2858]; "chemical affects gene association" -> "object context qualifier" [color=blue, label="object context qualifier", - lp="6780.4,221.5", - pos="e,6776.5,194.28 3703.2,251.65 3724.2,249.75 3745.9,248.06 3766.4,247 4082.3,230.6 6299.3,266.22 6613.4,229 6665.8,222.79 6724.1,\ -208.68 6766.6,197.03", + lp="6595.4,221.5", + pos="e,6591.5,194.28 3518.2,251.65 3539.2,249.75 3560.9,248.06 3581.4,247 3897.3,230.6 6114.3,266.22 6428.4,229 6480.8,222.79 6539.1,\ +208.68 6581.6,197.03", style=solid]; "causal mechanism qualifier" [height=0.5, - pos="7100.4,178", + pos="6915.4,178", width=3.8094]; "chemical affects gene association" -> "causal mechanism qualifier" [color=blue, label="causal mechanism qualifier", - lp="7055.9,221.5", - pos="e,7044,194.52 3703.2,251.64 3724.2,249.74 3745.9,248.06 3766.4,247 4110.5,229.23 6524.9,266.34 6867.4,229 6924.3,222.8 6987.7,208.7 \ -7034,197.04", + lp="6870.9,221.5", + pos="e,6859,194.52 3518.2,251.64 3539.2,249.74 3560.9,248.06 3581.4,247 3925.5,229.23 6339.9,266.34 6682.4,229 6739.3,222.8 6802.7,208.7 \ +6849,197.04", style=solid]; "anatomical context qualifier" [height=0.5, - pos="7396.4,178", + pos="7211.4,178", width=3.8997]; "chemical affects gene association" -> "anatomical context qualifier" [color=blue, label="anatomical context qualifier", - lp="7350.4,221.5", - pos="e,7338.5,194.53 3703.2,251.63 3724.2,249.73 3745.9,248.05 3766.4,247 3954.5,237.33 6970.1,248.89 7157.4,229 7215.8,222.8 7281.1,\ -208.65 7328.6,196.98", + lp="7165.4,221.5", + pos="e,7153.5,194.53 3518.2,251.63 3539.2,249.73 3560.9,248.05 3581.4,247 3769.5,237.33 6785.1,248.89 6972.4,229 7030.8,222.8 7096.1,\ +208.65 7143.6,196.98", style=solid]; "qualified predicate" [height=0.5, - pos="7652.4,178", + pos="7467.4,178", width=2.7081]; "chemical affects gene association" -> "qualified predicate" [color=blue, label="qualified predicate", - lp="7599.4,221.5", - pos="e,7606.6,193.94 3703.2,251.63 3724.2,249.72 3745.9,248.05 3766.4,247 3971,236.53 7251.1,254.77 7454.4,229 7503.4,222.79 7557.6,208.55 \ -7596.9,196.85", + lp="7414.4,221.5", + pos="e,7421.6,193.94 3518.2,251.63 3539.2,249.72 3560.9,248.05 3581.4,247 3786,236.53 7066.1,254.77 7269.4,229 7318.4,222.79 7372.6,208.55 \ +7411.9,196.85", style=solid]; subject [height=0.5, - pos="7812.4,178", + pos="7627.4,178", width=1.2277]; "chemical affects gene association" -> subject [color=blue, label=subject, - lp="7752.4,221.5", - pos="e,7784.3,192.04 3703.2,251.62 3724.2,249.72 3745.9,248.04 3766.4,247 3874.7,241.47 7563.5,247.52 7670.4,229 7707,222.65 7746.8,207.92 \ -7774.9,196.09", + lp="7567.4,221.5", + pos="e,7599.3,192.04 3518.2,251.62 3539.2,249.72 3560.9,248.04 3581.4,247 3689.7,241.47 7378.5,247.52 7485.4,229 7522,222.65 7561.8,207.92 \ +7589.9,196.09", style=solid]; predicate [height=0.5, - pos="7929.4,178", + pos="7744.4,178", width=1.5165]; "chemical affects gene association" -> predicate [color=blue, label=predicate, - lp="7874.4,221.5", - pos="e,7898.3,192.86 3703.2,251.62 3724.2,249.72 3745.9,248.04 3766.4,247 3877.8,241.32 7672.4,247.45 7782.4,229 7819.5,222.77 7859.9,\ -208.45 7888.9,196.72", + lp="7689.4,221.5", + pos="e,7713.3,192.86 3518.2,251.62 3539.2,249.72 3560.9,248.04 3581.4,247 3692.8,241.32 7487.4,247.45 7597.4,229 7634.5,222.77 7674.9,\ +208.45 7703.9,196.72", style=solid]; object [height=0.5, - pos="7879.4,91", + pos="7694.4,91", width=1.0832]; "chemical affects gene association" -> object [color=blue, label=object, - lp="8022.4,178", - pos="e,7908.9,102.76 3703.2,251.62 3724.2,249.72 3745.9,248.04 3766.4,247 3881.4,241.14 7799.4,251.38 7912.4,229 7950.5,221.44 7971.7,\ -228.26 7993.4,196 8018.8,158.28 7960.4,124.88 7918.2,106.64", + lp="7837.4,178", + pos="e,7723.9,102.76 3518.2,251.62 3539.2,249.72 3560.9,248.04 3581.4,247 3696.4,241.14 7614.4,251.38 7727.4,229 7765.5,221.44 7786.7,\ +228.26 7808.4,196 7833.8,158.28 7775.4,124.88 7733.2,106.64", style=solid]; "object direction qualifier" [height=0.5, - pos="8207.4,178", + pos="8022.4,178", width=3.4664]; "chemical affects gene association" -> "object direction qualifier" [color=blue, label="object direction qualifier", - lp="8190.4,221.5", - pos="e,8164.8,194.92 3703.2,251.61 3724.2,249.71 3745.9,248.04 3766.4,247 4003.2,234.96 7799.7,262.74 8034.4,229 8075.8,223.05 8121.2,\ -209.66 8155.1,198.23", + lp="8005.4,221.5", + pos="e,7979.8,194.92 3518.2,251.61 3539.2,249.71 3560.9,248.04 3581.4,247 3818.2,234.96 7614.7,262.74 7849.4,229 7890.8,223.05 7936.2,\ +209.66 7970.1,198.23", style=solid]; "species context qualifier" [height=0.5, - pos="8474.4,178", + pos="8289.4,178", width=3.4483]; "chemical affects gene association" -> "species context qualifier" [color=blue, label="species context qualifier", - lp="8443.9,221.5", - pos="e,8427.3,194.8 3703.2,251.61 3724.2,249.71 3745.9,248.04 3766.4,247 4017,234.29 8033.6,261.37 8282.4,229 8328.6,222.98 8379.7,209.34 \ -8417.5,197.83", + lp="8258.9,221.5", + pos="e,8242.3,194.8 3518.2,251.61 3539.2,249.71 3560.9,248.04 3581.4,247 3832,234.29 7848.6,261.37 8097.4,229 8143.6,222.98 8194.7,209.34 \ +8232.5,197.83", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3813.4,265", + pos="3628.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3944.4,265", + pos="3759.4,265", width=2.0762]; "chemical affects gene association_subject form or variant qualifier" [color=blue, height=0.5, label=ChemicalOrGeneOrGeneProductFormOrVariantEnum, - pos="4295.4,265", + pos="4110.4,265", width=7.1855]; "chemical affects gene association_subject part qualifier" [color=blue, height=0.5, label=GeneOrGeneProductOrChemicalPartQualifierEnum, - pos="4820.4,265", + pos="4635.4,265", width=6.8966]; "chemical affects gene association_subject derivative qualifier" [color=blue, height=0.5, label=ChemicalEntityDerivativeEnum, - pos="5244.4,265", + pos="5059.4,265", width=4.3871]; "chemical affects gene association_subject aspect qualifier" [color=blue, height=0.5, label=GeneOrGeneProductOrChemicalPartQualifierEnum, - pos="5668.4,265", + pos="5483.4,265", width=6.8966]; "chemical affects gene association_subject context qualifier" [color=blue, height=0.5, label="anatomical entity", - pos="6026.4,265", + pos="5841.4,265", width=2.5456]; "chemical affects gene association_subject direction qualifier" [color=blue, height=0.5, label=DirectionQualifierEnum, - pos="6257.4,265", + pos="6072.4,265", width=3.358]; "chemical affects gene association_object form or variant qualifier" [color=blue, height=0.5, label=ChemicalOrGeneOrGeneProductFormOrVariantEnum, - pos="6655.4,265", + pos="6470.4,265", width=7.1855]; "chemical affects gene association_object part qualifier" [color=blue, height=0.5, label=GeneOrGeneProductOrChemicalPartQualifierEnum, - pos="7180.4,265", + pos="6995.4,265", width=6.8966]; "chemical affects gene association_object aspect qualifier" [color=blue, height=0.5, label=GeneOrGeneProductOrChemicalPartQualifierEnum, - pos="7695.4,265", + pos="7510.4,265", width=6.8966]; "chemical affects gene association_object context qualifier" [color=blue, height=0.5, label="anatomical entity", - pos="8053.4,265", + pos="7868.4,265", width=2.5456]; "chemical affects gene association_causal mechanism qualifier" [color=blue, height=0.5, label=CausalMechanismQualifierEnum, - pos="8325.4,265", + pos="8140.4,265", width=4.5135]; "chemical affects gene association_anatomical context qualifier" [color=blue, height=0.5, label="anatomical entity", - pos="8597.4,265", + pos="8412.4,265", width=2.5456]; "chemical affects gene association_qualified predicate" [color=blue, height=0.5, label=string, - pos="8745.4,265", + pos="8560.4,265", width=1.0652]; subject -> object [label=relation, - lp="7878.4,134.5", - pos="e,7866.7,108.05 7825.3,160.61 7835.3,147.95 7849.3,130.24 7860.5,115.98"]; + lp="7693.4,134.5", + pos="e,7681.7,108.05 7640.3,160.61 7650.3,147.95 7664.3,130.24 7675.5,115.98"]; relation [height=0.5, - pos="7824.4,18", + pos="7639.4,18", width=1.2999]; - subject -> relation [pos="e,7823.1,36.188 7813.7,159.79 7815.8,132.48 7819.8,78.994 7822.3,46.38", + subject -> relation [pos="e,7638.1,36.188 7628.7,159.79 7630.8,132.48 7634.8,78.994 7637.3,46.38", style=dotted]; "chemical affects gene association_subject" [color=blue, height=0.5, label="chemical entity", - pos="8883.4,265", + pos="8698.4,265", width=2.2748]; "chemical affects gene association_predicate" [color=blue, height=0.5, label="predicate type", - pos="9061.4,265", + pos="8876.4,265", width=2.1665]; - object -> relation [pos="e,7837.2,35.54 7866.9,73.889 7860,64.939 7851.2,53.617 7843.4,43.584", + object -> relation [pos="e,7652.2,35.54 7681.9,73.889 7675,64.939 7666.2,53.617 7658.4,43.584", style=dotted]; "chemical affects gene association_object" [color=blue, height=0.5, label="gene or gene product", - pos="9267.4,265", + pos="9082.4,265", width=3.0692]; "chemical affects gene association_object direction qualifier" [color=blue, height=0.5, label=DirectionQualifierEnum, - pos="9516.4,265", + pos="9331.4,265", width=3.358]; "chemical affects gene association_species context qualifier" [color=blue, height=0.5, label="organism taxon", - pos="9738.4,265", + pos="9553.4,265", width=2.3109]; } diff --git a/graphviz/chemical_affects_gene_association.svg b/graphviz/chemical_affects_gene_association.svg index 5611c2887b..39550f4d4f 100644 --- a/graphviz/chemical_affects_gene_association.svg +++ b/graphviz/chemical_affects_gene_association.svg @@ -4,16 +4,16 @@ - + %3 - + chemical affects gene association - -chemical affects gene association + +chemical affects gene association @@ -24,8 +24,8 @@ chemical affects gene association->association - - + + is_a @@ -37,9 +37,9 @@ chemical affects gene association->id - - -id + + +id @@ -50,9 +50,9 @@ chemical affects gene association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ chemical affects gene association->name - - -name + + +name @@ -76,9 +76,9 @@ chemical affects gene association->description - - -description + + +description @@ -89,9 +89,9 @@ chemical affects gene association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ chemical affects gene association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ chemical affects gene association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ chemical affects gene association->publications - - -publications + + +publications @@ -141,648 +141,648 @@ chemical affects gene association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string chemical affects gene association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string chemical affects gene association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string chemical affects gene association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type chemical affects gene association->timepoint - - -timepoint + + +timepoint original subject - -string + +string chemical affects gene association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie chemical affects gene association->original predicate - - -original predicate + + +original predicate original object - -string + +string chemical affects gene association->original object - - -original object + + +original object subject category - -ontology class + +ontology class chemical affects gene association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class chemical affects gene association->object category - - -object category + + +object category subject closure - -string + +string chemical affects gene association->subject closure - - -subject closure + + +subject closure object closure - -string + +string chemical affects gene association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class chemical affects gene association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class chemical affects gene association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string chemical affects gene association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string chemical affects gene association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string chemical affects gene association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string chemical affects gene association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source chemical affects gene association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type chemical affects gene association->type - - -type + + +type category - -category + +category chemical affects gene association->category - - -category + + +category subject form or variant qualifier - -subject form or variant qualifier + +subject form or variant qualifier chemical affects gene association->subject form or variant qualifier - - -subject form or variant qualifier + + +subject form or variant qualifier subject part qualifier - -subject part qualifier + +subject part qualifier chemical affects gene association->subject part qualifier - - -subject part qualifier + + +subject part qualifier subject derivative qualifier - -subject derivative qualifier + +subject derivative qualifier chemical affects gene association->subject derivative qualifier - - -subject derivative qualifier + + +subject derivative qualifier subject aspect qualifier - -subject aspect qualifier + +subject aspect qualifier chemical affects gene association->subject aspect qualifier - - -subject aspect qualifier + + +subject aspect qualifier subject context qualifier - -subject context qualifier + +subject context qualifier chemical affects gene association->subject context qualifier - - -subject context qualifier + + +subject context qualifier subject direction qualifier - -subject direction qualifier + +subject direction qualifier chemical affects gene association->subject direction qualifier - - -subject direction qualifier + + +subject direction qualifier object form or variant qualifier - -object form or variant qualifier + +object form or variant qualifier chemical affects gene association->object form or variant qualifier - - -object form or variant qualifier + + +object form or variant qualifier object part qualifier - -object part qualifier + +object part qualifier chemical affects gene association->object part qualifier - - -object part qualifier + + +object part qualifier object aspect qualifier - -object aspect qualifier + +object aspect qualifier chemical affects gene association->object aspect qualifier - - -object aspect qualifier + + +object aspect qualifier object context qualifier - -object context qualifier + +object context qualifier chemical affects gene association->object context qualifier - - -object context qualifier + + +object context qualifier causal mechanism qualifier - -causal mechanism qualifier + +causal mechanism qualifier chemical affects gene association->causal mechanism qualifier - - -causal mechanism qualifier + + +causal mechanism qualifier anatomical context qualifier - -anatomical context qualifier + +anatomical context qualifier chemical affects gene association->anatomical context qualifier - - -anatomical context qualifier + + +anatomical context qualifier qualified predicate - -qualified predicate + +qualified predicate chemical affects gene association->qualified predicate - - -qualified predicate + + +qualified predicate subject - -subject + +subject chemical affects gene association->subject - - -subject + + +subject predicate - -predicate + +predicate chemical affects gene association->predicate - - -predicate + + +predicate object - -object + +object chemical affects gene association->object - - -object + + +object object direction qualifier - -object direction qualifier + +object direction qualifier chemical affects gene association->object direction qualifier - - -object direction qualifier + + +object direction qualifier species context qualifier - -species context qualifier + +species context qualifier chemical affects gene association->species context qualifier - - -species context qualifier + + +species context qualifier association_type - -string + +string association_category - -category type + +category type chemical affects gene association_subject form or variant qualifier - -ChemicalOrGeneOrGeneProductFormOrVariantEnum + +ChemicalOrGeneOrGeneProductFormOrVariantEnum chemical affects gene association_subject part qualifier - -GeneOrGeneProductOrChemicalPartQualifierEnum + +GeneOrGeneProductOrChemicalPartQualifierEnum chemical affects gene association_subject derivative qualifier - -ChemicalEntityDerivativeEnum + +ChemicalEntityDerivativeEnum chemical affects gene association_subject aspect qualifier - -GeneOrGeneProductOrChemicalPartQualifierEnum + +GeneOrGeneProductOrChemicalPartQualifierEnum chemical affects gene association_subject context qualifier - -anatomical entity + +anatomical entity chemical affects gene association_subject direction qualifier - -DirectionQualifierEnum + +DirectionQualifierEnum chemical affects gene association_object form or variant qualifier - -ChemicalOrGeneOrGeneProductFormOrVariantEnum + +ChemicalOrGeneOrGeneProductFormOrVariantEnum chemical affects gene association_object part qualifier - -GeneOrGeneProductOrChemicalPartQualifierEnum + +GeneOrGeneProductOrChemicalPartQualifierEnum chemical affects gene association_object aspect qualifier - -GeneOrGeneProductOrChemicalPartQualifierEnum + +GeneOrGeneProductOrChemicalPartQualifierEnum chemical affects gene association_object context qualifier - -anatomical entity + +anatomical entity chemical affects gene association_causal mechanism qualifier - -CausalMechanismQualifierEnum + +CausalMechanismQualifierEnum chemical affects gene association_anatomical context qualifier - -anatomical entity + +anatomical entity chemical affects gene association_qualified predicate - -string + +string subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + chemical affects gene association_subject - -chemical entity + +chemical entity chemical affects gene association_predicate - -predicate type + +predicate type object->relation - - + + chemical affects gene association_object - -gene or gene product + +gene or gene product chemical affects gene association_object direction qualifier - -DirectionQualifierEnum + +DirectionQualifierEnum chemical affects gene association_species context qualifier - -organism taxon + +organism taxon diff --git a/graphviz/chemical_entity_assesses_named_thing_association.gv b/graphviz/chemical_entity_assesses_named_thing_association.gv index 21abfc1ba7..d91b3ff806 100644 --- a/graphviz/chemical_entity_assesses_named_thing_association.gv +++ b/graphviz/chemical_entity_assesses_named_thing_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4748,283"]; + graph [bb="0,0,4563,283"]; node [label="\N"]; "chemical entity assesses named thing association" [height=0.5, label="chemical entity assesses named thing association", - pos="2468.4,265", + pos="2283.4,265", width=6.698]; association [height=0.5, pos="62.394,178", width=1.7332]; "chemical entity assesses named thing association" -> association [label=is_a, lp="280.39,221.5", - pos="e,102.91,191.79 2228.1,263.23 1697.2,261.07 456.29,253.47 266.39,229 213.1,222.13 153.57,206.61 112.64,194.66"]; + pos="e,102.91,191.77 2043.8,262.84 1547.4,260 438.05,251.24 266.39,229 213.11,222.1 153.58,206.57 112.65,194.64"]; id [color=blue, height=0.5, label=string, @@ -18,8 +18,8 @@ digraph { width=1.0652]; "chemical entity assesses named thing association" -> id [color=blue, label=id, - lp="396.39,221.5", - pos="e,210.38,189.98 2229.2,262.49 1721.5,258.91 567.62,248.7 389.39,229 317.23,221.02 299.34,215.5 229.39,196 226.29,195.13 223.09,194.17 \ + lp="395.39,221.5", + pos="e,210.38,189.98 2045.4,262.08 1573,257.92 548.52,246.94 388.39,229 316.67,220.97 298.9,215.43 229.39,196 226.29,195.13 223.09,194.17 \ 219.89,193.15", style=solid]; iri [color=blue, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "chemical entity assesses named thing association" -> iri [color=blue, label=iri, - lp="509.39,221.5", - pos="e,315.3,190.2 2230.2,262.15 1744,258.01 668.7,246.97 501.39,229 426.6,220.97 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ -325.06,193.15", + lp="501.39,221.5", + pos="e,315.32,190.15 2042.2,264.85 1625.1,265.38 785.84,262.11 493.39,229 422.11,220.93 404.75,214.31 335.39,196 332.02,195.11 328.55,\ +194.13 325.07,193.11", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "chemical entity assesses named thing association" -> name [color=blue, label=name, - lp="616.39,221.5", - pos="e,439.35,191.54 2229.2,262.62 1760.6,259.47 753.68,250.29 596.39,229 545.26,222.08 488.24,206.51 449.14,194.57", + lp="604.39,221.5", + pos="e,437.98,191.87 2044.6,262.34 1610.7,258.83 724.59,249.28 584.39,229 537.02,222.15 484.46,206.96 447.86,195.11", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "chemical entity assesses named thing association" -> description [color=blue, label=description, - lp="736.89,221.5", - pos="e,585.45,194.14 2228,263.41 1778.5,261.7 842.8,255.02 696.39,229 661.33,222.77 623.33,209.4 595.03,198.06", + lp="717.89,221.5", + pos="e,581.77,194.62 2042.9,263.46 1627.4,261.82 807.1,255.26 677.39,229 647.36,222.92 615.28,210.09 591.01,198.95", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "chemical entity assesses named thing association" -> "has attribute" [color=blue, label="has attribute", - lp="882.39,221.5", - pos="e,725.98,192.82 2228.5,263.13 1807.6,260.98 968.18,253.63 835.39,229 800.43,222.52 762.57,208.39 735.2,196.8", + lp="852.39,221.5", + pos="e,721.33,194.01 2042.7,263.62 1654.6,262.2 922.12,255.95 805.39,229 778.89,222.88 751.04,209.98 730.13,198.82", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "chemical entity assesses named thing association" -> negated [color=blue, label=negated, - lp="1038.4,221.5", - pos="e,847.59,190.46 2227.2,264.23 1875.1,263.53 1237.4,258.1 1009.4,229 956.09,222.2 896.47,205.66 857.14,193.46", + lp="990.39,221.5", + pos="e,843.03,191.96 2046.4,261.56 1694.6,257.36 1064.7,247.39 961.39,229 923.37,222.23 881.85,207.52 852.5,195.8", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "chemical entity assesses named thing association" -> qualifiers [color=blue, label=qualifiers, - lp="1178.9,221.5", - pos="e,996.68,193.07 2227.4,264.24 1904.1,263.42 1347.1,257.68 1145.4,229 1097.6,222.2 1044.5,207.74 1006.5,196.11", + lp="1101.9,221.5", + pos="e,982.4,194.93 2045.4,262.03 1718.6,258.58 1160.6,249.72 1068.4,229 1041.6,222.97 1013.3,210.59 991.57,199.66", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "chemical entity assesses named thing association" -> publications [color=blue, label=publications, - lp="1326.4,221.5", - pos="e,1148.1,192.71 2227.5,264.12 1934.7,263 1457.8,256.76 1282.4,229 1239.3,222.18 1191.8,207.69 1157.8,196.06", + lp="1202.4,221.5", + pos="e,1121.9,195.78 2047.4,261.25 1729.4,256.87 1198.1,246.93 1158.4,229 1146.3,223.57 1135.9,213.45 1128,203.73", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,274 +100,274 @@ digraph { width=2.0943]; "chemical entity assesses named thing association" -> "has evidence" [color=blue, label="has evidence", - lp="1480.9,221.5", - pos="e,1305.9,193.61 2228.5,262.99 1971.7,260.65 1581.3,253.07 1434.4,229 1393.5,222.3 1348.6,208.48 1315.7,197.06", + lp="1300.9,221.5", + pos="e,1255.9,195.88 2042.3,264.13 1746.7,263.07 1281.4,256.94 1254.4,229 1248.2,222.63 1248.8,213.73 1251.7,205.2", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1469.4,178", - width=3.015]; + label=string, + pos="1399.4,178", + width=1.0652]; "chemical entity assesses named thing association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1635.9,221.5", - pos="e,1495.5,195.59 2237,259.94 1992.6,254.85 1634.1,244.84 1571.4,229 1547.9,223.07 1523.5,211.31 1504.4,200.68", + lp="1419.9,221.5", + pos="e,1375.2,192.24 2043.5,263.13 1776.5,260.94 1379,253.55 1355.4,229 1345.9,219.09 1354.7,207.6 1366.9,198.13", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1704.4,178", - width=3.015]; + label=string, + pos="1494.4,178", + width=1.0652]; "chemical entity assesses named thing association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1807.4,221.5", - pos="e,1702.1,196.41 2235.7,260.28 2020.8,255.75 1731.9,246.46 1712.4,229 1706.1,223.34 1703.4,214.82 1702.5,206.41", + lp="1589.4,221.5", + pos="e,1489,196.04 2047,261.37 1821.6,257.67 1513.5,248.97 1494.4,229 1488.6,222.94 1487.2,214.32 1487.7,205.94", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1939.4,178", - width=3.015]; + label=string, + pos="1669.4,178", + width=1.0652]; "chemical entity assesses named thing association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2015.9,221.5", - pos="e,1918.7,195.97 2250.7,257.2 2098.9,251.35 1921.5,241.83 1909.4,229 1902.4,221.54 1905.6,212.18 1912,203.58", + lp="1809.9,221.5", + pos="e,1676.1,196.02 2052.6,259.69 1904.4,255.27 1734.1,246.43 1703.4,229 1693.8,223.55 1686.4,214.16 1680.9,204.98", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2121.4,178", + pos="1895.4,178", width=1.5346]; "chemical entity assesses named thing association" -> timepoint [color=blue, label=timepoint, - lp="2171.4,221.5", - pos="e,2121.9,196.47 2285.6,253.26 2215.5,247.53 2149,239.47 2136.4,229 2129.6,223.41 2125.9,214.91 2123.8,206.49", + lp="1972.4,221.5", + pos="e,1904.8,195.92 2075.5,255.83 2017.2,250.73 1962.8,242.44 1937.4,229 1926.7,223.32 1917.5,213.63 1910.6,204.28", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2233.4,178", + pos="2007.4,178", width=1.0652]; "chemical entity assesses named thing association" -> "original subject" [color=blue, label="original subject", - lp="2270.4,221.5", - pos="e,2219.6,194.92 2277.2,254.02 2248.3,248.68 2224.6,240.74 2214.4,229 2208.1,221.83 2209.9,212.39 2214.3,203.65", + lp="2076.4,221.5", + pos="e,2007.3,196.33 2095.9,253.68 2062.2,248.45 2033.5,240.64 2020.4,229 2013.9,223.25 2010.5,214.72 2008.7,206.31", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2347.4,178", + pos="2133.4,178", width=1.5887]; "chemical entity assesses named thing association" -> "original predicate" [color=blue, label="original predicate", - lp="2397.9,221.5", - pos="e,2336.3,195.76 2375.5,248.38 2356.5,243.27 2340.5,236.85 2334.4,229 2329.1,222.16 2329.6,213.39 2332.4,205.11", + lp="2207.9,221.5", + pos="e,2132.9,196.42 2190.8,248.36 2170,243.15 2151.8,236.68 2144.4,229 2138.6,222.99 2135.5,214.63 2134,206.47", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2461.4,178", + pos="2267.4,178", width=1.0652]; "chemical entity assesses named thing association" -> "original object" [color=blue, label="original object", - lp="2516.9,221.5", - pos="e,2462.8,196.18 2467,246.8 2466,235.16 2464.7,219.55 2463.6,206.24", + lp="2327.9,221.5", + pos="e,2270.6,196.18 2280.2,246.8 2278,235.16 2275,219.55 2272.5,206.24", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2594.4,178", + pos="2400.4,178", width=2.1304]; "chemical entity assesses named thing association" -> "subject category" [color=blue, label="subject category", - lp="2642.9,221.5", - pos="e,2590.6,196.4 2542.3,247.78 2553.3,243.03 2563.7,236.9 2572.4,229 2579.1,222.84 2583.9,214.24 2587.3,205.9", + lp="2452.9,221.5", + pos="e,2398.4,196.3 2355.6,247.77 2365.8,243.03 2375.6,236.9 2383.4,229 2389.5,222.8 2393.5,214.29 2396,206.04", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2765.4,178", + pos="2571.4,178", width=2.1304]; "chemical entity assesses named thing association" -> "object category" [color=blue, label="object category", - lp="2785.9,221.5", - pos="e,2750.6,195.73 2633.8,251.88 2658.8,246.6 2683.8,239.23 2706.4,229 2720,222.83 2733,212.54 2743.3,202.9", + lp="2593.9,221.5", + pos="e,2557.8,195.72 2447.8,251.78 2471.5,246.48 2495.1,239.14 2516.4,229 2529.3,222.88 2541.3,212.74 2550.8,203.17", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="2898.4,178", + pos="2704.4,178", width=1.0652]; "chemical entity assesses named thing association" -> "subject closure" [color=blue, label="subject closure", - lp="2921.9,221.5", - pos="e,2886,195.51 2645.7,252.76 2734.2,246.21 2826.5,237.56 2845.4,229 2858.3,223.16 2870.1,212.86 2879.2,203.11", + lp="2728.9,221.5", + pos="e,2692.6,195.5 2459.2,252.66 2545.6,246.12 2635,237.54 2653.4,229 2665.9,223.2 2677.1,213.04 2685.8,203.39", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="2998.4,178", + pos="2812.4,178", width=1.0652]; "chemical entity assesses named thing association" -> "object closure" [color=blue, label="object closure", - lp="3042.4,221.5", - pos="e,2996.9,196.19 2640.2,252.32 2788.9,242.21 2980.2,229.16 2980.4,229 2987.7,223.49 2992,214.74 2994.6,206.09", + lp="2851.4,221.5", + pos="e,2808.5,196.34 2455,252.33 2600.7,242.38 2786.5,229.59 2787.4,229 2795.5,223.6 2801.1,214.76 2804.9,206", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3131.4,178", + pos="2945.4,178", width=2.1304]; "chemical entity assesses named thing association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3200.9,221.5", - pos="e,3124.4,196.08 2636.8,252.08 2664.1,250.28 2692,248.53 2718.4,247 2760.4,244.57 3059.6,249.3 3096.4,229 3106.1,223.63 3113.8,214.25 \ -3119.4,205.06", + lp="3010.9,221.5", + pos="e,2936.7,196.13 2451.8,252.1 2479.1,250.3 2507,248.54 2533.4,247 2574.7,244.6 2868.5,247.82 2905.4,229 2916,223.58 2924.7,213.93 \ +2931.3,204.55", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3323.4,178", + pos="3138.4,178", width=2.1304]; "chemical entity assesses named thing association" -> "object category closure" [color=blue, label="object category closure", - lp="3390.9,221.5", - pos="e,3317.7,196.09 2634.1,251.88 2662.2,250.07 2691.1,248.35 2718.4,247 2750.3,245.42 3264.8,244.95 3292.4,229 3301.6,223.69 3308.4,\ -214.46 3313.3,205.36", + lp="3202.9,221.5", + pos="e,3131.1,196.16 2449.1,251.88 2477.2,250.07 2506.1,248.36 2533.4,247 2565,245.43 3074.5,243.86 3102.4,229 3112.4,223.67 3120.3,214.17 \ +3126.1,204.87", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3513.4,178", + pos="3328.4,178", width=1.0652]; "chemical entity assesses named thing association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3563.4,221.5", - pos="e,3506.4,196.18 2632.7,251.79 2661.3,249.96 2690.7,248.27 2718.4,247 2760.6,245.07 3441.2,248.95 3478.4,229 3488.2,223.75 3495.9,\ -214.39 3501.5,205.18", + lp="3375.4,221.5", + pos="e,3320.7,195.72 2447.7,251.79 2476.3,249.96 2505.7,248.27 2533.4,247 2575.4,245.07 3252.9,248.14 3290.4,229 3300.8,223.66 3309.2,\ +213.98 3315.4,204.54", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3672.4,178", + pos="3487.4,178", width=1.0652]; "chemical entity assesses named thing association" -> "object namespace" [color=blue, label="object namespace", - lp="3716.4,221.5", - pos="e,3665,195.73 2631.7,251.75 2660.6,249.92 2690.4,248.23 2718.4,247 2769.3,244.77 3590.1,252.38 3635.4,229 3645.7,223.67 3653.9,213.98 \ -3659.9,204.55", + lp="3529.4,221.5", + pos="e,3479.1,195.76 2446.7,251.76 2475.6,249.92 2505.4,248.23 2533.4,247 2584.1,244.78 3401.8,251.45 3447.4,229 3458.2,223.66 3467.1,\ +213.84 3473.7,204.3", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3823.4,178", + pos="3638.4,178", width=1.0652]; "chemical entity assesses named thing association" -> "subject label closure" [color=blue, label="subject label closure", - lp="3876.4,221.5", - pos="e,3815.4,195.76 2631.4,251.71 2660.4,249.87 2690.3,248.19 2718.4,247 2748,245.74 3757.9,242.22 3784.4,229 3795.1,223.66 3803.8,213.84 \ -3810.2,204.3", + lp="3689.4,221.5", + pos="e,3629.8,195.79 2446.4,251.71 2475.4,249.87 2505.3,248.19 2533.4,247 2592.5,244.49 3544.2,254.74 3597.4,229 3608.4,223.69 3617.4,\ +213.87 3624.2,204.33", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="3994.4,178", + pos="3809.4,178", width=1.0652]; "chemical entity assesses named thing association" -> "object label closure" [color=blue, label="object label closure", - lp="4041.9,221.5", - pos="e,3986.1,195.79 2631,251.68 2660.1,249.84 2690.1,248.17 2718.4,247 2752.7,245.58 3923.6,244.1 3954.4,229 3965.2,223.69 3974.1,213.87 \ -3980.7,204.33", + lp="3856.9,221.5", + pos="e,3800.5,195.81 2446,251.68 2475.1,249.84 2505.1,248.17 2533.4,247 2567.6,245.59 3736.4,243.71 3767.4,229 3778.5,223.71 3787.8,213.9 \ +3794.7,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4147.4,178", + pos="3962.4,178", width=2.347]; "chemical entity assesses named thing association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4200.9,221.5", - pos="e,4141.4,196.18 2630.7,251.66 2659.9,249.81 2690,248.15 2718.4,247 2757.2,245.43 4081.5,247.85 4115.4,229 4124.9,223.74 4131.9,214.39 \ -4137,205.18", + lp="4015.9,221.5", + pos="e,3956.4,196.18 2445.7,251.66 2474.9,249.81 2505,248.15 2533.4,247 2572.2,245.43 3896.5,247.85 3930.4,229 3939.9,223.74 3946.9,214.39 \ +3952,205.18", style=solid]; type [height=0.5, - pos="4281.4,178", + pos="4096.4,178", width=0.86659]; "chemical entity assesses named thing association" -> type [color=blue, label=type, - lp="4299.4,221.5", - pos="e,4284.1,195.98 2630.4,251.65 2659.7,249.8 2689.9,248.13 2718.4,247 2740,246.14 4258.2,243.28 4274.4,229 4280.9,223.32 4283.4,214.65 \ -4284.1,206.11", + lp="4114.4,221.5", + pos="e,4099.1,195.98 2445.4,251.65 2474.7,249.8 2504.9,248.13 2533.4,247 2555,246.14 4073.2,243.28 4089.4,229 4095.9,223.32 4098.4,214.65 \ +4099.1,206.11", style=solid]; category [height=0.5, - pos="4382.4,178", + pos="4197.4,178", width=1.4263]; "chemical entity assesses named thing association" -> category [color=blue, label=category, - lp="4377.9,221.5", - pos="e,4367.7,195.48 2630.4,251.64 2659.7,249.79 2689.9,248.13 2718.4,247 2762.8,245.24 4277.5,243.88 4319.4,229 4334.6,223.59 4349,212.83 \ -4360.1,202.68", + lp="4192.9,221.5", + pos="e,4182.7,195.48 2445.4,251.64 2474.7,249.79 2504.9,248.13 2533.4,247 2577.8,245.24 4092.5,243.88 4134.4,229 4149.6,223.59 4164,212.83 \ +4175.1,202.68", style=solid]; subject [height=0.5, - pos="4496.4,178", + pos="4311.4,178", width=1.2277]; "chemical entity assesses named thing association" -> subject [color=blue, label=subject, - lp="4473.4,221.5", - pos="e,4477.7,194.32 2630.4,251.63 2659.7,249.78 2689.9,248.12 2718.4,247 2812.5,243.3 4322.8,254.7 4413.4,229 4433.6,223.28 4453.7,211.29 \ -4469.2,200.49", + lp="4288.4,221.5", + pos="e,4292.7,194.32 2445.4,251.63 2474.7,249.78 2504.9,248.12 2533.4,247 2627.5,243.3 4137.8,254.7 4228.4,229 4248.6,223.28 4268.7,211.29 \ +4284.2,200.49", style=solid]; object [height=0.5, - pos="4539.4,91", + pos="4354.4,91", width=1.0832]; "chemical entity assesses named thing association" -> object [color=blue, label=object, - lp="4583.4,178", - pos="e,4552.8,108.09 2630,251.64 2659.4,249.78 2689.8,248.11 2718.4,247 2767.9,245.07 4456.3,244.42 4503.4,229 4527.3,221.18 4535.3,216.87 \ -4549.4,196 4563.2,175.52 4559.5,166.51 4562.4,142 4563.2,135.38 4564.3,133.39 4562.4,127 4561.4,123.55 4559.9,120.13 4558.1,116.85", + lp="4398.4,178", + pos="e,4367.8,108.09 2445,251.64 2474.4,249.78 2504.8,248.11 2533.4,247 2582.9,245.07 4271.3,244.42 4318.4,229 4342.3,221.18 4350.3,216.87 \ +4364.4,196 4378.2,175.52 4374.5,166.51 4377.4,142 4378.2,135.38 4379.3,133.39 4377.4,127 4376.4,123.55 4374.9,120.13 4373.1,116.85", style=solid]; predicate [height=0.5, - pos="4693.4,178", + pos="4508.4,178", width=1.5165]; "chemical entity assesses named thing association" -> predicate [color=blue, label=predicate, - lp="4666.4,221.5", - pos="e,4669.6,194.35 2630,251.62 2659.4,249.77 2689.8,248.11 2718.4,247 2822.3,242.97 4489.1,252.79 4590.4,229 4615.3,223.15 4641.2,210.56 \ -4660.8,199.47", + lp="4480.4,221.5", + pos="e,4484.6,194.35 2445,251.62 2474.4,249.77 2504.8,248.11 2533.4,247 2637.3,242.97 4304.1,252.79 4405.4,229 4430.3,223.15 4456.2,210.56 \ +4475.8,199.47", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2765.4,265", + pos="2580.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2896.4,265", + pos="2711.4,265", width=2.0762]; subject -> object [label=relation, - lp="4534.4,134.5", - pos="e,4521.5,107.23 4497.5,159.55 4498.7,149.57 4501.2,137.07 4506.4,127 4508.6,122.68 4511.5,118.52 4514.7,114.66"]; + lp="4349.4,134.5", + pos="e,4336.5,107.23 4312.5,159.55 4313.7,149.57 4316.2,137.07 4321.4,127 4323.6,122.68 4326.5,118.52 4329.7,114.66"]; relation [height=0.5, - pos="4484.4,18", + pos="4299.4,18", width=1.2999]; - subject -> relation [pos="e,4485.7,36.188 4495.1,159.79 4493,132.48 4489,78.994 4486.5,46.38", + subject -> relation [pos="e,4300.7,36.188 4310.1,159.79 4308,132.48 4304,78.994 4301.5,46.38", style=dotted]; "chemical entity assesses named thing association_subject" [color=blue, height=0.5, label="chemical entity", - pos="3071.4,265", + pos="2886.4,265", width=2.2748]; - object -> relation [pos="e,4497.2,35.54 4526.9,73.889 4520,64.939 4511.2,53.617 4503.4,43.584", + object -> relation [pos="e,4312.2,35.54 4341.9,73.889 4335,64.939 4326.2,53.617 4318.4,43.584", style=dotted]; "chemical entity assesses named thing association_object" [color=blue, height=0.5, label="named thing", - pos="3240.4,265", + pos="3055.4,265", width=1.9318]; "chemical entity assesses named thing association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3406.4,265", + pos="3221.4,265", width=2.1665]; } diff --git a/graphviz/chemical_entity_assesses_named_thing_association.svg b/graphviz/chemical_entity_assesses_named_thing_association.svg index dafec5d9bd..11ae41baed 100644 --- a/graphviz/chemical_entity_assesses_named_thing_association.svg +++ b/graphviz/chemical_entity_assesses_named_thing_association.svg @@ -4,16 +4,16 @@ - + %3 - + chemical entity assesses named thing association - -chemical entity assesses named thing association + +chemical entity assesses named thing association @@ -24,8 +24,8 @@ chemical entity assesses named thing association->association - - + + is_a @@ -37,9 +37,9 @@ chemical entity assesses named thing association->id - - -id + + +id @@ -50,9 +50,9 @@ chemical entity assesses named thing association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ chemical entity assesses named thing association->name - - -name + + +name @@ -76,9 +76,9 @@ chemical entity assesses named thing association->description - - -description + + +description @@ -89,9 +89,9 @@ chemical entity assesses named thing association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ chemical entity assesses named thing association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ chemical entity assesses named thing association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ chemical entity assesses named thing association->publications - - -publications + + +publications @@ -141,363 +141,363 @@ chemical entity assesses named thing association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string chemical entity assesses named thing association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string chemical entity assesses named thing association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string chemical entity assesses named thing association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type chemical entity assesses named thing association->timepoint - - -timepoint + + +timepoint original subject - -string + +string chemical entity assesses named thing association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie chemical entity assesses named thing association->original predicate - - -original predicate + + +original predicate original object - -string + +string chemical entity assesses named thing association->original object - - -original object + + +original object subject category - -ontology class + +ontology class chemical entity assesses named thing association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class chemical entity assesses named thing association->object category - - -object category + + +object category subject closure - -string + +string chemical entity assesses named thing association->subject closure - - -subject closure + + +subject closure object closure - -string + +string chemical entity assesses named thing association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class chemical entity assesses named thing association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class chemical entity assesses named thing association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string chemical entity assesses named thing association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string chemical entity assesses named thing association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string chemical entity assesses named thing association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string chemical entity assesses named thing association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source chemical entity assesses named thing association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type chemical entity assesses named thing association->type - - -type + + +type category - -category + +category chemical entity assesses named thing association->category - - -category + + +category subject - -subject + +subject chemical entity assesses named thing association->subject - - -subject + + +subject object - -object + +object chemical entity assesses named thing association->object - - -object + + +object predicate - -predicate + +predicate chemical entity assesses named thing association->predicate - - -predicate + + +predicate association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + chemical entity assesses named thing association_subject - -chemical entity + +chemical entity object->relation - - + + chemical entity assesses named thing association_object - -named thing + +named thing chemical entity assesses named thing association_predicate - -predicate type + +predicate type diff --git a/graphviz/chemical_entity_or_gene_or_gene_product_regulates_gene_association.gv b/graphviz/chemical_entity_or_gene_or_gene_product_regulates_gene_association.gv index f757588143..774730e682 100644 --- a/graphviz/chemical_entity_or_gene_or_gene_product_regulates_gene_association.gv +++ b/graphviz/chemical_entity_or_gene_or_gene_product_regulates_gene_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4996.4,283"]; + graph [bb="0,0,4811.4,283"]; node [label="\N"]; "chemical entity or gene or gene product regulates gene association" [height=0.5, label="chemical entity or gene or gene product regulates gene association", - pos="2531.4,265", + pos="2346.4,265", width=8.9909]; association [height=0.5, pos="62.394,178", width=1.7332]; "chemical entity or gene or gene product regulates gene association" -> association [label=is_a, lp="280.39,221.5", - pos="e,102.91,191.8 2209.5,263.03 1629.8,260.7 453.29,253.04 266.39,229 213.1,222.15 153.57,206.62 112.64,194.67"]; + pos="e,102.91,191.78 2025.6,262.54 1485.2,259.5 435.35,250.85 266.39,229 213.11,222.11 153.58,206.59 112.65,194.65"]; id [color=blue, height=0.5, label=string, @@ -19,8 +19,8 @@ digraph { "chemical entity or gene or gene product regulates gene association" -> id [color=blue, label=id, lp="395.39,221.5", - pos="e,210.38,189.98 2211.7,262.1 1658.3,258.32 563.98,248.48 388.39,229 316.66,221.04 298.9,215.43 229.39,196 226.29,195.13 223.09,194.17 \ -219.89,193.15", + pos="e,210.38,189.98 2028.5,261.57 1515.4,257.16 546.12,246.62 388.39,229 316.67,220.99 298.9,215.43 229.39,196 226.29,195.13 223.09,\ +194.17 219.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "chemical entity or gene or gene product regulates gene association" -> iri [color=blue, label=iri, - lp="508.39,221.5", - pos="e,315.3,190.19 2213.3,261.67 1684.3,257.32 665.27,246.76 500.39,229 426.04,220.99 407.78,214.78 335.39,196 332.02,195.12 328.54,\ -194.16 325.06,193.14", + lp="501.39,221.5", + pos="e,315.32,190.15 2029.5,261.24 1540.1,256.5 641.02,245.66 493.39,229 422.11,220.95 404.75,214.31 335.39,196 332.02,195.11 328.55,\ +194.13 325.07,193.11", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "chemical entity or gene or gene product regulates gene association" -> name [color=blue, label=name, - lp="615.39,221.5", - pos="e,439.15,191.54 2211.3,262.31 1702.4,259 750.31,250.07 595.39,229 544.62,222.09 488.03,206.58 449.14,194.65", + lp="604.39,221.5", + pos="e,437.98,191.87 2027.3,261.92 1558.1,258.22 722.46,248.92 584.39,229 537.02,222.16 484.45,206.98 447.86,195.12", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "chemical entity or gene or gene product regulates gene association" -> description [color=blue, label=description, - lp="735.89,221.5", - pos="e,585.2,194.15 2208.7,263.36 1721.5,261.55 839.47,254.72 695.39,229 660.55,222.78 622.82,209.42 594.72,198.07", + lp="717.89,221.5", + pos="e,581.52,194.51 2023.9,263.4 1575.7,261.62 805.01,254.78 677.39,229 647.25,222.91 615.06,210.01 590.76,198.84", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "chemical entity or gene or gene product regulates gene association" -> "has attribute" [color=blue, label="has attribute", - lp="881.39,221.5", - pos="e,726.02,192.95 2209.3,263.01 1754.6,260.75 965.08,253.34 834.39,229 799.92,222.58 762.64,208.62 735.52,197.07", + lp="852.39,221.5", + pos="e,721.33,194.01 2023.5,263.63 1606.4,262.07 920.22,255.45 805.39,229 778.88,222.89 751.04,210 730.13,198.83", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "chemical entity or gene or gene product regulates gene association" -> negated [color=blue, label=negated, - lp="1036.4,221.5", - pos="e,847.24,190.46 2207.8,264.53 1830.7,263.75 1230.8,257.75 1007.4,229 954.83,222.23 896.1,205.81 857.18,193.62", + lp="990.39,221.5", + pos="e,843.03,191.97 2030.6,261.01 1654.3,256.67 1063.3,247.07 961.39,229 923.37,222.26 881.85,207.54 852.49,195.81", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "chemical entity or gene or gene product regulates gene association" -> qualifiers [color=blue, label=qualifiers, - lp="1174.9,221.5", - pos="e,996.14,193.2 2207.6,264.66 1862.5,263.79 1339.2,257.52 1141.4,229 1094.7,222.26 1042.9,207.87 1005.7,196.25", + lp="1100.9,221.5", + pos="e,982.13,194.94 2028,261.71 1679.6,258.17 1158.3,249.52 1067.4,229 1040.8,222.99 1012.7,210.61 991.22,199.68", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "chemical entity or gene or gene product regulates gene association" -> publications [color=blue, label=publications, - lp="1320.4,221.5", - pos="e,1147.1,192.85 2207.6,264.73 1896.4,263.65 1448.6,256.98 1276.4,229 1235,222.28 1189.6,207.95 1156.8,196.35", + lp="1201.4,221.5", + pos="e,1121.6,195.78 2031.7,260.77 1692.9,256.38 1196.7,246.94 1157.4,229 1145.6,223.62 1135.5,213.65 1127.7,204.03", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,287 +100,287 @@ digraph { width=2.0943]; "chemical entity or gene or gene product regulates gene association" -> "has evidence" [color=blue, label="has evidence", - lp="1478.9,221.5", - pos="e,1305.4,193.63 2209.5,263.06 1939.7,260.55 1576.3,252.66 1432.4,229 1392,222.35 1347.6,208.52 1315.1,197.09", + lp="1299.9,221.5", + pos="e,1255.4,195.85 2022.6,264.48 1710.1,263.29 1280.1,256.6 1253.4,229 1247.1,222.53 1247.9,213.5 1251.1,204.89", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1469.4,178", - width=3.015]; + label=string, + pos="1399.4,178", + width=1.0652]; "chemical entity or gene or gene product regulates gene association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1633.9,221.5", - pos="e,1494.9,195.61 2224,259.33 1966.7,254.34 1631.7,244.91 1569.4,229 1546.3,223.1 1522.3,211.34 1503.6,200.71", + lp="1418.9,221.5", + pos="e,1375,191.97 2024.3,263.24 1743.6,260.94 1377.8,253.26 1354.4,229 1344.7,218.94 1353.9,207.35 1366.5,197.86", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1704.4,178", - width=3.015]; + label=string, + pos="1494.4,178", + width=1.0652]; "chemical entity or gene or gene product regulates gene association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1805.4,221.5", - pos="e,1701.4,196.33 2220.1,260.02 1995.9,255.65 1729.6,246.76 1710.4,229 1704.3,223.32 1701.9,214.91 1701.3,206.59", + lp="1588.4,221.5", + pos="e,1488.6,196.04 2030.1,261.14 1795.2,257.41 1512.4,248.81 1493.4,229 1487.6,222.94 1486.3,214.33 1487,205.95", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1939.4,178", - width=3.015]; + label=string, + pos="1669.4,178", + width=1.0652]; "chemical entity or gene or gene product regulates gene association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2013.9,221.5", - pos="e,1917.6,195.87 2245.4,256.57 2087.1,251.01 1919.8,242.08 1907.4,229 1900.2,221.43 1903.7,212.05 1910.6,203.46", + lp="1808.9,221.5", + pos="e,1675.8,196.03 2037.4,259.58 1887.3,255.18 1732.8,246.43 1702.4,229 1692.9,223.57 1685.7,214.18 1680.4,204.99", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2121.4,178", + pos="1895.4,178", width=1.5346]; "chemical entity or gene or gene product regulates gene association" -> timepoint [color=blue, label=timepoint, - lp="2168.4,221.5", - pos="e,2120.8,196.43 2282.8,253.46 2210.1,248.14 2146.5,240.32 2133.4,229 2126.9,223.36 2123.5,214.85 2122,206.44", + lp="1971.4,221.5", + pos="e,1904.5,195.99 2066.6,255.92 2010.7,250.64 1961.6,242.25 1936.4,229 1925.7,223.39 1916.8,213.72 1910.1,204.36", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2233.4,178", + pos="2007.4,178", width=1.0652]; "chemical entity or gene or gene product regulates gene association" -> "original subject" [color=blue, label="original subject", - lp="2266.4,221.5", - pos="e,2217.6,194.82 2318.6,251.43 2264.6,246.09 2219.2,238.78 2210.4,229 2203.7,221.56 2206.3,211.86 2211.8,202.98", + lp="2075.4,221.5", + pos="e,2006.8,196.38 2139.8,251.14 2081.1,245.64 2030,238.3 2019.4,229 2012.9,223.3 2009.6,214.78 2008,206.37", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2347.4,178", + pos="2133.4,178", width=1.5887]; "chemical entity or gene or gene product regulates gene association" -> "original predicate" [color=blue, label="original predicate", - lp="2392.9,221.5", - pos="e,2333.6,195.8 2373.3,249.17 2353,244.26 2336.7,237.71 2329.4,229 2323.5,222.05 2324.9,213.06 2328.7,204.62", + lp="2205.9,221.5", + pos="e,2131.9,196.09 2192.5,249.12 2169.8,244.2 2151.1,237.67 2142.4,229 2136.4,223.06 2133.6,214.58 2132.5,206.29", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2461.4,178", + pos="2267.4,178", width=1.0652]; "chemical entity or gene or gene product regulates gene association" -> "original object" [color=blue, label="original object", - lp="2516.9,221.5", - pos="e,2458.9,196.07 2484.7,247.02 2477.2,242.29 2470.2,236.37 2465.4,229 2461,222.32 2459.2,214 2458.8,206.08", + lp="2331.9,221.5", + pos="e,2268.4,196.29 2302.1,247.1 2293.9,242.3 2286.2,236.33 2280.4,229 2275.3,222.54 2272.2,214.29 2270.3,206.35", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2594.4,178", + pos="2400.4,178", width=2.1304]; "chemical entity or gene or gene product regulates gene association" -> "subject category" [color=blue, label="subject category", - lp="2640.9,221.5", - pos="e,2589,196.22 2555.3,246.74 2561.4,241.53 2567.6,235.46 2572.4,229 2577.6,221.97 2581.9,213.49 2585.3,205.54", + lp="2453.9,221.5", + pos="e,2398.5,196.23 2371.4,246.86 2377.4,241.72 2383.2,235.66 2387.4,229 2391.7,222.13 2394.6,213.88 2396.5,206.07", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2765.4,178", + pos="2571.4,178", width=2.1304]; "chemical entity or gene or gene product regulates gene association" -> "object category" [color=blue, label="object category", - lp="2783.9,221.5", - pos="e,2749.3,195.91 2649.3,248.2 2668.2,243.4 2687.2,237.15 2704.4,229 2718,222.54 2731.2,212.41 2741.8,202.94", + lp="2594.9,221.5", + pos="e,2557.5,195.94 2466.1,248.23 2483.8,243.43 2501.5,237.17 2517.4,229 2529.8,222.64 2541.4,212.65 2550.7,203.26", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="2898.4,178", + pos="2704.4,178", width=1.0652]; "chemical entity or gene or gene product regulates gene association" -> "subject closure" [color=blue, label="subject closure", - lp="2920.9,221.5", - pos="e,2885.3,195.42 2733.6,250.93 2780.1,245.74 2822.1,238.63 2843.4,229 2856.6,223.04 2868.7,212.72 2878.3,203", + lp="2729.9,221.5", + pos="e,2692.8,195.41 2550.3,250.99 2594.6,245.83 2634.2,238.73 2654.4,229 2666.7,223.09 2677.7,212.91 2686.2,203.27", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="2998.4,178", + pos="2812.4,178", width=1.0652]; "chemical entity or gene or gene product regulates gene association" -> "object closure" [color=blue, label="object closure", - lp="3041.4,221.5", - pos="e,2996.5,196.18 2752.4,251.83 2860.4,244.99 2969.5,236.38 2979.4,229 2986.8,223.48 2991.3,214.73 2994,206.08", + lp="2851.4,221.5", + pos="e,2808.8,196.29 2562.3,251.56 2669.5,244.58 2778.3,235.91 2788.4,229 2796.4,223.54 2801.8,214.69 2805.4,205.94", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3131.4,178", + pos="2945.4,178", width=2.1304]; "chemical entity or gene or gene product regulates gene association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3199.9,221.5", - pos="e,3124,196.04 2758,252.13 2911.4,243.73 3087.7,233.25 3095.4,229 3105.2,223.57 3113.1,214.19 3118.9,205", + lp="3010.9,221.5", + pos="e,2936.7,196.07 2570.9,251.99 2722.9,243.53 2897.7,233.02 2905.4,229 2916,223.51 2924.7,213.85 2931.3,204.47", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3323.4,178", + pos="3138.4,178", width=2.1304]; "chemical entity or gene or gene product regulates gene association" -> "object category closure" [color=blue, label="object category closure", - lp="3390.9,221.5", - pos="e,3317.3,196.06 2758.4,252.14 2793.9,250.36 2830.1,248.6 2864.4,247 2911.8,244.79 3250.2,252.67 3291.4,229 3300.8,223.61 3307.8,\ -214.23 3312.9,205.04", + lp="3202.9,221.5", + pos="e,3131,196.12 2573.4,252.15 2608.9,250.38 2645.1,248.6 2679.4,247 2726.4,244.8 3061,251.33 3102.4,229 3112.4,223.61 3120.3,214.1 \ +3126.1,204.81", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3513.4,178", + pos="3328.4,178", width=1.0652]; "chemical entity or gene or gene product regulates gene association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3563.4,221.5", - pos="e,3506.4,196.16 2754.4,251.95 2791.1,250.15 2828.8,248.43 2864.4,247 2898.5,245.63 3448.4,245.2 3478.4,229 3488.2,223.72 3495.8,\ -214.36 3501.4,205.15", + lp="3375.4,221.5", + pos="e,3320.7,195.7 2569.4,251.95 2606.1,250.16 2643.8,248.43 2679.4,247 2713.3,245.63 3260.2,244.54 3290.4,229 3300.8,223.63 3309.2,\ +213.94 3315.4,204.51", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3672.4,178", + pos="3487.4,178", width=1.0652]; "chemical entity or gene or gene product regulates gene association" -> "object namespace" [color=blue, label="object namespace", - lp="3716.4,221.5", - pos="e,3665,195.71 2752.6,251.85 2789.9,250.05 2828.2,248.34 2864.4,247 2907.2,245.41 3597.4,248.73 3635.4,229 3645.7,223.65 3653.9,213.96 \ -3659.9,204.53", + lp="3529.4,221.5", + pos="e,3479.1,195.75 2567.6,251.85 2604.9,250.05 2643.2,248.35 2679.4,247 2722,245.41 3409.1,247.94 3447.4,229 3458.2,223.64 3467.1,213.81 \ +3473.7,204.28", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3823.4,178", + pos="3638.4,178", width=1.0652]; "chemical entity or gene or gene product regulates gene association" -> "subject label closure" [color=blue, label="subject label closure", - lp="3876.4,221.5", - pos="e,3815.4,195.75 2751.7,251.78 2789.3,249.97 2827.9,248.29 2864.4,247 2915.5,245.2 3738.7,251.88 3784.4,229 3795.1,223.64 3803.7,\ -213.82 3810.1,204.29", + lp="3689.4,221.5", + pos="e,3629.8,195.77 2566.7,251.78 2604.3,249.97 2642.9,248.29 2679.4,247 2730.4,245.2 3551.5,251.27 3597.4,229 3608.4,223.67 3617.4,\ +213.85 3624.2,204.32", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="3994.4,178", + pos="3809.4,178", width=1.0652]; "chemical entity or gene or gene product regulates gene association" -> "object label closure" [color=blue, label="object label closure", - lp="4041.9,221.5", - pos="e,3986.1,195.78 2750.8,251.72 2788.7,249.91 2827.7,248.24 2864.4,247 2894.7,245.98 3927.2,242.34 3954.4,229 3965.2,223.67 3974.1,\ -213.85 3980.7,204.32", + lp="3856.9,221.5", + pos="e,3800.5,195.8 2565.8,251.72 2603.7,249.91 2642.7,248.24 2679.4,247 2709.6,245.98 3740.1,241.99 3767.4,229 3778.5,223.7 3787.8,213.89 \ +3794.7,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4138.4,178", + pos="3953.4,178", width=2.347]; "chemical entity or gene or gene product regulates gene association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4197.9,221.5", - pos="e,4135.4,196 2749.9,251.7 2788,249.88 2827.4,248.21 2864.4,247 2899.1,245.86 4086.3,247.96 4115.4,229 4123.5,223.7 4128.8,214.72 \ -4132.3,205.81", + lp="4012.9,221.5", + pos="e,3950.4,196 2564.9,251.7 2603,249.88 2642.4,248.21 2679.4,247 2714.1,245.86 3901.3,247.96 3930.4,229 3938.5,223.7 3943.8,214.72 \ +3947.3,205.81", style=solid]; type [height=0.5, - pos="4272.4,178", + pos="4087.4,178", width=0.86659]; "chemical entity or gene or gene product regulates gene association" -> type [color=blue, label=type, - lp="4294.4,221.5", - pos="e,4277.5,196.18 2749.4,251.67 2787.7,249.85 2827.2,248.19 2864.4,247 2883.9,246.38 4257.5,242.77 4271.4,229 4277.4,223.09 4279,214.51 \ -4278.6,206.12", + lp="4109.4,221.5", + pos="e,4092.5,196.18 2564.4,251.67 2602.7,249.85 2642.2,248.19 2679.4,247 2698.9,246.38 4072.5,242.77 4086.4,229 4092.4,223.09 4094,214.51 \ +4093.6,206.12", style=solid]; category [height=0.5, - pos="4373.4,178", + pos="4188.4,178", width=1.4263]; "chemical entity or gene or gene product regulates gene association" -> category [color=blue, label=category, - lp="4371.9,221.5", - pos="e,4359.8,195.45 2749.4,251.66 2787.7,249.84 2827.2,248.18 2864.4,247 2904.7,245.72 4276.7,243.1 4314.4,229 4329,223.55 4342.4,212.79 \ -4352.8,202.65", + lp="4186.9,221.5", + pos="e,4174.8,195.45 2564.4,251.66 2602.7,249.84 2642.2,248.18 2679.4,247 2719.7,245.72 4091.7,243.1 4129.4,229 4144,223.55 4157.4,212.79 \ +4167.8,202.65", style=solid]; "object direction qualifier" [height=0.5, - pos="4567.4,178", + pos="4382.4,178", width=3.4664]; "chemical entity or gene or gene product regulates gene association" -> "object direction qualifier" [color=blue, label="object direction qualifier", - lp="4558.4,221.5", - pos="e,4527.4,195.08 2749,251.66 2787.4,249.83 2827.1,248.17 2864.4,247 3035.8,241.63 4238.1,255.85 4407.4,229 4445.3,222.99 4486.5,209.93 \ -4517.7,198.66", + lp="4373.4,221.5", + pos="e,4342.4,195.08 2564,251.66 2602.4,249.83 2642.1,248.17 2679.4,247 2850.8,241.63 4053.1,255.85 4222.4,229 4260.3,222.99 4301.5,209.93 \ +4332.7,198.66", style=solid]; predicate [height=0.5, - pos="4764.4,178", + pos="4579.4,178", width=1.5165]; "chemical entity or gene or gene product regulates gene association" -> predicate [color=blue, label=predicate, - lp="4730.4,221.5", - pos="e,4738.2,194.11 2748.5,251.63 2787.1,249.8 2826.9,248.14 2864.4,247 2963.6,243.97 4553.4,249.85 4650.4,229 4678.1,223.04 4707.4,\ -210.05 4729.3,198.8", + lp="4545.4,221.5", + pos="e,4553.2,194.11 2563.5,251.63 2602.1,249.8 2641.9,248.14 2679.4,247 2778.6,243.97 4368.4,249.85 4465.4,229 4493.1,223.04 4522.4,\ +210.05 4544.3,198.8", style=solid]; subject [height=0.5, - pos="4881.4,178", + pos="4696.4,178", width=1.2277]; "chemical entity or gene or gene product regulates gene association" -> subject [color=blue, label=subject, - lp="4839.4,221.5", - pos="e,4857.3,193.16 2748.5,251.61 2787.1,249.78 2826.9,248.13 2864.4,247 2970.1,243.8 4665,251.36 4768.4,229 4796.6,222.89 4826.5,209.36 \ -4848.4,197.91", + lp="4654.4,221.5", + pos="e,4672.3,193.16 2563.5,251.61 2602.1,249.78 2641.9,248.13 2679.4,247 2785.1,243.8 4480,251.36 4583.4,229 4611.6,222.89 4641.5,209.36 \ +4663.4,197.91", style=solid]; object [height=0.5, - pos="4924.4,91", + pos="4739.4,91", width=1.0832]; "chemical entity or gene or gene product regulates gene association" -> object [color=blue, label=object, - lp="4974.4,178", - pos="e,4937.8,108.09 2748.1,251.62 2786.8,249.78 2826.8,248.13 2864.4,247 2975.7,243.66 4761.2,255.41 4869.4,229 4900.9,221.32 4914.3,\ -221.42 4934.4,196 4953.7,171.51 4956.3,156.9 4947.4,127 4946.4,123.55 4944.9,120.13 4943.1,116.85", + lp="4789.4,178", + pos="e,4752.8,108.09 2563.1,251.62 2601.8,249.78 2641.8,248.13 2679.4,247 2790.7,243.66 4576.2,255.41 4684.4,229 4715.9,221.32 4729.3,\ +221.42 4749.4,196 4768.7,171.51 4771.3,156.9 4762.4,127 4761.4,123.55 4759.9,120.13 4758.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2911.4,265", + pos="2726.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3042.4,265", + pos="2857.4,265", width=2.0762]; "chemical entity or gene or gene product regulates gene association_object direction qualifier" [color=blue, height=0.5, label=DirectionQualifierEnum, - pos="3256.4,265", + pos="3071.4,265", width=3.358]; "chemical entity or gene or gene product regulates gene association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3473.4,265", + pos="3288.4,265", width=2.1665]; subject -> object [label=relation, - lp="4919.4,134.5", - pos="e,4906.5,107.23 4882.5,159.55 4883.7,149.57 4886.2,137.07 4891.4,127 4893.6,122.68 4896.5,118.52 4899.7,114.66"]; + lp="4734.4,134.5", + pos="e,4721.5,107.23 4697.5,159.55 4698.7,149.57 4701.2,137.07 4706.4,127 4708.6,122.68 4711.5,118.52 4714.7,114.66"]; relation [height=0.5, - pos="4869.4,18", + pos="4684.4,18", width=1.2999]; - subject -> relation [pos="e,4870.7,36.188 4880.1,159.79 4878,132.48 4874,78.994 4871.5,46.38", + subject -> relation [pos="e,4685.7,36.188 4695.1,159.79 4693,132.48 4689,78.994 4686.5,46.38", style=dotted]; "chemical entity or gene or gene product regulates gene association_subject" [color=blue, height=0.5, label="chemical entity or gene or gene product", - pos="3766.4,265", + pos="3581.4,265", width=5.4703]; - object -> relation [pos="e,4882.2,35.54 4911.9,73.889 4905,64.939 4896.2,53.617 4888.4,43.584", + object -> relation [pos="e,4697.2,35.54 4726.9,73.889 4720,64.939 4711.2,53.617 4703.4,43.584", style=dotted]; "chemical entity or gene or gene product regulates gene association_object" [color=blue, height=0.5, label="gene or gene product", - pos="4091.4,265", + pos="3906.4,265", width=3.0692]; } diff --git a/graphviz/chemical_entity_or_gene_or_gene_product_regulates_gene_association.svg b/graphviz/chemical_entity_or_gene_or_gene_product_regulates_gene_association.svg index 03f7ad1888..5b7ddb050b 100644 --- a/graphviz/chemical_entity_or_gene_or_gene_product_regulates_gene_association.svg +++ b/graphviz/chemical_entity_or_gene_or_gene_product_regulates_gene_association.svg @@ -4,16 +4,16 @@ - + %3 - + chemical entity or gene or gene product regulates gene association - -chemical entity or gene or gene product regulates gene association + +chemical entity or gene or gene product regulates gene association @@ -24,8 +24,8 @@ chemical entity or gene or gene product regulates gene association->association - - + + is_a @@ -37,7 +37,7 @@ chemical entity or gene or gene product regulates gene association->id - + id @@ -50,9 +50,9 @@ chemical entity or gene or gene product regulates gene association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ chemical entity or gene or gene product regulates gene association->name - - -name + + +name @@ -76,9 +76,9 @@ chemical entity or gene or gene product regulates gene association->description - - -description + + +description @@ -89,9 +89,9 @@ chemical entity or gene or gene product regulates gene association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ chemical entity or gene or gene product regulates gene association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ chemical entity or gene or gene product regulates gene association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ chemical entity or gene or gene product regulates gene association->publications - - -publications + + +publications @@ -141,382 +141,382 @@ chemical entity or gene or gene product regulates gene association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string chemical entity or gene or gene product regulates gene association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string chemical entity or gene or gene product regulates gene association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string chemical entity or gene or gene product regulates gene association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type chemical entity or gene or gene product regulates gene association->timepoint - - -timepoint + + +timepoint original subject - -string + +string chemical entity or gene or gene product regulates gene association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie chemical entity or gene or gene product regulates gene association->original predicate - - -original predicate + + +original predicate original object - -string + +string chemical entity or gene or gene product regulates gene association->original object - - -original object + + +original object subject category - -ontology class + +ontology class chemical entity or gene or gene product regulates gene association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class chemical entity or gene or gene product regulates gene association->object category - - -object category + + +object category subject closure - -string + +string chemical entity or gene or gene product regulates gene association->subject closure - - -subject closure + + +subject closure object closure - -string + +string chemical entity or gene or gene product regulates gene association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class chemical entity or gene or gene product regulates gene association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class chemical entity or gene or gene product regulates gene association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string chemical entity or gene or gene product regulates gene association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string chemical entity or gene or gene product regulates gene association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string chemical entity or gene or gene product regulates gene association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string chemical entity or gene or gene product regulates gene association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source chemical entity or gene or gene product regulates gene association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type chemical entity or gene or gene product regulates gene association->type - - -type + + +type category - -category + +category chemical entity or gene or gene product regulates gene association->category - - -category + + +category object direction qualifier - -object direction qualifier + +object direction qualifier chemical entity or gene or gene product regulates gene association->object direction qualifier - - -object direction qualifier + + +object direction qualifier predicate - -predicate + +predicate chemical entity or gene or gene product regulates gene association->predicate - - -predicate + + +predicate subject - -subject + +subject chemical entity or gene or gene product regulates gene association->subject - - -subject + + +subject object - -object + +object chemical entity or gene or gene product regulates gene association->object - - -object + + +object association_type - -string + +string association_category - -category type + +category type chemical entity or gene or gene product regulates gene association_object direction qualifier - -DirectionQualifierEnum + +DirectionQualifierEnum chemical entity or gene or gene product regulates gene association_predicate - -predicate type + +predicate type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + chemical entity or gene or gene product regulates gene association_subject - -chemical entity or gene or gene product + +chemical entity or gene or gene product object->relation - - + + chemical entity or gene or gene product regulates gene association_object - -gene or gene product + +gene or gene product diff --git a/graphviz/chemical_gene_interaction_association.gv b/graphviz/chemical_gene_interaction_association.gv index cc8e289b36..3318110996 100644 --- a/graphviz/chemical_gene_interaction_association.gv +++ b/graphviz/chemical_gene_interaction_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,7388.4,283"]; + graph [bb="0,0,7170.4,283"]; node [label="\N"]; "chemical gene interaction association" [height=0.5, label="chemical gene interaction association", - pos="3309.4,265", + pos="3091.4,265", width=5.1454]; association [height=0.5, pos="62.394,178", width=1.7332]; "chemical gene interaction association" -> association [label=is_a, lp="495.39,221.5", - pos="e,107.14,190.57 3124.5,263.71 2581.6,262.52 998.21,256.73 481.39,229 326.7,220.7 287.25,221.19 134.39,196 128.71,195.06 122.81,193.93 \ + pos="e,107.14,190.57 2906.7,263.48 2392.9,261.72 953.98,254.6 481.39,229 326.7,220.62 287.25,221.19 134.39,196 128.71,195.06 122.81,193.93 \ 116.94,192.71"]; "chemical to entity association mixin" [height=0.5, pos="320.39,178", width=4.9287]; "chemical gene interaction association" -> "chemical to entity association mixin" [label=uses, - lp="650.89,221.5", - pos="e,396.47,194.28 3124.7,263.13 2560.1,260.27 880.16,250.06 634.39,229 556.74,222.34 469.22,207.82 406.35,196.13"]; + lp="649.89,221.5", + pos="e,396.55,194.32 2907.3,262.91 2374.8,259.55 857.15,248.36 633.39,229 556.11,222.31 469.04,207.83 406.39,196.16"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "chemical gene interaction association" -> id [color=blue, label=id, - lp="769.39,221.5", - pos="e,583.38,189.98 3124.4,263.49 2577.9,261.68 994.57,254.31 762.39,229 690.21,221.13 672.34,215.5 602.39,196 599.29,195.13 596.09,\ -194.17 592.89,193.15", + lp="767.39,221.5", + pos="e,583.38,189.97 2906.7,263.26 2392.9,260.9 970.7,252.33 760.39,229 689.09,221.09 671.47,215.35 602.39,196 599.29,195.13 596.09,194.16 \ +592.89,193.14", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,9 @@ digraph { width=1.2277]; "chemical gene interaction association" -> iri [color=blue, label=iri, - lp="882.39,221.5", - pos="e,688.3,190.2 3124.6,263.28 2594.9,260.95 1095.3,252.35 874.39,229 799.59,221.09 781.22,214.85 708.39,196 705.02,195.13 701.54,194.16 \ -698.06,193.15", + lp="872.39,221.5", + pos="e,688.32,190.13 2906.9,263.14 2409.5,260.54 1064.2,251.49 864.39,229 793.97,221.07 776.89,214.18 708.39,196 705.02,195.11 701.55,\ +194.12 698.07,193.1", style=solid]; name [color=blue, height=0.5, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "chemical gene interaction association" -> name [color=blue, label=name, - lp="989.39,221.5", - pos="e,811.98,191.47 3124.4,263.74 2608.9,262.65 1180,257.11 969.39,229 918.09,222.15 860.88,206.49 821.77,194.51", + lp="974.39,221.5", + pos="e,810.36,191.92 2906.5,263.66 2422.8,262.4 1144.3,256.47 954.39,229 907.74,222.25 856.05,207.05 820.07,195.17", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "chemical gene interaction association" -> description [color=blue, label=description, - lp="1109.9,221.5", - pos="e,958.44,194.19 3124.1,264.46 2623.7,265.22 1268.7,263.99 1069.4,229 1034.3,222.84 996.32,209.47 968.03,198.11", + lp="1086.9,221.5", + pos="e,953.99,194.78 2907.4,262.7 2421.8,259.01 1136.5,247.55 1046.4,229 1017.4,223.04 986.63,210.36 963.22,199.26", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "chemical gene interaction association" -> "has attribute" [color=blue, label="has attribute", - lp="1255.4,221.5", - pos="e,1099,192.87 3124,264.38 2645.6,264.88 1393.5,262.88 1208.4,229 1173.4,222.6 1135.6,208.47 1108.2,196.85", + lp="1218.4,221.5", + pos="e,1093,194.29 2907.3,262.8 2442.9,259.5 1254.7,249.12 1171.4,229 1146.7,223.04 1121.1,210.45 1101.7,199.39", style=solid]; negated [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=1.2999]; "chemical gene interaction association" -> negated [color=blue, label=negated, - lp="1410.4,221.5", - pos="e,1220.4,190.52 3125.3,262.89 2676.6,259.88 1551,250.28 1381.4,229 1328.4,222.36 1269.3,205.85 1230.2,193.61", + lp="1351.4,221.5", + pos="e,1214.5,192.49 2906.5,263.81 2484.4,262.88 1474.6,257.64 1322.4,229 1287.9,222.51 1250.7,208.27 1223.9,196.64", style=solid]; qualifiers [color=blue, height=0.5, @@ -87,8 +87,8 @@ digraph { width=2.1304]; "chemical gene interaction association" -> qualifiers [color=blue, label=qualifiers, - lp="1549.9,221.5", - pos="e,1369.2,193.15 3125.3,262.9 2699.7,260 1672.2,250.81 1516.4,229 1469,222.37 1416.5,207.89 1378.9,196.21", + lp="1455.9,221.5", + pos="e,1350.7,195.24 2907.8,262.41 2489,258.48 1493.2,247.28 1422.4,229 1400.1,223.25 1377.2,211.41 1359.5,200.7", style=solid]; publications [color=blue, height=0.5, @@ -97,8 +97,8 @@ digraph { width=1.7332]; "chemical gene interaction association" -> publications [color=blue, label=publications, - lp="1697.4,221.5", - pos="e,1520.7,192.8 3125.2,262.87 2724,260.01 1795.3,251.08 1653.4,229 1610.7,222.36 1563.8,207.86 1530.2,196.17", + lp="1549.4,221.5", + pos="e,1486.8,196.42 2907.6,262.55 2496,258.95 1534,248.47 1505.4,229 1497.6,223.69 1492.7,214.87 1489.6,206.1", style=solid]; "has evidence" [color=blue, height=0.5, @@ -107,384 +107,385 @@ digraph { width=2.0943]; "chemical gene interaction association" -> "has evidence" [color=blue, label="has evidence", - lp="1858.9,221.5", - pos="e,1679.4,193.48 3125.9,262.37 2754.6,258.7 1938.7,248.5 1812.4,229 1769.9,222.44 1723.1,208.37 1689,196.82", + lp="1647.9,221.5", + pos="e,1615.2,195.05 2907.1,263 2513.4,260.42 1623.9,252.04 1601.4,229 1593.3,220.67 1598.5,210.7 1607.5,201.85", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1842.4,178", - width=3.015]; + label=string, + pos="1772.4,178", + width=1.0652]; "chemical gene interaction association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2016.9,221.5", - pos="e,1870.2,195.45 3124.8,263.33 2780.1,261.46 2063.4,254.54 1952.4,229 1926.9,223.12 1900.1,211.08 1879.3,200.29", + lp="1765.9,221.5", + pos="e,1743.1,189.79 2907.6,262.67 2534.6,259.54 1722.2,250.29 1701.4,229 1696.7,224.23 1697.9,219.66 1701.4,214 1705.4,207.54 1719.2,\ +200.12 1733.6,193.78", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2077.4,178", - width=3.015]; + label=string, + pos="1867.4,178", + width=1.0652]; "chemical gene interaction association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2191.4,221.5", - pos="e,2079.1,196.34 3124.4,264.02 2795,263.31 2137.5,258.21 2096.4,229 2088.9,223.66 2084.3,214.95 2081.6,206.29", + lp="1933.4,221.5", + pos="e,1848.9,194.29 2908.4,262.15 2565,258.24 1856.8,247.89 1838.4,229 1830.8,221.21 1834.8,211.06 1842,201.95", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2312.4,178", - width=3.015]; + label=string, + pos="2009.4,178", + width=1.0652]; "chemical gene interaction association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2400.9,221.5", - pos="e,2298.2,196.19 3124.2,264.18 2839.1,263.53 2322.7,258.29 2294.4,229 2288.1,222.47 2289.3,213.57 2293.2,205.09", + lp="2155.9,221.5", + pos="e,2017.7,195.71 2909,261.82 2620.4,257.8 2087,247.87 2049.4,229 2038.6,223.58 2029.7,213.75 2023.2,204.23", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2494.4,178", + pos="2236.4,178", width=1.5346]; "chemical gene interaction association" -> timepoint [color=blue, label=timepoint, - lp="2560.4,221.5", - pos="e,2500.1,196.04 3124.1,264.73 2908.6,264.18 2575.6,258.46 2525.4,229 2516.2,223.63 2509.4,214.39 2504.5,205.29", + lp="2321.4,221.5", + pos="e,2247.8,195.74 2907,263 2686.9,260.72 2341.5,253.26 2286.4,229 2273.9,223.52 2262.9,213.4 2254.4,203.69", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2606.4,178", + pos="2348.4,178", width=1.0652]; "chemical gene interaction association" -> "original subject" [color=blue, label="original subject", - lp="2661.4,221.5", - pos="e,2600.6,196.02 3128.3,261.14 2925.7,257.02 2623.3,247.77 2605.4,229 2599.6,222.92 2598.3,214.3 2599,205.92", + lp="2428.4,221.5", + pos="e,2351.9,196.39 2906,264.71 2707.7,263.94 2415.8,257.81 2372.4,229 2364.4,223.66 2358.9,214.83 2355.3,206.07", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2720.4,178", + pos="2473.4,178", width=1.5887]; "chemical gene interaction association" -> "original predicate" [color=blue, label="original predicate", - lp="2792.9,221.5", - pos="e,2718.6,196.41 3124.2,264.09 2965.7,262.34 2758.7,255.01 2729.4,229 2723,223.34 2720.2,214.82 2719.1,206.41", + lp="2565.9,221.5", + pos="e,2478.5,195.95 2909.1,261.78 2749,258.43 2536.5,250.03 2502.4,229 2493.5,223.53 2487.1,214.26 2482.5,205.18", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2834.4,178", + pos="2602.4,178", width=1.0652]; "chemical gene interaction association" -> "original object" [color=blue, label="original object", - lp="2929.9,221.5", - pos="e,2844.1,195.53 3125.5,262.64 3028.7,259.26 2921.3,250.51 2878.4,229 2867,223.3 2857.3,213.29 2849.9,203.72", + lp="2705.9,221.5", + pos="e,2614.5,195.57 2909.4,261.61 2810.4,257.93 2699.3,249.2 2654.4,229 2641.6,223.24 2630,212.95 2621.1,203.19", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2967.4,178", + pos="2735.4,178", width=2.1304]; "chemical gene interaction association" -> "subject category" [color=blue, label="subject category", - lp="3059.9,221.5", - pos="e,2974.2,196.29 3141,257.47 3082.2,252.57 3024.8,243.99 3000.4,229 2991.3,223.43 2984.2,214.31 2979,205.38", + lp="2838.9,221.5", + pos="e,2745.5,195.89 2928.6,256.35 2867.3,251.27 2806,242.85 2779.4,229 2768.4,223.27 2758.9,213.58 2751.6,204.24", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3138.4,178", + pos="2906.4,178", width=2.1304]; "chemical gene interaction association" -> "object category" [color=blue, label="object category", - lp="3182.9,221.5", - pos="e,3128.1,195.99 3183.6,251.66 3157.8,246.51 3135.8,239.23 3127.4,229 3121.9,222.4 3122.2,213.69 3124.5,205.39", + lp="2963.9,221.5", + pos="e,2902.1,196.23 2966.1,251.68 2939.7,246.51 2917.2,239.23 2908.4,229 2903.1,222.8 2901.4,214.39 2901.4,206.24", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3271.4,178", + pos="3039.4,178", width=1.0652]; "chemical gene interaction association" -> "subject closure" [color=blue, label="subject closure", - lp="3298.9,221.5", - pos="e,3254.2,194.51 3263.3,247.41 3255.7,242.63 3248.9,236.59 3244.4,229 3239.3,220.49 3242.4,210.95 3248,202.51", + lp="3080.9,221.5", + pos="e,3028.9,195.67 3045.3,247.41 3037.7,242.63 3030.9,236.59 3026.4,229 3022.1,221.77 3022.7,213.13 3025.2,205.07", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3371.4,178", + pos="3152.4,178", width=1.0652]; "chemical gene interaction association" -> "object closure" [color=blue, label="object closure", - lp="3411.4,221.5", - pos="e,3367.7,196.33 3335.8,246.85 3342.2,241.72 3348.6,235.66 3353.4,229 3358.3,222.15 3362,213.81 3364.7,205.93", + lp="3193.4,221.5", + pos="e,3149.1,196.33 3117.9,246.91 3124.3,241.78 3130.7,235.7 3135.4,229 3140.2,222.22 3143.7,214 3146.2,206.19", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3504.4,178", + pos="3285.4,178", width=2.1304]; "chemical gene interaction association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3569.9,221.5", - pos="e,3495.4,195.9 3416.5,250.27 3433.7,245.23 3450.6,238.36 3465.4,229 3475.1,222.84 3483.4,213.37 3489.8,204.32", + lp="3351.9,221.5", + pos="e,3276.7,195.89 3199,250.31 3216,245.26 3232.8,238.37 3247.4,229 3256.9,222.9 3264.9,213.56 3271.1,204.6", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3696.4,178", + pos="3478.4,178", width=2.1304]; "chemical gene interaction association" -> "object category closure" [color=blue, label="object category closure", - lp="3760.9,221.5", - pos="e,3689,196.37 3440.4,252.24 3538.4,243.23 3656.5,231.88 3661.4,229 3670.9,223.46 3678.4,214.23 3684,205.19", + lp="3542.9,221.5", + pos="e,3471,196.37 3222.4,252.24 3320.4,243.23 3438.5,231.88 3443.4,229 3452.9,223.46 3460.4,214.23 3466,205.19", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3886.4,178", + pos="3668.4,178", width=1.0652]; "chemical gene interaction association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3933.4,221.5", - pos="e,3878.4,196.1 3438.6,252.1 3460.6,250.26 3483.1,248.48 3504.4,247 3542.6,244.34 3814.6,246.9 3848.4,229 3858.6,223.59 3866.9,214.08 \ -3873.1,204.79", + lp="3715.4,221.5", + pos="e,3660.4,196.1 3220.6,252.1 3242.6,250.26 3265.1,248.48 3286.4,247 3324.6,244.34 3596.6,246.9 3630.4,229 3640.6,223.59 3648.9,214.08 \ +3655.1,204.79", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4045.4,178", + pos="3827.4,178", width=1.0652]; "chemical gene interaction association" -> "object namespace" [color=blue, label="object namespace", - lp="4087.4,221.5", - pos="e,4037.1,195.7 3437,251.93 3459.5,250.08 3482.6,248.34 3504.4,247 3560,243.58 3955.6,254.03 4005.4,229 4016.2,223.57 4025,213.73 \ -4031.6,204.21", + lp="3869.4,221.5", + pos="e,3819.1,195.7 3219,251.93 3241.5,250.08 3264.6,248.34 3286.4,247 3342,243.58 3737.6,254.03 3787.4,229 3798.2,223.57 3807,213.73 \ +3813.6,204.21", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4140.4,178", + pos="3922.4,178", width=1.0652]; "chemical gene interaction association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4234.4,221.5", - pos="e,4152.6,195.36 3436.2,251.84 3458.9,249.98 3482.3,248.27 3504.4,247 3522.5,245.96 4142.8,241.97 4155.4,229 4161.8,222.42 4160.8,\ -213.21 4157.2,204.49", + lp="4016.4,221.5", + pos="e,3934.6,195.36 3218.2,251.84 3240.9,249.98 3264.3,248.27 3286.4,247 3304.5,245.96 3924.8,241.97 3937.4,229 3943.8,222.42 3942.8,\ +213.21 3939.2,204.49", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4235.4,178", + pos="4017.4,178", width=1.0652]; "chemical gene interaction association" -> "object label closure" [color=blue, label="object label closure", - lp="4385.9,221.5", - pos="e,4263.8,190.16 3435.4,251.81 3458.4,249.93 3482.1,248.22 3504.4,247 3526.8,245.77 4296.7,245.05 4312.4,229 4317.1,224.23 4316,219.61 \ -4312.4,214 4309.9,210.14 4291.4,201.68 4273.2,194.05", + lp="4167.9,221.5", + pos="e,4045.8,190.16 3217.4,251.81 3240.4,249.93 3264.1,248.22 3286.4,247 3308.8,245.77 4078.7,245.05 4094.4,229 4099.1,224.23 4098,219.61 \ +4094.4,214 4091.9,210.14 4073.4,201.68 4055.2,194.05", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4376.4,178", + pos="4158.4,178", width=2.347]; "chemical gene interaction association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4534.9,221.5", - pos="e,4428.6,192.27 3435.2,251.77 3458.2,249.89 3482,248.19 3504.4,247 3530.9,245.6 4440.8,247.94 4459.4,229 4472.6,215.57 4458.4,204.33 \ -4438.2,195.93", + lp="4316.9,221.5", + pos="e,4210.6,192.27 3217.2,251.77 3240.2,249.89 3264,248.19 3286.4,247 3312.9,245.6 4222.8,247.94 4241.4,229 4254.6,215.57 4240.4,204.33 \ +4220.2,195.93", style=solid]; type [height=0.5, - pos="4510.4,178", + pos="4292.4,178", width=0.86659]; "chemical gene interaction association" -> type [color=blue, label=type, - lp="4628.4,221.5", - pos="e,4534.5,189.42 3434.9,251.74 3458,249.86 3481.9,248.16 3504.4,247 3535,245.42 4586.9,250.86 4608.4,229 4613.1,224.25 4612.3,219.38 \ -4608.4,214 4592.7,192.57 4576.4,205.1 4551.4,196 4549,195.12 4546.5,194.19 4544,193.22", + lp="4410.4,221.5", + pos="e,4316.5,189.42 3216.9,251.74 3240,249.86 3263.9,248.16 3286.4,247 3317,245.42 4368.9,250.86 4390.4,229 4395.1,224.25 4394.3,219.38 \ +4390.4,214 4374.7,192.57 4358.4,205.1 4333.4,196 4331,195.12 4328.5,194.19 4326,193.22", style=solid]; category [height=0.5, - pos="4611.4,178", + pos="4393.4,178", width=1.4263]; "chemical gene interaction association" -> category [color=blue, label=category, - lp="4684.9,221.5", - pos="e,4634.4,194.31 3434.9,251.73 3458,249.85 3481.9,248.16 3504.4,247 3536.1,245.37 4626.1,251.65 4648.4,229 4656.7,220.54 4651.1,210.12 \ -4641.9,200.99", + lp="4466.9,221.5", + pos="e,4416.4,194.31 3216.9,251.73 3240,249.85 3263.9,248.16 3286.4,247 3318.1,245.37 4408.1,251.65 4430.4,229 4438.7,220.54 4433.1,210.12 \ +4423.9,200.99", style=solid]; "subject form or variant qualifier" [height=0.5, - pos="4840.4,178", + pos="4622.4,178", width=4.4232]; "chemical gene interaction association" -> "subject form or variant qualifier" [color=blue, label="subject form or variant qualifier", - lp="4882.9,221.5", - pos="e,4809.4,195.79 3434.7,251.73 3457.8,249.85 3481.8,248.15 3504.4,247 3639.3,240.13 4588.1,256.48 4720.4,229 4748.2,223.23 4777.6,\ -211.08 4800.4,200.19", + lp="4664.9,221.5", + pos="e,4591.4,195.79 3216.7,251.73 3239.8,249.85 3263.8,248.15 3286.4,247 3421.3,240.13 4370.1,256.48 4502.4,229 4530.2,223.23 4559.6,\ +211.08 4582.4,200.19", style=solid]; "subject part qualifier" [height=0.5, - pos="5126.4,178", + pos="4908.4,178", width=3.015]; "chemical gene interaction association" -> "subject part qualifier" [color=blue, label="subject part qualifier", - lp="5126.9,221.5", - pos="e,5095,195.32 3434.4,251.7 3457.6,249.81 3481.7,248.12 3504.4,247 3587.5,242.89 4919.8,245.22 5001.4,229 5030.7,223.17 5062,210.66 \ -5085.9,199.62", + lp="4908.9,221.5", + pos="e,4877,195.32 3216.4,251.7 3239.6,249.81 3263.7,248.12 3286.4,247 3369.5,242.89 4701.8,245.22 4783.4,229 4812.7,223.17 4844,210.66 \ +4867.9,199.62", style=solid]; "subject derivative qualifier" [height=0.5, - pos="5388.4,178", + pos="5170.4,178", width=3.7733]; "chemical gene interaction association" -> "subject derivative qualifier" [color=blue, label="subject derivative qualifier", - lp="5373.9,221.5", - pos="e,5342.7,195.08 3434.4,251.68 3457.6,249.79 3481.7,248.11 3504.4,247 3693.3,237.78 5019.1,255.27 5206.4,229 5249.7,222.93 5297.3,\ -209.6 5333,198.23", + lp="5155.9,221.5", + pos="e,5124.7,195.08 3216.4,251.68 3239.6,249.79 3263.7,248.11 3286.4,247 3475.3,237.78 4801.1,255.27 4988.4,229 5031.7,222.93 5079.3,\ +209.6 5115,198.23", style=solid]; "subject context qualifier" [height=0.5, - pos="5665.4,178", + pos="5447.4,178", width=3.4303]; "chemical gene interaction association" -> "subject context qualifier" [color=blue, label="subject context qualifier", - lp="5636.4,221.5", - pos="e,5618.6,194.73 3434.1,251.67 3457.5,249.78 3481.7,248.09 3504.4,247 3723,236.49 5257.4,257.94 5474.4,229 5520.4,222.86 5571.2,209.23 \ -5608.8,197.75", + lp="5418.4,221.5", + pos="e,5400.6,194.73 3216.1,251.67 3239.5,249.78 3263.7,248.09 3286.4,247 3505,236.49 5039.4,257.94 5256.4,229 5302.4,222.86 5353.2,209.23 \ +5390.8,197.75", style=solid]; "object form or variant qualifier" [height=0.5, - pos="5961.4,178", + pos="5743.4,178", width=4.2788]; "chemical gene interaction association" -> "object form or variant qualifier" [color=blue, label="object form or variant qualifier", - lp="5928.9,221.5", - pos="e,5903.7,194.73 3434.1,251.65 3457.5,249.76 3481.7,248.08 3504.4,247 3751.1,235.26 5481.9,255.95 5727.4,229 5784.1,222.77 5847.4,\ -208.82 5893.8,197.24", + lp="5710.9,221.5", + pos="e,5685.7,194.73 3216.1,251.65 3239.5,249.76 3263.7,248.08 3286.4,247 3533.1,235.26 5263.9,255.95 5509.4,229 5566.1,222.77 5629.4,\ +208.82 5675.8,197.24", style=solid]; "object part qualifier" [height=0.5, - pos="6236.4,178", + pos="6018.4,178", width=2.8525]; "chemical gene interaction association" -> "object part qualifier" [color=blue, label="object part qualifier", - lp="6190.4,221.5", - pos="e,6191,194.15 3433.9,251.66 3457.3,249.76 3481.6,248.07 3504.4,247 3645.3,240.37 5903.5,247.33 6043.4,229 6090.7,222.81 6142.9,208.81 \ -6181.1,197.2", + lp="5972.4,221.5", + pos="e,5973,194.15 3215.9,251.66 3239.3,249.76 3263.6,248.07 3286.4,247 3427.3,240.37 5685.5,247.33 5825.4,229 5872.7,222.81 5924.9,208.81 \ +5963.1,197.2", style=solid]; "object context qualifier" [height=0.5, - pos="6475.4,178", + pos="6257.4,178", width=3.2858]; "chemical gene interaction association" -> "object context qualifier" [color=blue, label="object context qualifier", - lp="6430.4,221.5", - pos="e,6425.1,194.4 3433.9,251.64 3457.3,249.75 3481.6,248.07 3504.4,247 3657.6,239.83 6113.1,247.38 6265.4,229 6316.7,222.8 6373.7,208.77 \ -6415.3,197.14", + lp="6212.4,221.5", + pos="e,6207.1,194.4 3215.9,251.64 3239.3,249.75 3263.6,248.07 3286.4,247 3439.6,239.83 5895.1,247.38 6047.4,229 6098.7,222.8 6155.7,208.77 \ +6197.3,197.14", style=solid]; "anatomical context qualifier" [height=0.5, - pos="6752.4,178", + pos="6534.4,178", width=3.8997]; "chemical gene interaction association" -> "anatomical context qualifier" [color=blue, label="anatomical context qualifier", - lp="6709.4,221.5", - pos="e,6695.5,194.52 3433.9,251.63 3457.3,249.74 3481.6,248.06 3504.4,247 3838.8,231.45 6184.6,265.02 6517.4,229 6574.9,222.78 6639,208.63 \ -6685.8,196.97", + lp="6491.4,221.5", + pos="e,6477.5,194.52 3215.9,251.63 3239.3,249.74 3263.6,248.06 3286.4,247 3620.8,231.45 5966.6,265.02 6299.4,229 6356.9,222.78 6421,208.63 \ +6467.8,196.97", style=solid]; subject [height=0.5, - pos="6955.4,178", + pos="6737.4,178", width=1.2277]; "chemical gene interaction association" -> subject [color=blue, label=subject, - lp="6895.4,221.5", - pos="e,6927.3,192.03 3433.6,251.65 3457.1,249.74 3481.5,248.06 3504.4,247 3688,238.51 6632.3,260.46 6813.4,229 6850,222.64 6889.8,207.91 \ -6917.9,196.08", + lp="6677.4,221.5", + pos="e,6709.3,192.03 3215.6,251.65 3239.1,249.74 3263.5,248.06 3286.4,247 3470,238.51 6414.3,260.46 6595.4,229 6632,222.64 6671.8,207.91 \ +6699.9,196.08", style=solid]; object [height=0.5, - pos="6998.4,91", + pos="6780.4,91", width=1.0832]; "chemical gene interaction association" -> object [color=blue, label=object, - lp="7048.4,178", - pos="e,7011.8,108.09 3433.6,251.64 3457.1,249.74 3481.5,248.06 3504.4,247 3599.3,242.62 6832.1,247.12 6925.4,229 6964.4,221.43 6982.4,\ -225.99 7008.4,196 7028.8,172.42 7030.3,156.9 7021.4,127 7020.4,123.55 7018.9,120.13 7017.1,116.85", + lp="6830.4,178", + pos="e,6793.8,108.09 3215.6,251.64 3239.1,249.74 3263.5,248.06 3286.4,247 3381.3,242.62 6614.1,247.12 6707.4,229 6746.4,221.43 6764.4,\ +225.99 6790.4,196 6810.8,172.42 6812.3,156.9 6803.4,127 6802.4,123.55 6800.9,120.13 6799.1,116.85", style=solid]; predicate [height=0.5, - pos="7152.4,178", + pos="6934.4,178", width=1.5165]; "chemical gene interaction association" -> predicate [color=blue, label=predicate, - lp="7125.4,221.5", - pos="e,7128.6,194.39 3433.6,251.64 3457.1,249.74 3481.5,248.06 3504.4,247 3602.8,242.47 6953.5,251.31 7049.4,229 7074.3,223.21 7100.2,\ -210.61 7119.8,199.51", + lp="6907.4,221.5", + pos="e,6910.6,194.39 3215.6,251.64 3239.1,249.74 3263.5,248.06 3286.4,247 3384.8,242.47 6735.5,251.31 6831.4,229 6856.3,223.21 6882.2,\ +210.61 6901.8,199.51", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3551.4,265", + pos="3333.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3682.4,265", + pos="3464.4,265", width=2.0762]; "chemical gene interaction association_subject form or variant qualifier" [color=blue, height=0.5, label=ChemicalOrGeneOrGeneProductFormOrVariantEnum, - pos="4033.4,265", + pos="3815.4,265", width=7.1855]; "chemical gene interaction association_subject part qualifier" [color=blue, height=0.5, label=GeneOrGeneProductOrChemicalPartQualifierEnum, - pos="4558.4,265", + pos="4340.4,265", width=6.8966]; "chemical gene interaction association_subject derivative qualifier" [color=blue, height=0.5, label=ChemicalEntityDerivativeEnum, - pos="4982.4,265", + pos="4764.4,265", width=4.3871]; "chemical gene interaction association_subject context qualifier" [color=blue, height=0.5, label="anatomical entity", - pos="5250.4,265", + pos="5032.4,265", width=2.5456]; "chemical gene interaction association_object form or variant qualifier" [color=blue, height=0.5, label=ChemicalOrGeneOrGeneProductFormOrVariantEnum, - pos="5618.4,265", + pos="5400.4,265", width=7.1855]; "chemical gene interaction association_object part qualifier" [color=blue, height=0.5, label=GeneOrGeneProductOrChemicalPartQualifierEnum, - pos="6143.4,265", + pos="5925.4,265", width=6.8966]; "chemical gene interaction association_object context qualifier" [color=blue, height=0.5, label="anatomical entity", - pos="6501.4,265", + pos="6283.4,265", width=2.5456]; "chemical gene interaction association_anatomical context qualifier" [color=blue, height=0.5, label="anatomical entity", - pos="6702.4,265", + pos="6484.4,265", width=2.5456]; subject -> object [label=relation, - lp="6993.4,134.5", - pos="e,6980.5,107.23 6956.5,159.55 6957.7,149.57 6960.2,137.07 6965.4,127 6967.6,122.68 6970.5,118.52 6973.7,114.66"]; + lp="6775.4,134.5", + pos="e,6762.5,107.23 6738.5,159.55 6739.7,149.57 6742.2,137.07 6747.4,127 6749.6,122.68 6752.5,118.52 6755.7,114.66"]; relation [height=0.5, - pos="6943.4,18", + pos="6725.4,18", width=1.2999]; - subject -> relation [pos="e,6944.7,36.188 6954.1,159.79 6952,132.48 6948,78.994 6945.5,46.38", + subject -> relation [pos="e,6726.7,36.188 6736.1,159.79 6734,132.48 6730,78.994 6727.5,46.38", style=dotted]; "chemical gene interaction association_subject" [color=blue, height=0.5, label="chemical entity", - pos="6894.4,265", + pos="6676.4,265", width=2.2748]; - object -> relation [pos="e,6956.2,35.54 6985.9,73.889 6979,64.939 6970.2,53.617 6962.4,43.584", + object -> relation [pos="e,6738.2,35.54 6767.9,73.889 6761,64.939 6752.2,53.617 6744.4,43.584", style=dotted]; "chemical gene interaction association_object" [color=blue, height=0.5, label="gene or gene product", - pos="7104.4,265", + pos="6886.4,265", width=3.0692]; "chemical gene interaction association_predicate" [color=blue, height=0.5, label="predicate type", - pos="7310.4,265", + pos="7092.4,265", width=2.1665]; } diff --git a/graphviz/chemical_gene_interaction_association.svg b/graphviz/chemical_gene_interaction_association.svg index 3df081f3a4..fc4f1acaee 100644 --- a/graphviz/chemical_gene_interaction_association.svg +++ b/graphviz/chemical_gene_interaction_association.svg @@ -4,16 +4,16 @@ - + %3 - + chemical gene interaction association - -chemical gene interaction association + +chemical gene interaction association @@ -24,7 +24,7 @@ chemical gene interaction association->association - + is_a @@ -37,9 +37,9 @@ chemical gene interaction association->chemical to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ chemical gene interaction association->id - - -id + + +id @@ -63,9 +63,9 @@ chemical gene interaction association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ chemical gene interaction association->name - - -name + + +name @@ -89,9 +89,9 @@ chemical gene interaction association->description - - -description + + +description @@ -102,9 +102,9 @@ chemical gene interaction association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ chemical gene interaction association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ chemical gene interaction association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ chemical gene interaction association->publications - - -publications + + +publications @@ -154,515 +154,515 @@ chemical gene interaction association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string chemical gene interaction association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string chemical gene interaction association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string chemical gene interaction association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type chemical gene interaction association->timepoint - - -timepoint + + +timepoint original subject - -string + +string chemical gene interaction association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie chemical gene interaction association->original predicate - - -original predicate + + +original predicate original object - -string + +string chemical gene interaction association->original object - - -original object + + +original object subject category - -ontology class + +ontology class chemical gene interaction association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class chemical gene interaction association->object category - - -object category + + +object category subject closure - -string + +string chemical gene interaction association->subject closure - - -subject closure + + +subject closure object closure - -string + +string chemical gene interaction association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class chemical gene interaction association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class chemical gene interaction association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string chemical gene interaction association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string chemical gene interaction association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string chemical gene interaction association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string chemical gene interaction association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source chemical gene interaction association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type chemical gene interaction association->type - - -type + + +type category - -category + +category chemical gene interaction association->category - - -category + + +category subject form or variant qualifier - -subject form or variant qualifier + +subject form or variant qualifier chemical gene interaction association->subject form or variant qualifier - - -subject form or variant qualifier + + +subject form or variant qualifier subject part qualifier - -subject part qualifier + +subject part qualifier chemical gene interaction association->subject part qualifier - - -subject part qualifier + + +subject part qualifier subject derivative qualifier - -subject derivative qualifier + +subject derivative qualifier chemical gene interaction association->subject derivative qualifier - - -subject derivative qualifier + + +subject derivative qualifier subject context qualifier - -subject context qualifier + +subject context qualifier chemical gene interaction association->subject context qualifier - - -subject context qualifier + + +subject context qualifier object form or variant qualifier - -object form or variant qualifier + +object form or variant qualifier chemical gene interaction association->object form or variant qualifier - - -object form or variant qualifier + + +object form or variant qualifier object part qualifier - -object part qualifier + +object part qualifier chemical gene interaction association->object part qualifier - - -object part qualifier + + +object part qualifier object context qualifier - -object context qualifier + +object context qualifier chemical gene interaction association->object context qualifier - - -object context qualifier + + +object context qualifier anatomical context qualifier - -anatomical context qualifier + +anatomical context qualifier chemical gene interaction association->anatomical context qualifier - - -anatomical context qualifier + + +anatomical context qualifier subject - -subject + +subject chemical gene interaction association->subject - - -subject + + +subject object - -object + +object chemical gene interaction association->object - - -object + + +object predicate - -predicate + +predicate chemical gene interaction association->predicate - - -predicate + + +predicate association_type - -string + +string association_category - -category type + +category type chemical gene interaction association_subject form or variant qualifier - -ChemicalOrGeneOrGeneProductFormOrVariantEnum + +ChemicalOrGeneOrGeneProductFormOrVariantEnum chemical gene interaction association_subject part qualifier - -GeneOrGeneProductOrChemicalPartQualifierEnum + +GeneOrGeneProductOrChemicalPartQualifierEnum chemical gene interaction association_subject derivative qualifier - -ChemicalEntityDerivativeEnum + +ChemicalEntityDerivativeEnum chemical gene interaction association_subject context qualifier - -anatomical entity + +anatomical entity chemical gene interaction association_object form or variant qualifier - -ChemicalOrGeneOrGeneProductFormOrVariantEnum + +ChemicalOrGeneOrGeneProductFormOrVariantEnum chemical gene interaction association_object part qualifier - -GeneOrGeneProductOrChemicalPartQualifierEnum + +GeneOrGeneProductOrChemicalPartQualifierEnum chemical gene interaction association_object context qualifier - -anatomical entity + +anatomical entity chemical gene interaction association_anatomical context qualifier - -anatomical entity + +anatomical entity subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + chemical gene interaction association_subject - -chemical entity + +chemical entity object->relation - - + + chemical gene interaction association_object - -gene or gene product + +gene or gene product chemical gene interaction association_predicate - -predicate type + +predicate type diff --git a/graphviz/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association.gv b/graphviz/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association.gv index b536b5c966..dfab6d6bac 100644 --- a/graphviz/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association.gv +++ b/graphviz/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,6632,283"]; + graph [bb="0,0,6374,283"]; node [label="\N"]; "chemical or drug or treatment side effect disease or phenotypic feature association" [height=0.5, label="chemical or drug or treatment side effect disease or phenotypic feature association", - pos="3901.4,265", + pos="3643.4,265", width=11.049]; "chemical or drug or treatment to disease or phenotypic feature association" [height=0.5, pos="359.42,178", width=9.9838]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "chemical or drug or treatment to disease or phenotypic feature association" [label=is_a, lp="1321.4,221.5", - pos="e,571.57,192.57 3505,263.48 2996,261.69 2085.7,254.77 1307.4,229 1058.8,220.77 773.84,204.87 581.79,193.2"]; + pos="e,572.52,192.54 3249.1,262.62 2784.6,259.95 1989.7,252.1 1307.4,229 1059.2,220.6 774.78,204.77 582.73,193.16"]; "chemical to entity association mixin" [height=0.5, pos="914.42,178", width=4.9287]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "chemical to entity association mixin" [label=uses, lp="1627.9,221.5", - pos="e,1039.4,190.81 3504.4,263.87 3047.6,262.34 2275,255.52 1611.4,229 1384.5,219.93 1327.9,213.62 1101.4,196 1084.6,194.69 1067,193.22 \ + pos="e,1039.4,190.81 3248.5,262.73 2838.9,260.12 2180.1,252.28 1611.4,229 1384.5,219.71 1327.9,213.62 1101.4,196 1084.6,194.69 1067,193.22 \ 1049.6,191.71"]; "entity to disease or phenotypic feature association mixin" [height=0.5, pos="1384.4,178", width=7.6188]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "entity to disease or phenotypic feature association mixin" [label=uses, lp="1810.9,221.5", - pos="e,1488.2,194.7 3507.7,262.39 2992,259.42 2115.8,251.2 1794.4,229 1694,222.06 1580.4,207.69 1498.3,196.13"]; + pos="e,1488.6,194.7 3254.1,261.32 2797.2,257.34 2067.5,248.19 1794.4,229 1694.2,221.96 1580.8,207.64 1498.7,196.12"]; id [color=blue, height=0.5, label=string, @@ -32,7 +32,7 @@ digraph { "chemical or drug or treatment side effect disease or phenotypic feature association" -> id [color=blue, label=id, lp="1928.4,221.5", - pos="e,1744.4,189.97 3513,261.06 2981.1,256.43 2074.3,246.16 1921.4,229 1850.1,221 1832.5,215.35 1763.4,196 1760.3,195.13 1757.1,194.16 \ + pos="e,1744.4,189.97 3245.5,264.45 2818.4,263.41 2167.9,257 1921.4,229 1850.1,220.9 1832.5,215.35 1763.4,196 1760.3,195.13 1757.1,194.16 \ 1753.9,193.14", style=solid]; iri [color=blue, @@ -43,7 +43,7 @@ digraph { "chemical or drug or treatment side effect disease or phenotypic feature association" -> iri [color=blue, label=iri, lp="2024.4,221.5", - pos="e,1849.6,190.01 3513.4,260.99 3004.8,256.39 2160.1,246.28 2016.4,229 1961.2,222.36 1899.4,205.37 1859.3,193.03", + pos="e,1849.6,189.98 3245.8,264.52 2842.1,263.41 2245,256.83 2016.4,229 1961.2,222.28 1899.4,205.31 1859.3,193", style=solid]; name [color=blue, height=0.5, @@ -53,7 +53,7 @@ digraph { "chemical or drug or treatment side effect disease or phenotypic feature association" -> name [color=blue, label=name, lp="2120.4,221.5", - pos="e,1969.5,192.36 3508.9,262.08 3020.8,258.81 2235,250.28 2100.4,229 2058.4,222.35 2012.1,207.65 1979.3,195.9", + pos="e,1969.9,192.44 3257,260.69 2837.1,256.22 2211.2,246.7 2100.4,229 2058.5,222.3 2012.4,207.68 1979.6,195.97", style=solid]; description [color=blue, height=0.5, @@ -63,7 +63,7 @@ digraph { "chemical or drug or treatment side effect disease or phenotypic feature association" -> description [color=blue, label=description, lp="2223.9,221.5", - pos="e,2109.6,195.24 3516.2,260.51 3029.4,255.46 2246.8,244.93 2183.4,229 2160.4,223.23 2136.7,211.31 2118.4,200.56", + pos="e,2109.6,195.22 3246.9,263.54 2849.8,261.63 2283.7,254.39 2183.4,229 2160.4,223.19 2136.7,211.27 2118.4,200.53", style=solid]; "has attribute" [color=blue, height=0.5, @@ -73,7 +73,7 @@ digraph { "chemical or drug or treatment side effect disease or phenotypic feature association" -> "has attribute" [color=blue, label="has attribute", lp="2342.4,221.5", - pos="e,2245.8,195.42 3510.4,261.57 3053.4,257.82 2351.8,248.87 2295.4,229 2279.7,223.46 2264.8,212.55 2253.2,202.32", + pos="e,2245.8,195.4 3262,259.88 2879.5,254.86 2340.6,245.02 2295.4,229 2279.7,223.43 2264.8,212.51 2253.2,202.29", style=solid]; subject [color=blue, height=0.5, @@ -83,7 +83,7 @@ digraph { "chemical or drug or treatment side effect disease or phenotypic feature association" -> subject [color=blue, label=subject, lp="2436.4,221.5", - pos="e,2379,196.24 3506,262.96 3080.9,260.6 2458.9,253.03 2410.4,229 2399.7,223.71 2391,214.09 2384.4,204.68", + pos="e,2379,196.22 3256.3,260.83 2909.1,256.77 2448.3,247.86 2410.4,229 2399.8,223.69 2391,214.06 2384.4,204.66", style=solid]; object [color=blue, height=0.5, @@ -93,8 +93,8 @@ digraph { "chemical or drug or treatment side effect disease or phenotypic feature association" -> object [color=blue, label=object, lp="2507.4,178", - pos="e,2465.7,109.09 3533.1,258.16 3241.3,252.61 2857.6,243.02 2702.4,229 2605.3,220.23 2554.8,264.6 2485.4,196 2465.5,176.25 2463.3,\ -142.8 2464.8,119.17", + pos="e,2465.9,109.28 3275.8,258.08 3040.3,252.96 2757.1,243.95 2637.4,229 2568.8,220.43 2533,246.13 2485.4,196 2466.2,175.75 2463.8,142.68 \ +2465.1,119.27", style=solid]; negated [color=blue, height=0.5, @@ -103,8 +103,8 @@ digraph { width=1.2999]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> negated [color=blue, label=negated, - lp="2812.4,221.5", - pos="e,2620,190.39 3519.3,259.98 3252.7,255.66 2920.9,246.84 2783.4,229 2729.6,222.02 2669.4,205.52 2629.6,193.37", + lp="2707.4,221.5", + pos="e,2606.8,194.16 3271.6,258.58 3024.7,253.58 2735.7,244.53 2678.4,229 2656,222.91 2632.9,210.58 2615.4,199.68", style=solid]; qualifiers [color=blue, height=0.5, @@ -113,8 +113,8 @@ digraph { width=2.1304]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> qualifiers [color=blue, label=qualifiers, - lp="2945.9,221.5", - pos="e,2768.3,193.2 3523,259.45 3294.9,254.97 3026.9,246.18 2912.4,229 2866.1,222.05 2814.8,207.75 2777.9,196.22", + lp="2786.9,221.5", + pos="e,2730.8,195.99 3278.1,257.84 3042.8,252.52 2776.5,243.38 2753.4,229 2744.8,223.63 2738.8,214.51 2734.6,205.52", style=solid]; publications [color=blue, height=0.5, @@ -123,8 +123,8 @@ digraph { width=1.7332]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> publications [color=blue, label=publications, - lp="3083.4,221.5", - pos="e,2918,193.08 3528.2,258.73 3339.7,254.08 3131.7,245.35 3039.4,229 3000.8,222.15 2958.4,208.15 2927.6,196.7", + lp="2872.4,221.5", + pos="e,2850.5,193.31 3266.7,259.2 3061,254.66 2844.6,245.88 2828.4,229 2818.4,218.5 2827.8,207.57 2841.5,198.61", style=solid]; "has evidence" [color=blue, height=0.5, @@ -133,234 +133,236 @@ digraph { width=2.0943]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "has evidence" [color=blue, label="has evidence", - lp="3229.9,221.5", - pos="e,3073.9,194.09 3553,256.3 3406.6,251.14 3254,242.68 3183.4,229 3148.9,222.31 3111.4,209.1 3083.4,197.94", + lp="2969.9,221.5", + pos="e,2981.7,189.71 3285.5,257.13 3111.6,251.97 2937,243.27 2923.4,229 2918.8,224.17 2919.4,219.35 2923.4,214 2929.9,205.25 2950.2,197.84 \ +2972,192.13", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="3241.4,178", - width=3.015]; + label=string, + pos="3171.4,178", + width=1.0652]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "knowledge source" [color=blue, label="knowledge source", - lp="3368.9,221.5", - pos="e,3257,195.95 3589.2,253.81 3459.7,248.06 3332.8,239.82 3304.4,229 3289.6,223.35 3275.6,212.89 3264.5,202.99", + lp="3100.9,221.5", + pos="e,3142.4,189.98 3319.4,254.56 3180.5,248.87 3047.3,240.48 3036.4,229 2990.9,180.74 2976.1,237.12 3123.4,196 3126.5,195.13 3129.7,\ +194.17 3132.9,193.15", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="3476.4,178", - width=3.015]; + label=string, + pos="3266.4,178", + width=1.0652]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="3535.4,221.5", - pos="e,3452.2,195.77 3574.4,254.73 3506.6,249.55 3452,241.49 3440.4,229 3433,220.97 3437.2,211.37 3445,202.74", + lp="3267.4,221.5", + pos="e,3236.8,189.56 3310.2,255.15 3240.5,249.97 3184.3,241.81 3172.4,229 3167.9,224.11 3168.6,219.48 3172.4,214 3173.3,212.74 3201.9,\ +202.19 3227.3,193", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="3711.4,178", - width=3.015]; + label=string, + pos="3361.4,178", + width=1.0652]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="3744.9,221.5", - pos="e,3662.2,194.17 3681.9,249.98 3662,244.87 3646.3,238.05 3638.4,229 3628,217.1 3637.8,206.69 3653.2,198.49", + lp="3481.9,221.5", + pos="e,3361.7,196.37 3429.8,249.76 3405.6,244.75 3385.8,238.02 3375.4,229 3368.8,223.29 3365.2,214.77 3363.3,206.36", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="3893.4,178", + pos="3587.4,178", width=1.5346]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> timepoint [color=blue, label=timepoint, - lp="3891.4,221.5", - pos="e,3870.6,194.47 3871.3,246.83 3865.3,241.89 3859.8,235.93 3856.4,229 3851.7,219.42 3856.2,209.79 3863.4,201.57", + lp="3633.4,221.5", + pos="e,3588.3,196.31 3615.3,246.98 3608.9,241.92 3602.8,235.86 3598.4,229 3594.2,222.28 3591.6,214.16 3589.9,206.44", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="4005.4,178", + pos="3699.4,178", width=1.0652]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "original subject" [color=blue, label="original subject", - lp="4005.4,221.5", - pos="e,3981.4,192.24 3916,246.75 3925.1,236.6 3937.3,223.86 3949.4,214 3956.6,208.17 3964.8,202.54 3972.7,197.56", + lp="3734.4,221.5", + pos="e,3689.4,195.84 3656.1,246.71 3660.1,241.11 3664.5,234.84 3668.4,229 3673.7,221.09 3679.2,212.33 3684.1,204.38", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="4119.4,178", + pos="3825.4,178", width=1.5887]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "original predicate" [color=blue, label="original predicate", - lp="4147.9,221.5", - pos="e,4104.3,195.85 4011.1,247.63 4028.4,242.9 4045.8,236.82 4061.4,229 4074.5,222.46 4087,212.32 4097.1,202.87", + lp="3872.9,221.5", + pos="e,3818.8,196.33 3758.1,247.71 3771.1,242.95 3783.5,236.84 3794.4,229 3802.7,223.06 3809.3,214.14 3814.1,205.48", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="4233.4,178", + pos="3954.4,178", width=1.0652]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "original object" [color=blue, label="original object", - lp="4275.9,221.5", - pos="e,4230.4,196.13 4145.7,250.74 4174.5,245.61 4198.4,238.59 4211.4,229 4219.1,223.36 4224.1,214.47 4227.4,205.74", + lp="4001.9,221.5", + pos="e,3954.2,196.41 3883.8,250.59 3908.9,245.44 3929.4,238.45 3940.4,229 3947,223.33 3950.7,214.82 3952.6,206.41", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="4366.4,178", + pos="4087.4,178", width=2.1304]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "subject category" [color=blue, label="subject category", - lp="4406.9,221.5", - pos="e,4359.3,195.95 4164.2,251.47 4243.9,245.91 4314.9,238.45 4331.4,229 4341.1,223.47 4348.7,214.06 4354.3,204.89", + lp="4131.9,221.5", + pos="e,4081.7,196.37 3902.5,251.31 3976.9,245.82 4042.3,238.44 4057.4,229 4066.2,223.52 4072.8,214.42 4077.5,205.47", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="4537.4,178", + pos="4258.4,178", width=2.1304]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "object category" [color=blue, label="object category", - lp="4552.9,221.5", - pos="e,4520.9,195.7 4160.6,251.34 4303.4,243.8 4455,234.64 4470.4,229 4486.1,223.24 4501.3,212.51 4513.2,202.47", + lp="4275.9,221.5", + pos="e,4243.1,195.68 3937.9,252.86 4055.6,246.98 4169.7,238.91 4195.4,229 4210.3,223.27 4224.5,212.7 4235.6,202.74", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="4670.4,178", + pos="4391.4,178", width=1.0652]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "subject closure" [color=blue, label="subject closure", - lp="4688.9,221.5", - pos="e,4654.7,194.68 4182.2,252.25 4376.5,243.78 4602,233.15 4612.4,229 4620.3,225.85 4634.7,213.43 4647.2,201.76", + lp="4412.9,221.5", + pos="e,4378.6,195.24 3920.6,252.06 4108.8,243.62 4325.4,233.1 4335.4,229 4349.3,223.32 4361.9,212.68 4371.7,202.68", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="4766.4,178", + pos="4504.4,178", width=1.0652]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "object closure" [color=blue, label="object closure", - lp="4807.4,221.5", - pos="e,4763.9,196.35 4182.2,252.25 4224.5,250.49 4267.6,248.69 4308.4,247 4332.7,245.99 4725.5,242.86 4745.4,229 4753.2,223.61 4758.1,\ -214.78 4761.2,206.02", + lp="4537.4,221.5", + pos="e,4498,196.08 3924.1,252.23 4164.1,242.14 4471,229.22 4471.4,229 4480.9,223.62 4488.2,214.25 4493.4,205.05", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="4899.4,178", + pos="4637.4,178", width=2.1304]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "subject category closure" [color=blue, label="subject category closure", - lp="4965.9,221.5", - pos="e,4891.4,196.18 4178.6,252.08 4222.1,250.31 4266.5,248.56 4308.4,247 4339.1,245.86 4834.1,243.11 4861.4,229 4871.7,223.69 4880,214.2 \ -4886.2,204.89", + lp="4698.9,221.5", + pos="e,4626.9,196.25 3920.9,252.09 3964.3,250.33 4008.5,248.57 4050.4,247 4110.5,244.74 4536.8,254.08 4591.4,229 4603,223.67 4613,213.91 \ +4620.7,204.41", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="5088.4,178", + pos="4830.4,178", width=2.1304]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "object category closure" [color=blue, label="object category closure", - lp="5155.9,221.5", - pos="e,5082.7,196.12 4174.8,251.92 4219.4,250.13 4265.2,248.42 4308.4,247 4350,245.63 5021.3,249.68 5057.4,229 5066.6,223.73 5073.5,214.5 \ -5078.3,205.39", + lp="4891.9,221.5", + pos="e,4821.8,196.24 3917.1,251.92 3961.6,250.14 4007.3,248.42 4050.4,247 4091.5,245.64 4753.6,247.26 4790.4,229 4801.1,223.71 4809.8,\ +214.08 4816.4,204.68", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="5278.4,178", + pos="5020.4,178", width=1.0652]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "subject namespace" [color=blue, label="subject namespace", - lp="5328.4,221.5", - pos="e,5271.4,196.2 4172.6,251.82 4217.9,250.03 4264.5,248.34 4308.4,247 4334.4,246.21 5220.5,241.22 5243.4,229 5253.2,223.77 5260.9,\ -214.42 5266.5,205.2", + lp="5065.4,221.5", + pos="e,5011.8,195.78 3914.6,251.83 3959.9,250.03 4006.5,248.34 4050.4,247 4102,245.42 4933,251.53 4979.4,229 4990.4,223.67 4999.4,213.85 \ +5006.2,204.32", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="5437.4,178", + pos="5179.4,178", width=1.0652]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "object namespace" [color=blue, label="object namespace", - lp="5481.4,221.5", - pos="e,5430.1,195.74 4171.2,251.77 4217,249.97 4264.1,248.29 4308.4,247 4338.7,246.12 5373.4,242.88 5400.4,229 5410.8,223.68 5418.9,214 \ -5425,204.57", + lp="5221.4,221.5", + pos="e,5170.5,195.8 3913.5,251.76 3959.2,249.97 4006.1,248.29 4050.4,247 4080.6,246.12 5110.2,241.98 5137.4,229 5148.5,223.7 5157.8,213.89 \ +5164.8,204.35", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="5588.4,178", + pos="5330.4,178", width=1.0652]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "subject label closure" [color=blue, label="subject label closure", - lp="5641.4,221.5", - pos="e,5580.4,195.77 4170.4,251.73 4216.4,249.93 4263.8,248.26 4308.4,247 4342.9,246.03 5518.5,244.35 5549.4,229 5560.1,223.67 5568.8,\ -213.85 5575.2,204.31", + lp="5383.4,221.5", + pos="e,5321.8,195.8 3912.4,251.73 3958.4,249.93 4005.8,248.26 4050.4,247 4084.8,246.03 5258.4,243.95 5289.4,229 5300.4,223.7 5309.5,213.88 \ +5316.2,204.34", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="5759.4,178", + pos="5501.4,178", width=1.0652]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "object label closure" [color=blue, label="object label closure", - lp="5806.9,221.5", - pos="e,5751.1,195.79 4169.6,251.69 4215.9,249.89 4263.5,248.22 4308.4,247 4347.6,245.93 5684.2,246.2 5719.4,229 5730.3,223.7 5739.1,213.88 \ -5745.7,204.34", + lp="5548.9,221.5", + pos="e,5493.1,195.79 3911.6,251.69 3957.9,249.89 4005.5,248.22 4050.4,247 4089.6,245.93 5426.2,246.2 5461.4,229 5472.3,223.7 5481.1,213.88 \ +5487.7,204.34", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="5921.4,178", + pos="5663.4,178", width=2.347]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="5969.9,221.5", - pos="e,5912.5,196.3 4169,251.67 4215.5,249.86 4263.3,248.2 4308.4,247 4352.1,245.84 5841.1,247.9 5880.4,229 5891.3,223.79 5900.2,214.18 \ -5907,204.76", + lp="5711.9,221.5", + pos="e,5654.5,196.3 3911,251.67 3957.5,249.86 4005.3,248.2 4050.4,247 4094.1,245.84 5583.1,247.9 5622.4,229 5633.3,223.79 5642.2,214.18 \ +5649,204.76", style=solid]; type [height=0.5, - pos="6055.4,178", + pos="5797.4,178", width=0.86659]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> type [color=blue, label=type, - lp="6069.4,221.5", - pos="e,6056.3,196.18 4168.5,251.65 4215.1,249.83 4263.2,248.18 4308.4,247 4332.5,246.37 6024.6,244.02 6043.4,229 6050.3,223.54 6053.6,\ -214.92 6055.2,206.37", + lp="5811.4,221.5", + pos="e,5798.3,196.18 3910.5,251.65 3957.1,249.83 4005.2,248.18 4050.4,247 4074.5,246.37 5766.6,244.02 5785.4,229 5792.3,223.54 5795.6,\ +214.92 5797.2,206.37", style=solid]; category [height=0.5, - pos="6156.4,178", + pos="5898.4,178", width=1.4263]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> category [color=blue, label=category, - lp="6149.9,221.5", - pos="e,6140.8,195.25 4168.2,251.65 4214.9,249.83 4263.1,248.18 4308.4,247 4357.9,245.72 6042.5,244.83 6089.4,229 6105.6,223.53 6121.1,\ -212.51 6133.1,202.2", + lp="5891.9,221.5", + pos="e,5882.8,195.25 3910.2,251.65 3956.9,249.83 4005.1,248.18 4050.4,247 4099.9,245.72 5784.5,244.83 5831.4,229 5847.6,223.53 5863.1,\ +212.51 5875.1,202.2", style=solid]; "FDA adverse event level" [color=blue, height=0.5, label=FDAIDAAdverseEventEnum, - pos="6365.4,178", + pos="6107.4,178", width=3.8816]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> "FDA adverse event level" [color=blue, label="FDA adverse event level", - lp="6343.9,221.5", - pos="e,6320.2,195.09 4168.2,251.63 4214.9,249.81 4263.1,248.16 4308.4,247 4516.9,241.65 5978.9,258.16 6185.4,229 6228.3,222.95 6275.4,\ -209.62 6310.6,198.24", + lp="6085.9,221.5", + pos="e,6062.2,195.09 3910.2,251.63 3956.9,249.81 4005.1,248.16 4050.4,247 4258.9,241.65 5720.9,258.16 5927.4,229 5970.3,222.95 6017.4,\ +209.62 6052.6,198.24", style=solid]; predicate [height=0.5, - pos="6577.4,178", + pos="6319.4,178", width=1.5165]; "chemical or drug or treatment side effect disease or phenotypic feature association" -> predicate [color=blue, label=predicate, - lp="6524.4,221.5", - pos="e,6546.9,193.06 4167.6,251.61 4214.5,249.79 4262.9,248.14 4308.4,247 4426.6,244.03 6319,249.4 6435.4,229 6471,222.76 6509.5,208.69 \ -6537.5,197.06", + lp="6266.4,221.5", + pos="e,6288.9,193.06 3909.6,251.61 3956.5,249.79 4004.9,248.14 4050.4,247 4168.6,244.03 6061,249.4 6177.4,229 6213,222.76 6251.5,208.69 \ +6279.5,197.06", style=solid]; subject -> object [label=relation, lp="2434.4,134.5", @@ -375,16 +377,16 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="4355.4,265", + pos="4097.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="4486.4,265", + pos="4228.4,265", width=2.0762]; "chemical or drug or treatment side effect disease or phenotypic feature association_predicate" [color=blue, height=0.5, label="predicate type", - pos="4657.4,265", + pos="4399.4,265", width=2.1665]; } diff --git a/graphviz/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association.svg b/graphviz/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association.svg index 095e1c57ea..48bea1c8fd 100644 --- a/graphviz/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association.svg +++ b/graphviz/chemical_or_drug_or_treatment_side_effect_disease_or_phenotypic_feature_association.svg @@ -4,16 +4,16 @@ - + %3 - + chemical or drug or treatment side effect disease or phenotypic feature association - -chemical or drug or treatment side effect disease or phenotypic feature association + +chemical or drug or treatment side effect disease or phenotypic feature association @@ -24,8 +24,8 @@ chemical or drug or treatment side effect disease or phenotypic feature association->chemical or drug or treatment to disease or phenotypic feature association - - + + is_a @@ -37,7 +37,7 @@ chemical or drug or treatment side effect disease or phenotypic feature association->chemical to entity association mixin - + uses @@ -50,8 +50,8 @@ chemical or drug or treatment side effect disease or phenotypic feature association->entity to disease or phenotypic feature association mixin - - + + uses @@ -63,7 +63,7 @@ chemical or drug or treatment side effect disease or phenotypic feature association->id - + id @@ -76,8 +76,8 @@ chemical or drug or treatment side effect disease or phenotypic feature association->iri - - + + iri @@ -89,8 +89,8 @@ chemical or drug or treatment side effect disease or phenotypic feature association->name - - + + name @@ -102,8 +102,8 @@ chemical or drug or treatment side effect disease or phenotypic feature association->description - - + + description @@ -115,8 +115,8 @@ chemical or drug or treatment side effect disease or phenotypic feature association->has attribute - - + + has attribute @@ -128,8 +128,8 @@ chemical or drug or treatment side effect disease or phenotypic feature association->subject - - + + subject @@ -141,8 +141,8 @@ chemical or drug or treatment side effect disease or phenotypic feature association->object - - + + object @@ -154,9 +154,9 @@ chemical or drug or treatment side effect disease or phenotypic feature association->negated - - -negated + + +negated @@ -167,9 +167,9 @@ chemical or drug or treatment side effect disease or phenotypic feature association->qualifiers - - -qualifiers + + +qualifiers @@ -180,9 +180,9 @@ chemical or drug or treatment side effect disease or phenotypic feature association->publications - - -publications + + +publications @@ -193,295 +193,295 @@ chemical or drug or treatment side effect disease or phenotypic feature association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string chemical or drug or treatment side effect disease or phenotypic feature association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string chemical or drug or treatment side effect disease or phenotypic feature association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string chemical or drug or treatment side effect disease or phenotypic feature association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type chemical or drug or treatment side effect disease or phenotypic feature association->timepoint - - -timepoint + + +timepoint original subject - -string + +string chemical or drug or treatment side effect disease or phenotypic feature association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie chemical or drug or treatment side effect disease or phenotypic feature association->original predicate - - -original predicate + + +original predicate original object - -string + +string chemical or drug or treatment side effect disease or phenotypic feature association->original object - - -original object + + +original object subject category - -ontology class + +ontology class chemical or drug or treatment side effect disease or phenotypic feature association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class chemical or drug or treatment side effect disease or phenotypic feature association->object category - - -object category + + +object category subject closure - -string + +string chemical or drug or treatment side effect disease or phenotypic feature association->subject closure - - -subject closure + + +subject closure object closure - -string + +string chemical or drug or treatment side effect disease or phenotypic feature association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class chemical or drug or treatment side effect disease or phenotypic feature association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class chemical or drug or treatment side effect disease or phenotypic feature association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string chemical or drug or treatment side effect disease or phenotypic feature association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string chemical or drug or treatment side effect disease or phenotypic feature association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string chemical or drug or treatment side effect disease or phenotypic feature association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string chemical or drug or treatment side effect disease or phenotypic feature association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source chemical or drug or treatment side effect disease or phenotypic feature association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type chemical or drug or treatment side effect disease or phenotypic feature association->type - - -type + + +type category - -category + +category chemical or drug or treatment side effect disease or phenotypic feature association->category - - -category + + +category FDA adverse event level - -FDAIDAAdverseEventEnum + +FDAIDAAdverseEventEnum chemical or drug or treatment side effect disease or phenotypic feature association->FDA adverse event level - - -FDA adverse event level + + +FDA adverse event level predicate - -predicate + +predicate chemical or drug or treatment side effect disease or phenotypic feature association->predicate - - -predicate + + +predicate @@ -511,20 +511,20 @@ association_type - -string + +string association_category - -category type + +category type chemical or drug or treatment side effect disease or phenotypic feature association_predicate - -predicate type + +predicate type diff --git a/graphviz/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association.gv b/graphviz/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association.gv index 1cd6b7a62a..bfb71049f5 100644 --- a/graphviz/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association.gv +++ b/graphviz/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association.gv @@ -1,30 +1,30 @@ digraph { - graph [bb="0,0,6038,283"]; + graph [bb="0,0,5780,283"]; node [label="\N"]; "chemical or drug or treatment to disease or phenotypic feature association" [height=0.5, label="chemical or drug or treatment to disease or phenotypic feature association", - pos="3307.4,265", + pos="3049.4,265", width=9.9838]; association [height=0.5, pos="62.394,178", width=1.7332]; "chemical or drug or treatment to disease or phenotypic feature association" -> association [label=is_a, lp="727.39,221.5", - pos="e,106.71,190.75 2948.2,264.08 2447.5,263.07 1511.1,257.1 713.39,229 455.8,219.93 389.46,233.09 134.39,196 128.61,195.16 122.61,194.08 \ -116.66,192.88"]; + pos="e,106.71,190.75 2691.1,263.29 2232.5,261.32 1413.6,254.19 713.39,229 455.81,219.73 389.46,233.09 134.39,196 128.61,195.16 122.61,\ +194.08 116.66,192.88"]; "chemical to entity association mixin" [height=0.5, pos="320.39,178", width=4.9287]; "chemical or drug or treatment to disease or phenotypic feature association" -> "chemical to entity association mixin" [label=uses, lp="1033.9,221.5", - pos="e,445.34,190.81 2948.3,263.98 2497.3,262.71 1699.8,256.27 1017.4,229 790.44,219.93 733.85,213.62 507.39,196 490.62,194.69 473,193.22 \ + pos="e,445.34,190.81 2692.3,262.96 2286.3,260.6 1603.9,253.01 1017.4,229 790.44,219.71 733.85,213.62 507.39,196 490.62,194.69 473,193.22 \ 455.57,191.71"]; "entity to disease or phenotypic feature association mixin" [height=0.5, pos="790.39,178", width=7.6188]; "chemical or drug or treatment to disease or phenotypic feature association" -> "entity to disease or phenotypic feature association mixin" [label=uses, lp="1216.9,221.5", - pos="e,894.16,194.7 2951.1,262.6 2441.5,259.82 1529.7,251.75 1200.4,229 1100,222.06 986.37,207.69 904.27,196.13"]; + pos="e,894.59,194.7 2695.9,261.62 2242.3,257.82 1480.7,248.7 1200.4,229 1100.1,221.96 986.77,207.64 904.69,196.12"]; id [color=blue, height=0.5, label=string, @@ -33,7 +33,7 @@ digraph { "chemical or drug or treatment to disease or phenotypic feature association" -> id [color=blue, label=id, lp="1334.4,221.5", - pos="e,1150.4,189.97 2955.1,261.37 2429.3,256.9 1483.8,246.56 1327.4,229 1256.1,221 1238.5,215.35 1169.4,196 1166.3,195.13 1163.1,194.16 \ + pos="e,1150.4,189.97 2690,264.53 2264.4,263.78 1581.4,257.86 1327.4,229 1256.1,220.9 1238.5,215.35 1169.4,196 1166.3,195.13 1163.1,194.16 \ 1159.9,193.14", style=solid]; iri [color=blue, @@ -44,7 +44,7 @@ digraph { "chemical or drug or treatment to disease or phenotypic feature association" -> iri [color=blue, label=iri, lp="1430.4,221.5", - pos="e,1255.5,190.01 2955.5,261.31 2451.8,256.87 1569.5,246.7 1422.4,229 1367.2,222.36 1305.3,205.37 1265.2,193.03", + pos="e,1255.5,189.98 2689.7,264.61 2286.5,263.81 1658.2,257.72 1422.4,229 1367.2,222.28 1305.4,205.31 1265.2,193", style=solid]; name [color=blue, height=0.5, @@ -54,7 +54,7 @@ digraph { "chemical or drug or treatment to disease or phenotypic feature association" -> name [color=blue, label=name, lp="1526.4,221.5", - pos="e,1375.5,192.36 2951.8,262.32 2467.5,259.23 1644.4,250.82 1506.4,229 1464.3,222.35 1418.1,207.65 1385.2,195.9", + pos="e,1375.8,192.44 2698.6,261.06 2279.5,256.76 1620.3,247.21 1506.4,229 1464.5,222.3 1418.4,207.68 1385.6,195.97", style=solid]; description [color=blue, height=0.5, @@ -64,7 +64,7 @@ digraph { "chemical or drug or treatment to disease or phenotypic feature association" -> description [color=blue, label=description, lp="1629.9,221.5", - pos="e,1515.5,195.24 2957.5,260.87 2474.3,255.97 1654.4,245.32 1589.4,229 1566.4,223.23 1542.7,211.31 1524.3,200.56", + pos="e,1515.5,195.22 2690.6,263.71 2292.7,262.08 1692.9,255.2 1589.4,229 1566.4,223.19 1542.7,211.27 1524.4,200.53", style=solid]; "has attribute" [color=blue, height=0.5, @@ -74,7 +74,7 @@ digraph { "chemical or drug or treatment to disease or phenotypic feature association" -> "has attribute" [color=blue, label="has attribute", lp="1748.4,221.5", - pos="e,1651.7,195.42 2953.3,261.87 2498.2,258.3 1759.3,249.41 1701.4,229 1685.7,223.46 1670.8,212.55 1659.2,202.32", + pos="e,1651.7,195.4 2702.2,260.32 2318.4,255.45 1747.9,245.5 1701.4,229 1685.7,223.43 1670.8,212.51 1659.2,202.29", style=solid]; subject [color=blue, height=0.5, @@ -84,7 +84,7 @@ digraph { "chemical or drug or treatment to disease or phenotypic feature association" -> subject [color=blue, label=subject, lp="1842.4,221.5", - pos="e,1785,196.24 2949.6,263.16 2524.6,261.04 1866.4,253.75 1816.4,229 1805.7,223.71 1797,214.09 1790.4,204.68", + pos="e,1785,196.22 2697.7,261.23 2347.3,257.37 1855.6,248.51 1816.4,229 1805.7,223.69 1797,214.06 1790.4,204.66", style=solid]; object [color=blue, height=0.5, @@ -94,8 +94,8 @@ digraph { "chemical or drug or treatment to disease or phenotypic feature association" -> object [color=blue, label=object, lp="1913.4,178", - pos="e,1871.7,109.09 2970.2,258.74 2675.1,253.29 2269.2,243.52 2108.4,229 2011.2,220.23 1960.8,264.6 1891.4,196 1871.4,176.25 1869.3,\ -142.8 1870.8,119.17", + pos="e,1871.8,109.28 2712.2,258.73 2471.2,253.73 2168.3,244.6 2043.4,229 1974.8,220.43 1939,246.13 1891.4,196 1872.2,175.75 1869.8,142.68 \ +1871.1,119.27", style=solid]; negated [color=blue, height=0.5, @@ -104,8 +104,8 @@ digraph { width=1.2999]; "chemical or drug or treatment to disease or phenotypic feature association" -> negated [color=blue, label=negated, - lp="2218.4,221.5", - pos="e,2026,190.39 2959.2,260.52 2687.5,256.41 2332.7,247.6 2189.4,229 2135.6,222.02 2075.4,205.52 2035.6,193.37", + lp="2113.4,221.5", + pos="e,2012.7,194.16 2709.1,259.2 2455.9,254.35 2144.1,245.19 2084.4,229 2061.9,222.91 2038.9,210.58 2021.4,199.68", style=solid]; qualifiers [color=blue, height=0.5, @@ -114,8 +114,8 @@ digraph { width=2.1304]; "chemical or drug or treatment to disease or phenotypic feature association" -> qualifiers [color=blue, label=qualifiers, - lp="2351.9,221.5", - pos="e,2174.3,193.2 2961.7,260.06 2727.1,255.8 2438.4,247.01 2318.4,229 2272.1,222.05 2220.8,207.75 2183.8,196.22", + lp="2192.9,221.5", + pos="e,2136.8,195.99 2714,258.5 2471.9,253.29 2183.4,243.99 2159.4,229 2150.8,223.63 2144.7,214.51 2140.6,205.52", style=solid]; publications [color=blue, height=0.5, @@ -124,8 +124,8 @@ digraph { width=1.7332]; "chemical or drug or treatment to disease or phenotypic feature association" -> publications [color=blue, label=publications, - lp="2489.4,221.5", - pos="e,2324,193.08 2965.4,259.47 2769.1,255.02 2542.8,246.26 2445.4,229 2406.7,222.15 2364.4,208.15 2333.6,196.7", + lp="2278.4,221.5", + pos="e,2256.5,193.31 2704.7,259.88 2490,255.55 2251.4,246.76 2234.4,229 2224.3,218.5 2233.8,207.57 2247.5,198.61", style=solid]; "has evidence" [color=blue, height=0.5, @@ -134,234 +134,237 @@ digraph { width=2.0943]; "chemical or drug or treatment to disease or phenotypic feature association" -> "has evidence" [color=blue, label="has evidence", - lp="2635.9,221.5", - pos="e,2479.8,194.09 2983.7,257.15 2830,252.08 2664,243.46 2589.4,229 2554.9,222.31 2517.4,209.1 2489.3,197.94", + lp="2375.9,221.5", + pos="e,2387.7,189.71 2718.9,257.92 2536.4,252.87 2343.7,244.02 2329.4,229 2324.8,224.17 2325.4,219.35 2329.4,214 2335.9,205.25 2356.2,\ +197.84 2378,192.13", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2647.4,178", - width=3.015]; + label=string, + pos="2577.4,178", + width=1.0652]; "chemical or drug or treatment to disease or phenotypic feature association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2774.9,221.5", - pos="e,2663,195.95 3013.5,254.61 2877.8,248.83 2740.1,240.33 2710.4,229 2695.6,223.35 2681.5,212.89 2670.5,202.99", + lp="2506.9,221.5", + pos="e,2548.4,189.98 2745.4,255.36 2599.6,249.67 2453.8,241.03 2442.4,229 2396.8,180.74 2382.1,237.12 2529.4,196 2532.5,195.13 2535.7,\ +194.17 2538.9,193.15", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2882.4,178", - width=3.015]; + label=string, + pos="2672.4,178", + width=1.0652]; "chemical or drug or treatment to disease or phenotypic feature association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2941.4,221.5", - pos="e,2858.2,195.77 2996.7,255.92 2921.5,250.8 2858.9,242.48 2846.4,229 2839,220.97 2843.2,211.37 2851,202.74", + lp="2673.4,221.5", + pos="e,2642.8,189.56 2733.6,256.37 2656,251.27 2591.3,242.86 2578.4,229 2573.9,224.11 2574.6,219.48 2578.4,214 2579.3,212.74 2607.9,202.19 \ +2633.3,193", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="3117.4,178", - width=3.015]; + label=string, + pos="2767.4,178", + width=1.0652]; "chemical or drug or treatment to disease or phenotypic feature association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="3150.9,221.5", - pos="e,3068.2,194.17 3090.4,250.63 3069.3,245.45 3052.7,238.44 3044.4,229 3034,217.1 3043.7,206.69 3059.1,198.49", + lp="2887.9,221.5", + pos="e,2767.6,196.37 2838.9,250.39 2813.3,245.32 2792.3,238.41 2781.4,229 2774.8,223.29 2771.2,214.77 2769.3,206.36", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="3299.4,178", + pos="2993.4,178", width=1.5346]; "chemical or drug or treatment to disease or phenotypic feature association" -> timepoint [color=blue, label=timepoint, - lp="3297.4,221.5", - pos="e,3276.6,194.47 3277.3,246.83 3271.3,241.89 3265.8,235.93 3262.4,229 3257.7,219.42 3262.1,209.79 3269.4,201.57", + lp="3039.4,221.5", + pos="e,2994.3,196.31 3021.3,246.98 3014.9,241.92 3008.7,235.86 3004.4,229 3000.2,222.28 2997.5,214.16 2995.9,206.44", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="3411.4,178", + pos="3105.4,178", width=1.0652]; "chemical or drug or treatment to disease or phenotypic feature association" -> "original subject" [color=blue, label="original subject", - lp="3411.4,221.5", - pos="e,3387.4,192.24 3322,246.75 3331.1,236.6 3343.3,223.86 3355.4,214 3362.6,208.17 3370.8,202.54 3378.7,197.56", + lp="3140.4,221.5", + pos="e,3095.3,195.84 3062.1,246.71 3066.1,241.11 3070.5,234.84 3074.4,229 3079.7,221.09 3085.2,212.33 3090.1,204.38", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3525.4,178", + pos="3231.4,178", width=1.5887]; "chemical or drug or treatment to disease or phenotypic feature association" -> "original predicate" [color=blue, label="original predicate", - lp="3553.9,221.5", - pos="e,3510.2,195.85 3416.6,247.74 3434.1,243 3451.6,236.88 3467.4,229 3480.5,222.46 3493,212.32 3503.1,202.87", + lp="3278.9,221.5", + pos="e,3224.8,196.33 3163.7,247.85 3176.8,243.07 3189.3,236.92 3200.4,229 3208.7,223.06 3215.2,214.14 3220.1,205.48", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3639.4,178", + pos="3360.4,178", width=1.0652]; "chemical or drug or treatment to disease or phenotypic feature association" -> "original object" [color=blue, label="original object", - lp="3681.9,221.5", - pos="e,3636.4,196.13 3546.9,251.56 3577.9,246.37 3603.7,239.11 3617.4,229 3625.1,223.36 3630.1,214.47 3633.4,205.74", + lp="3407.9,221.5", + pos="e,3360.2,196.41 3285.7,251.41 3312.7,246.18 3334.8,238.96 3346.4,229 3353,223.33 3356.6,214.82 3358.6,206.41", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3772.4,178", + pos="3493.4,178", width=2.1304]; "chemical or drug or treatment to disease or phenotypic feature association" -> "subject category" [color=blue, label="subject category", - lp="3812.9,221.5", - pos="e,3765.3,195.95 3559.8,252.18 3643.7,246.55 3720.2,238.86 3737.4,229 3747,223.47 3754.7,214.06 3760.3,204.89", + lp="3537.9,221.5", + pos="e,3487.7,196.37 3298.8,252.01 3377.2,246.45 3447.6,238.85 3463.4,229 3472.2,223.52 3478.8,214.42 3483.5,205.47", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3943.4,178", + pos="3664.4,178", width=2.1304]; "chemical or drug or treatment to disease or phenotypic feature association" -> "object category" [color=blue, label="object category", - lp="3958.9,221.5", - pos="e,3926.9,195.7 3555.2,251.93 3701.3,244.29 3860.6,234.78 3876.4,229 3892.1,223.24 3907.3,212.51 3919.2,202.47", + lp="3681.9,221.5", + pos="e,3649.1,195.68 3293.8,251.77 3434.4,244.18 3586.3,234.8 3601.4,229 3616.3,223.27 3630.4,212.7 3641.5,202.74", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="4076.4,178", + pos="3797.4,178", width=1.0652]; "chemical or drug or treatment to disease or phenotypic feature association" -> "subject closure" [color=blue, label="subject closure", - lp="4094.9,221.5", - pos="e,4060.6,194.68 3558.7,252.09 3762.2,242.38 4015.7,230.1 4018.4,229 4026.3,225.85 4040.7,213.43 4053.2,201.76", + lp="3818.9,221.5", + pos="e,3784.6,195.24 3302,252.18 3497.5,242.89 3736.2,231.15 3741.4,229 3755.2,223.32 3767.9,212.68 3777.7,202.68", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="4172.4,178", + pos="3910.4,178", width=1.0652]; "chemical or drug or treatment to disease or phenotypic feature association" -> "object closure" [color=blue, label="object closure", - lp="4213.4,221.5", - pos="e,4169.9,196.36 3559,252.13 3598.3,250.36 3638.4,248.59 3676.4,247 3702.8,245.89 4129.7,244.03 4151.4,229 4159.2,223.63 4164.1,214.79 \ -4167.2,206.03", + lp="3943.4,221.5", + pos="e,3904,196.09 3301.5,252.16 3340.6,250.38 3380.6,248.61 3418.4,247 3469.4,244.83 3832.9,254.06 3877.4,229 3886.9,223.64 3894.2,214.26 \ +3899.4,205.07", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="4305.4,178", + pos="4043.4,178", width=2.1304]; "chemical or drug or treatment to disease or phenotypic feature association" -> "subject category closure" [color=blue, label="subject category closure", - lp="4371.9,221.5", - pos="e,4297.4,196.19 3556.5,251.99 3596.6,250.22 3637.6,248.48 3676.4,247 3709.2,245.74 4238.2,244.04 4267.4,229 4277.7,223.7 4286,214.21 \ -4292.1,204.91", + lp="4104.9,221.5", + pos="e,4032.9,196.26 3298.5,252.02 3338.6,250.23 3379.6,248.5 3418.4,247 3450.6,245.76 3968.1,242.39 3997.4,229 4009,223.69 4019,213.92 \ +4026.7,204.42", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="4494.4,178", + pos="4236.4,178", width=2.1304]; "chemical or drug or treatment to disease or phenotypic feature association" -> "object category closure" [color=blue, label="object category closure", - lp="4561.9,221.5", - pos="e,4488.7,196.12 3553.5,251.87 3594.5,250.07 3636.7,248.37 3676.4,247 3720.1,245.49 4425.4,250.71 4463.4,229 4472.6,223.73 4479.4,\ -214.5 4484.3,205.4", + lp="4297.9,221.5", + pos="e,4227.8,196.24 3295.5,251.88 3336.5,250.08 3378.7,248.37 3418.4,247 3461.6,245.51 4157.6,248.18 4196.4,229 4207.1,223.71 4215.8,\ +214.09 4222.4,204.69", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4684.4,178", + pos="4426.4,178", width=1.0652]; "chemical or drug or treatment to disease or phenotypic feature association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4734.4,221.5", - pos="e,4677.4,196.2 3552,251.78 3593.5,249.98 3636.2,248.3 3676.4,247 3703.4,246.13 4625.5,241.71 4649.4,229 4659.2,223.77 4666.9,214.42 \ -4672.5,205.21", + lp="4471.4,221.5", + pos="e,4417.8,195.78 3294,251.79 3335.5,249.98 3378.2,248.3 3418.4,247 3472.1,245.26 4337,252.43 4385.4,229 4396.4,223.68 4405.4,213.86 \ +4412.2,204.32", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4843.4,178", + pos="4585.4,178", width=1.0652]; "chemical or drug or treatment to disease or phenotypic feature association" -> "object namespace" [color=blue, label="object namespace", - lp="4887.4,221.5", - pos="e,4836,195.74 3551,251.74 3592.8,249.93 3635.9,248.26 3676.4,247 3707.8,246.03 4778.5,243.35 4806.4,229 4816.7,223.69 4824.9,214.01 \ -4830.9,204.57", + lp="4627.4,221.5", + pos="e,4576.5,195.8 3293,251.74 3334.8,249.93 3377.9,248.26 3418.4,247 3449.6,246.03 4515.2,242.43 4543.4,229 4554.5,223.7 4563.8,213.89 \ +4570.7,204.35", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4994.4,178", + pos="4736.4,178", width=1.0652]; "chemical or drug or treatment to disease or phenotypic feature association" -> "subject label closure" [color=blue, label="subject label closure", - lp="5047.4,221.5", - pos="e,4986.4,195.78 3550,251.72 3592.1,249.9 3635.5,248.23 3676.4,247 3711.9,245.93 4923.6,244.81 4955.4,229 4966.1,223.67 4974.8,213.85 \ -4981.2,204.32", + lp="4789.4,221.5", + pos="e,4727.8,195.8 3292,251.72 3334.1,249.9 3377.5,248.23 3418.4,247 3453.9,245.93 4663.4,244.4 4695.4,229 4706.4,223.7 4715.4,213.89 \ +4722.2,204.35", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="5165.4,178", + pos="4907.4,178", width=1.0652]; "chemical or drug or treatment to disease or phenotypic feature association" -> "object label closure" [color=blue, label="object label closure", - lp="5212.9,221.5", - pos="e,5157.1,195.79 3549.5,251.68 3591.8,249.86 3635.4,248.2 3676.4,247 3716.6,245.82 5089.2,246.66 5125.4,229 5136.3,223.7 5145.1,213.88 \ -5151.7,204.34", + lp="4954.9,221.5", + pos="e,4899.1,195.79 3291.5,251.68 3333.8,249.86 3377.4,248.2 3418.4,247 3458.6,245.82 4831.2,246.66 4867.4,229 4878.3,223.7 4887.1,213.88 \ +4893.7,204.34", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="5327.4,178", + pos="5069.4,178", width=2.347]; "chemical or drug or treatment to disease or phenotypic feature association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="5375.9,221.5", - pos="e,5318.5,196.31 3549,251.66 3591.5,249.84 3635.2,248.18 3676.4,247 3721.1,245.72 5246.1,248.36 5286.4,229 5297.2,223.79 5306.2,214.18 \ -5312.9,204.76", + lp="5117.9,221.5", + pos="e,5060.5,196.31 3291,251.66 3333.5,249.84 3377.2,248.18 3418.4,247 3463.1,245.72 4988.1,248.36 5028.4,229 5039.2,223.79 5048.2,214.18 \ +5054.9,204.76", style=solid]; type [height=0.5, - pos="5461.4,178", + pos="5203.4,178", width=0.86659]; "chemical or drug or treatment to disease or phenotypic feature association" -> type [color=blue, label=type, - lp="5475.4,221.5", - pos="e,5462.2,196.18 3548.5,251.64 3591.1,249.82 3635,248.16 3676.4,247 3701,246.31 5430.1,244.34 5449.4,229 5456.2,223.54 5459.6,214.92 \ -5461.1,206.37", + lp="5217.4,221.5", + pos="e,5204.2,196.18 3290.5,251.64 3333.1,249.82 3377,248.16 3418.4,247 3443,246.31 5172.1,244.34 5191.4,229 5198.2,223.54 5201.6,214.92 \ +5203.1,206.37", style=solid]; category [height=0.5, - pos="5562.4,178", + pos="5304.4,178", width=1.4263]; "chemical or drug or treatment to disease or phenotypic feature association" -> category [color=blue, label=category, - lp="5555.9,221.5", - pos="e,5546.8,195.25 3548.5,251.64 3591.1,249.81 3635,248.16 3676.4,247 3726.9,245.59 5447.5,245.16 5495.4,229 5511.6,223.53 5527.1,212.51 \ -5539.1,202.2", + lp="5297.9,221.5", + pos="e,5288.8,195.25 3290.5,251.64 3333.1,249.81 3377,248.16 3418.4,247 3468.9,245.59 5189.5,245.16 5237.4,229 5253.6,223.53 5269.1,212.51 \ +5281.1,202.2", style=solid]; "FDA adverse event level" [color=blue, height=0.5, label=FDAIDAAdverseEventEnum, - pos="5771.4,178", + pos="5513.4,178", width=3.8816]; "chemical or drug or treatment to disease or phenotypic feature association" -> "FDA adverse event level" [color=blue, label="FDA adverse event level", - lp="5749.9,221.5", - pos="e,5726.2,195.1 3548.5,251.62 3591.1,249.79 3635,248.15 3676.4,247 3889.1,241.1 5380.7,258.73 5591.4,229 5634.3,222.95 5681.3,209.62 \ -5716.6,198.25", + lp="5491.9,221.5", + pos="e,5468.2,195.1 3290.5,251.62 3333.1,249.79 3377,248.15 3418.4,247 3631.1,241.1 5122.7,258.73 5333.4,229 5376.3,222.95 5423.3,209.62 \ +5458.6,198.25", style=solid]; predicate [height=0.5, - pos="5983.4,178", + pos="5725.4,178", width=1.5165]; "chemical or drug or treatment to disease or phenotypic feature association" -> predicate [color=blue, label=predicate, - lp="5930.4,221.5", - pos="e,5952.9,193.06 3548,251.6 3590.8,249.77 3634.9,248.13 3676.4,247 3796.6,243.73 5722.9,249.76 5841.4,229 5877,222.77 5915.5,208.69 \ -5943.5,197.06", + lp="5672.4,221.5", + pos="e,5694.9,193.06 3290,251.6 3332.8,249.77 3376.9,248.13 3418.4,247 3538.6,243.73 5464.9,249.76 5583.4,229 5619,222.77 5657.5,208.69 \ +5685.5,197.06", style=solid]; subject -> object [label=relation, lp="1840.4,134.5", @@ -376,16 +379,16 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="3723.4,265", + pos="3465.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3854.4,265", + pos="3596.4,265", width=2.0762]; "chemical or drug or treatment to disease or phenotypic feature association_predicate" [color=blue, height=0.5, label="predicate type", - pos="4025.4,265", + pos="3767.4,265", width=2.1665]; } diff --git a/graphviz/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association.svg b/graphviz/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association.svg index 48913aacac..78a8da6ce3 100644 --- a/graphviz/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association.svg +++ b/graphviz/chemical_or_drug_or_treatment_to_disease_or_phenotypic_feature_association.svg @@ -4,16 +4,16 @@ - + %3 - + chemical or drug or treatment to disease or phenotypic feature association - -chemical or drug or treatment to disease or phenotypic feature association + +chemical or drug or treatment to disease or phenotypic feature association @@ -24,7 +24,7 @@ chemical or drug or treatment to disease or phenotypic feature association->association - + is_a @@ -37,7 +37,7 @@ chemical or drug or treatment to disease or phenotypic feature association->chemical to entity association mixin - + uses @@ -50,8 +50,8 @@ chemical or drug or treatment to disease or phenotypic feature association->entity to disease or phenotypic feature association mixin - - + + uses @@ -63,7 +63,7 @@ chemical or drug or treatment to disease or phenotypic feature association->id - + id @@ -76,8 +76,8 @@ chemical or drug or treatment to disease or phenotypic feature association->iri - - + + iri @@ -89,8 +89,8 @@ chemical or drug or treatment to disease or phenotypic feature association->name - - + + name @@ -102,8 +102,8 @@ chemical or drug or treatment to disease or phenotypic feature association->description - - + + description @@ -115,8 +115,8 @@ chemical or drug or treatment to disease or phenotypic feature association->has attribute - - + + has attribute @@ -128,8 +128,8 @@ chemical or drug or treatment to disease or phenotypic feature association->subject - - + + subject @@ -141,8 +141,8 @@ chemical or drug or treatment to disease or phenotypic feature association->object - - + + object @@ -154,9 +154,9 @@ chemical or drug or treatment to disease or phenotypic feature association->negated - - -negated + + +negated @@ -167,9 +167,9 @@ chemical or drug or treatment to disease or phenotypic feature association->qualifiers - - -qualifiers + + +qualifiers @@ -180,9 +180,9 @@ chemical or drug or treatment to disease or phenotypic feature association->publications - - -publications + + +publications @@ -193,295 +193,295 @@ chemical or drug or treatment to disease or phenotypic feature association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string chemical or drug or treatment to disease or phenotypic feature association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string chemical or drug or treatment to disease or phenotypic feature association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string chemical or drug or treatment to disease or phenotypic feature association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type chemical or drug or treatment to disease or phenotypic feature association->timepoint - - -timepoint + + +timepoint original subject - -string + +string chemical or drug or treatment to disease or phenotypic feature association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie chemical or drug or treatment to disease or phenotypic feature association->original predicate - - -original predicate + + +original predicate original object - -string + +string chemical or drug or treatment to disease or phenotypic feature association->original object - - -original object + + +original object subject category - -ontology class + +ontology class chemical or drug or treatment to disease or phenotypic feature association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class chemical or drug or treatment to disease or phenotypic feature association->object category - - -object category + + +object category subject closure - -string + +string chemical or drug or treatment to disease or phenotypic feature association->subject closure - - -subject closure + + +subject closure object closure - -string + +string chemical or drug or treatment to disease or phenotypic feature association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class chemical or drug or treatment to disease or phenotypic feature association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class chemical or drug or treatment to disease or phenotypic feature association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string chemical or drug or treatment to disease or phenotypic feature association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string chemical or drug or treatment to disease or phenotypic feature association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string chemical or drug or treatment to disease or phenotypic feature association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string chemical or drug or treatment to disease or phenotypic feature association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source chemical or drug or treatment to disease or phenotypic feature association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type chemical or drug or treatment to disease or phenotypic feature association->type - - -type + + +type category - -category + +category chemical or drug or treatment to disease or phenotypic feature association->category - - -category + + +category FDA adverse event level - -FDAIDAAdverseEventEnum + +FDAIDAAdverseEventEnum chemical or drug or treatment to disease or phenotypic feature association->FDA adverse event level - - -FDA adverse event level + + +FDA adverse event level predicate - -predicate + +predicate chemical or drug or treatment to disease or phenotypic feature association->predicate - - -predicate + + +predicate @@ -511,20 +511,20 @@ association_type - -string + +string association_category - -category type + +category type chemical or drug or treatment to disease or phenotypic feature association_predicate - -predicate type + +predicate type diff --git a/graphviz/chemical_to_chemical_association.gv b/graphviz/chemical_to_chemical_association.gv index a563126ed6..11866b0b6d 100644 --- a/graphviz/chemical_to_chemical_association.gv +++ b/graphviz/chemical_to_chemical_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,5202.4,283"]; + graph [bb="0,0,4944.4,283"]; node [label="\N"]; "chemical to chemical association" [height=0.5, label="chemical to chemical association", - pos="2834.4,265", + pos="2576.4,265", width=4.5135]; association [height=0.5, pos="62.394,178", width=1.7332]; "chemical to chemical association" -> association [label=is_a, - lp="496.39,221.5", - pos="e,107.14,190.57 2672.5,263.27 2213.5,260.94 909.66,252.4 482.39,229 327.27,220.5 287.69,221.24 134.39,196 128.71,195.06 122.81,193.93 \ -116.94,192.71"]; + lp="495.39,221.5", + pos="e,107.14,190.57 2414.9,262.94 1991.6,259.89 856.74,249.95 481.39,229 326.72,220.37 287.25,221.19 134.39,196 128.71,195.06 122.81,\ +193.93 116.94,192.71"]; "chemical to entity association mixin" [height=0.5, pos="320.39,178", width=4.9287]; "chemical to chemical association" -> "chemical to entity association mixin" [label=uses, - lp="652.89,221.5", - pos="e,397.29,194.28 2671.7,264.39 2232.8,264.95 1031.3,263.22 636.39,229 558.39,222.24 470.48,207.77 407.23,196.12"]; + lp="650.89,221.5", + pos="e,397.12,194.3 2413.9,264 2011.8,263.52 977.86,259.29 634.39,229 557.02,222.18 469.83,207.75 406.99,196.13"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "chemical to chemical association" -> id [color=blue, label=id, - lp="773.39,221.5", - pos="e,583.37,190.01 2672.6,262.95 2218.5,259.78 953.32,249.22 766.39,229 692.48,221 674.06,215.79 602.39,196 599.28,195.14 596.08,194.18 \ -592.89,193.17", + lp="770.39,221.5", + pos="e,583.38,189.99 2413.8,264.67 2030.8,265.62 1080.3,264.24 763.39,229 690.8,220.93 672.77,215.57 602.39,196 599.29,195.14 596.09,\ +194.17 592.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,9 @@ digraph { width=1.2277]; "chemical to chemical association" -> iri [color=blue, label=iri, - lp="891.39,221.5", - pos="e,688.01,190.16 2671.9,264.61 2268.3,265.55 1228.2,264.35 883.39,229 804.66,220.93 785.11,215.46 708.39,196 704.97,195.13 701.43,\ -194.16 697.9,193.14", + lp="885.39,221.5", + pos="e,688.3,190.21 2413.9,264.22 2048.7,264.14 1171.8,260.53 877.39,229 801.3,220.85 782.51,215.05 708.39,196 705.02,195.13 701.54,194.17 \ +698.05,193.16", style=solid]; name [color=blue, height=0.5, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "chemical to chemical association" -> name [color=blue, label=name, - lp="1005.4,221.5", - pos="e,813.59,191.06 2673,262.84 2253.4,259.55 1150,249.08 985.39,229 929,222.12 865.78,205.98 823.37,193.88", + lp="995.39,221.5", + pos="e,812.8,191.31 2415.2,262.47 2037.2,258.59 1115.1,247.37 975.39,229 922.2,222 862.74,206.18 822.38,194.19", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "chemical to chemical association" -> description [color=blue, label=description, - lp="1136.9,221.5", - pos="e,963.36,193.52 2672.4,263.16 2270.6,260.74 1249.2,252.33 1096.4,229 1053.9,222.51 1007.1,208.43 973.04,196.86", + lp="1120.9,221.5", + pos="e,960.53,193.86 2415.1,262.83 2055.3,259.86 1208.9,250.64 1080.4,229 1042.3,222.59 1000.7,208.91 970.08,197.48", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "chemical to chemical association" -> "has attribute" [color=blue, label="has attribute", - lp="1298.4,221.5", - pos="e,1104.4,191.41 2673.2,262.67 2298.3,259.24 1389,248.98 1251.4,229 1203.7,222.07 1150.7,206.59 1114.2,194.67", + lp="1273.4,221.5", + pos="e,1101.5,192.18 2415.6,262.38 2083,258.65 1340.6,248.27 1226.4,229 1186.3,222.24 1142.3,207.57 1111.2,195.87", style=solid]; subject [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=1.9318]; "chemical to chemical association" -> subject [color=blue, label=subject, - lp="1463.4,221.5", - pos="e,1254.8,191.65 2672.1,263.82 2356.8,262.83 1671.7,257.36 1437.4,229 1377.6,221.76 1310.4,206.08 1264.5,194.2", + lp="1422.4,221.5", + pos="e,1249.7,192.68 2414.2,263.83 2138,262.75 1587.7,257.03 1396.4,229 1349.1,222.07 1296.6,207.4 1259.3,195.73", style=solid]; predicate [color=blue, height=0.5, @@ -87,8 +87,8 @@ digraph { width=2.1665]; "chemical to chemical association" -> predicate [color=blue, label=predicate, - lp="1601.4,221.5", - pos="e,1418.3,193.17 2671.9,264.1 2379.5,263.51 1775.7,258.6 1567.4,229 1519.5,222.19 1466.4,207.8 1428.2,196.2", + lp="1536.4,221.5", + pos="e,1406.3,194.64 2416.3,261.8 2138.7,257.53 1589.2,246.94 1502.4,229 1472.3,222.78 1440.1,210.01 1415.6,198.94", style=solid]; negated [color=blue, height=0.5, @@ -97,8 +97,8 @@ digraph { width=1.2999]; "chemical to chemical association" -> negated [color=blue, label=negated, - lp="1745.4,221.5", - pos="e,1553,190.39 2673,262.83 2409,260.26 1896.3,252.34 1716.4,229 1662.6,222.02 1602.4,205.52 1562.6,193.37", + lp="1640.4,221.5", + pos="e,1539.7,194.16 2415.8,262.15 2161.3,258.62 1686.6,249.39 1611.4,229 1588.9,222.91 1565.9,210.58 1548.4,199.68", style=solid]; qualifiers [color=blue, height=0.5, @@ -107,8 +107,8 @@ digraph { width=2.1304]; "chemical to chemical association" -> qualifiers [color=blue, label=qualifiers, - lp="1878.9,221.5", - pos="e,1701.3,193.2 2673,262.73 2434.7,260.11 2000,252.21 1845.4,229 1799.1,222.05 1747.8,207.75 1710.8,196.22", + lp="1719.9,221.5", + pos="e,1663.8,195.99 2416.5,261.79 2168.6,257.79 1716.8,247.93 1686.4,229 1677.8,223.63 1671.7,214.51 1667.6,205.52", style=solid]; publications [color=blue, height=0.5, @@ -117,8 +117,8 @@ digraph { width=1.7332]; "chemical to chemical association" -> publications [color=blue, label=publications, - lp="2016.4,221.5", - pos="e,1851,193.08 2672.9,262.63 2461.4,259.93 2102.3,252.01 1972.4,229 1933.7,222.15 1891.4,208.15 1860.6,196.7", + lp="1805.4,221.5", + pos="e,1783.5,193.31 2415.1,262.73 2184,260.1 1783.6,252.2 1761.4,229 1751.3,218.5 1760.8,207.57 1774.5,198.61", style=solid]; "has evidence" [color=blue, height=0.5, @@ -127,226 +127,229 @@ digraph { width=2.0943]; "chemical to chemical association" -> "has evidence" [color=blue, label="has evidence", - lp="2162.9,221.5", - pos="e,2006.8,194.09 2674.7,261.51 2496.4,257.79 2219.3,248.95 2116.4,229 2081.9,222.31 2044.4,209.1 2016.3,197.94", + lp="1902.9,221.5", + pos="e,1914.7,189.71 2416.3,261.75 2210,258.04 1875.4,248.98 1856.4,229 1851.8,224.17 1852.4,219.35 1856.4,214 1862.9,205.25 1883.2,197.84 \ +1905,192.13", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2174.4,178", - width=3.015]; + label=string, + pos="2104.4,178", + width=1.0652]; "chemical to chemical association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2301.9,221.5", - pos="e,2190,195.95 2678.7,259.73 2515.6,254.48 2277.6,244.33 2237.4,229 2222.6,223.35 2208.5,212.89 2197.5,202.99", + lp="2033.9,221.5", + pos="e,2075.4,189.98 2419.4,260.25 2244.7,255.29 1984.7,245.23 1969.4,229 1923.8,180.74 1909.1,237.12 2056.4,196 2059.5,195.13 2062.7,\ +194.17 2065.9,193.15", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2409.4,178", - width=3.015]; + label=string, + pos="2199.4,178", + width=1.0652]; "chemical to chemical association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2468.4,221.5", - pos="e,2385.2,195.77 2673.6,262.33 2548.9,259.31 2393.9,251.09 2373.4,229 2366,220.97 2370.2,211.37 2378,202.74", + lp="2200.4,221.5", + pos="e,2169.8,189.56 2415.3,262.64 2287.3,259.83 2126.5,251.74 2105.4,229 2100.9,224.11 2101.6,219.48 2105.4,214 2106.3,212.74 2134.9,\ +202.19 2160.3,193", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2644.4,178", - width=3.015]; + label=string, + pos="2294.4,178", + width=1.0652]; "chemical to chemical association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2677.9,221.5", - pos="e,2595.2,194.17 2677.7,260.19 2630.2,255.5 2586.6,246.37 2571.4,229 2561,217.1 2570.7,206.69 2586.1,198.49", + lp="2414.9,221.5", + pos="e,2294.6,196.37 2424.7,258.53 2374.5,253.75 2326.8,244.98 2308.4,229 2301.8,223.29 2298.2,214.77 2296.3,206.36", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2826.4,178", + pos="2520.4,178", width=1.5346]; "chemical to chemical association" -> timepoint [color=blue, label=timepoint, - lp="2824.4,221.5", - pos="e,2803.6,194.47 2804.8,247.2 2798.6,242.2 2792.9,236.11 2789.4,229 2784.7,219.42 2789.1,209.79 2796.4,201.57", + lp="2566.4,221.5", + pos="e,2521.3,196.31 2548.3,246.98 2541.9,241.92 2535.7,235.86 2531.4,229 2527.2,222.28 2524.5,214.16 2522.9,206.44", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2938.4,178", + pos="2632.4,178", width=1.0652]; "chemical to chemical association" -> "original subject" [color=blue, label="original subject", - lp="2938.4,221.5", - pos="e,2914.4,192.24 2849,246.75 2858.1,236.6 2870.3,223.86 2882.4,214 2889.6,208.17 2897.8,202.54 2905.7,197.56", + lp="2667.4,221.5", + pos="e,2622.3,195.84 2589.1,246.71 2593.1,241.11 2597.5,234.84 2601.4,229 2606.7,221.09 2612.2,212.33 2617.1,204.38", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3052.4,178", + pos="2758.4,178", width=1.5887]; "chemical to chemical association" -> "original predicate" [color=blue, label="original predicate", - lp="3080.9,221.5", - pos="e,3037.2,195.85 2932.6,250.55 2953.7,245.48 2975.3,238.53 2994.4,229 3007.5,222.46 3020,212.32 3030.1,202.87", + lp="2805.9,221.5", + pos="e,2751.8,196.33 2681,251.15 2697.5,246.01 2713.6,238.88 2727.4,229 2735.7,223.06 2742.2,214.14 2747.1,205.48", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3166.4,178", + pos="2892.4,178", width=1.0652]; "chemical to chemical association" -> "original object" [color=blue, label="original object", - lp="3208.9,221.5", - pos="e,3163.4,196.13 2949.9,252.29 3036.3,243.32 3140.3,231.98 3144.4,229 3152.1,223.36 3157.1,214.47 3160.4,205.74", + lp="2936.9,221.5", + pos="e,2890.4,196.05 2689.6,252.01 2771.9,243.08 2869.6,231.94 2873.4,229 2880.7,223.33 2885.1,214.55 2887.9,205.92", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3299.4,178", + pos="3025.4,178", width=2.1304]; "chemical to chemical association" -> "subject category" [color=blue, label="subject category", - lp="3339.9,221.5", - pos="e,3292.3,196 2949.1,252.2 2968.2,250.37 2987.9,248.56 3006.4,247 3063.7,242.17 3214.4,257.3 3264.4,229 3274.1,223.52 3281.7,214.13 \ -3287.3,204.95", + lp="3067.9,221.5", + pos="e,3018.9,195.96 2691.5,252.22 2710.5,250.39 2730,248.59 2748.4,247 2802.6,242.33 2945.5,256.51 2992.4,229 3001.8,223.47 3009.1,214.07 \ +3014.3,204.9", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3470.4,178", + pos="3196.4,178", width=2.1304]; "chemical to chemical association" -> "object category" [color=blue, label="object category", - lp="3485.9,221.5", - pos="e,3453.9,195.79 2947.2,251.98 2966.9,250.13 2987.2,248.38 3006.4,247 3094.5,240.65 3320.2,258.72 3403.4,229 3419.2,223.36 3434.3,\ -212.65 3446.2,202.59", + lp="3212.9,221.5", + pos="e,3180.5,195.78 2689.2,252.01 2708.9,250.16 2729.2,248.4 2748.4,247 2833.4,240.81 3051.4,258.32 3131.4,229 3146.8,223.35 3161.5,\ +212.63 3173.1,202.57", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3603.4,178", + pos="3329.4,178", width=1.0652]; "chemical to chemical association" -> "subject closure" [color=blue, label="subject closure", - lp="3621.9,221.5", - pos="e,3587.7,194.71 2946.3,251.88 2966.3,250.01 2986.9,248.29 3006.4,247 3066.2,243.05 3489.6,250.8 3545.4,229 3553.3,225.92 3567.7,\ -213.5 3580.2,201.81", + lp="3351.9,221.5", + pos="e,3316.3,195.33 2688.3,251.89 2708.3,250.03 2728.9,248.29 2748.4,247 2806.5,243.13 3218.2,250.46 3272.4,229 3286.4,223.44 3299.3,\ +212.81 3309.3,202.79", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3699.4,178", + pos="3437.4,178", width=1.0652]; "chemical to chemical association" -> "object closure" [color=blue, label="object closure", - lp="3741.4,221.5", - pos="e,3697,196.4 2945.8,251.81 2965.9,249.94 2986.8,248.23 3006.4,247 3043.7,244.66 3647.6,250.09 3678.4,229 3686.2,223.67 3691.1,214.85 \ -3694.2,206.08", + lp="3474.4,221.5", + pos="e,3433,196.04 2687.8,251.82 2707.9,249.95 2728.8,248.23 2748.4,247 2785.1,244.69 3379.1,248.28 3410.4,229 3419,223.69 3425.1,214.58 \ +3429.2,205.58", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3832.4,178", + pos="3570.4,178", width=2.1304]; "chemical to chemical association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3899.9,221.5", - pos="e,3824.8,196.21 2945.3,251.79 2965.6,249.91 2986.6,248.2 3006.4,247 3050.2,244.34 3756.5,249.18 3795.4,229 3805.6,223.73 3813.7,\ -214.24 3819.7,204.93", + lp="3634.9,221.5", + pos="e,3561.2,196.26 2687.3,251.8 2707.6,249.92 2728.6,248.2 2748.4,247 2791.7,244.37 3489.3,247.76 3528.4,229 3539.3,223.74 3548.5,214.12 \ +3555.4,204.71", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="4021.4,178", + pos="3763.4,178", width=2.1304]; "chemical to chemical association" -> "object category closure" [color=blue, label="object category closure", - lp="4089.9,221.5", - pos="e,4016.1,196.12 2944.9,251.76 2965.3,249.87 2986.5,248.16 3006.4,247 3033.7,245.4 3967.7,242.7 3991.4,229 4000.5,223.73 4007.2,214.51 \ -4011.9,205.4", + lp="3826.9,221.5", + pos="e,3755.8,196.23 2686.9,251.76 2707.3,249.87 2728.5,248.17 2748.4,247 2802.6,243.82 3678.1,253.9 3726.4,229 3736.6,223.75 3744.7,\ +214.26 3750.7,204.95", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4211.4,178", + pos="3953.4,178", width=1.0652]; "chemical to chemical association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4261.4,221.5", - pos="e,4204.7,196.2 2944.9,251.71 2965.3,249.83 2986.5,248.14 3006.4,247 3038.9,245.15 4148.8,244.44 4177.4,229 4187.1,223.77 4194.6,\ -214.42 4200,205.21", + lp="4000.4,221.5", + pos="e,3945.4,195.77 2686.9,251.71 2707.3,249.83 2728.5,248.14 2748.4,247 2780.7,245.16 3885.4,243.44 3914.4,229 3925.1,223.67 3933.8,\ +213.84 3940.2,204.31", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4370.4,178", + pos="4112.4,178", width=1.0652]; "chemical to chemical association" -> "object namespace" [color=blue, label="object namespace", - lp="4414.4,221.5", - pos="e,4363,195.75 2944.4,251.73 2965,249.83 2986.3,248.13 3006.4,247 3043.2,244.94 4300.6,245.82 4333.4,229 4343.7,223.7 4351.9,214.02 \ -4357.9,204.58", + lp="4154.4,221.5", + pos="e,4104.1,195.79 2686.4,251.73 2707,249.83 2728.3,248.13 2748.4,247 2785.1,244.94 4039.4,245.16 4072.4,229 4083.3,223.69 4092.1,213.87 \ +4098.7,204.33", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4521.4,178", + pos="4263.4,178", width=1.0652]; "chemical to chemical association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4574.4,221.5", - pos="e,4513.4,195.78 2944.4,251.7 2965,249.81 2986.3,248.11 3006.4,247 3047.3,244.73 4445.7,247.21 4482.4,229 4493.1,223.68 4501.8,213.86 \ -4508.2,204.33", + lp="4316.4,221.5", + pos="e,4254.8,195.81 2686.4,251.7 2707,249.81 2728.3,248.11 2748.4,247 2789.3,244.73 4185.5,246.74 4222.4,229 4233.4,223.71 4242.4,213.9 \ +4249.2,204.36", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4692.4,178", + pos="4434.4,178", width=1.0652]; "chemical to chemical association" -> "object label closure" [color=blue, label="object label closure", - lp="4740.9,221.5", - pos="e,4684.1,195.8 2944.4,251.68 2965,249.79 2986.3,248.1 3006.4,247 3052.1,244.5 4611.3,249.03 4652.4,229 4663.3,223.71 4672.1,213.89 \ -4678.7,204.35", + lp="4482.9,221.5", + pos="e,4426.1,195.8 2686.4,251.68 2707,249.79 2728.3,248.1 2748.4,247 2794.1,244.5 4353.3,249.03 4394.4,229 4405.3,223.71 4414.1,213.89 \ +4420.7,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4854.4,178", + pos="4596.4,178", width=2.347]; "chemical to chemical association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4902.9,221.5", - pos="e,4845.8,196.3 2944.4,251.67 2965,249.77 2986.3,248.09 3006.4,247 3056.5,244.28 4769.2,250.98 4814.4,229 4825.1,223.78 4833.9,214.17 \ -4840.4,204.76", + lp="4644.9,221.5", + pos="e,4587.8,196.3 2686.4,251.67 2707,249.77 2728.3,248.09 2748.4,247 2798.5,244.28 4511.2,250.98 4556.4,229 4567.1,223.78 4575.9,214.17 \ +4582.4,204.76", style=solid]; type [height=0.5, - pos="4988.4,178", + pos="4730.4,178", width=0.86659]; "chemical to chemical association" -> type [color=blue, label=type, - lp="5002.4,221.5", - pos="e,4989.2,196.19 2943.9,251.69 2964.7,249.79 2986.2,248.09 3006.4,247 3033.7,245.53 4955,246.04 4976.4,229 4983.2,223.55 4986.6,214.93 \ -4988.2,206.37", + lp="4744.4,221.5", + pos="e,4731.2,196.19 2685.9,251.69 2706.7,249.79 2728.2,248.09 2748.4,247 2775.7,245.53 4697,246.04 4718.4,229 4725.2,223.55 4728.6,214.93 \ +4730.2,206.37", style=solid]; category [height=0.5, - pos="5089.4,178", + pos="4831.4,178", width=1.4263]; "chemical to chemical association" -> category [color=blue, label=category, - lp="5081.9,221.5", - pos="e,5073.8,195.26 2943.9,251.69 2964.7,249.78 2986.2,248.09 3006.4,247 3062.3,243.99 4969.3,246.88 5022.4,229 5038.6,223.54 5054.1,\ -212.52 5066.1,202.21", + lp="4823.9,221.5", + pos="e,4815.8,195.26 2685.9,251.69 2706.7,249.78 2728.2,248.09 2748.4,247 2804.3,243.99 4711.3,246.88 4764.4,229 4780.6,223.54 4796.1,\ +212.52 4808.1,202.21", style=solid]; object [height=0.5, pos="1276.4,91", width=1.0832]; "chemical to chemical association" -> object [color=blue, label=object, - lp="5180.4,178", - pos="e,1315.5,91.926 2943.9,251.68 2964.7,249.78 2986.2,248.08 3006.4,247 3065,243.86 5063.5,252.09 5117.4,229 5148.5,215.69 5173.1,184.11 \ -5149.4,160 5079.1,88.423 1771.3,91.209 1325.8,91.91", + lp="4922.4,178", + pos="e,1315.6,91.976 2685.9,251.68 2706.7,249.78 2728.2,248.08 2748.4,247 2807,243.86 4805.5,252.09 4859.4,229 4890.5,215.69 4915.1,184.13 \ +4891.4,160 4826,93.321 1754.3,91.853 1325.8,91.973", style=solid]; subject -> object [label=relation, lp="1275.4,134.5", @@ -359,18 +362,18 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="3053.4,265", + pos="2795.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3184.4,265", + pos="2926.4,265", width=2.0762]; object -> relation [pos="e,1234.2,35.54 1263.9,73.889 1257,64.939 1248.2,53.617 1240.4,43.584", style=dotted]; "chemical to chemical association_object" [color=blue, height=0.5, label="chemical entity", - pos="3359.4,265", + pos="3101.4,265", width=2.2748]; } diff --git a/graphviz/chemical_to_chemical_association.svg b/graphviz/chemical_to_chemical_association.svg index 21b1998a9b..42f7de98bd 100644 --- a/graphviz/chemical_to_chemical_association.svg +++ b/graphviz/chemical_to_chemical_association.svg @@ -4,16 +4,16 @@ - + %3 - + chemical to chemical association - -chemical to chemical association + +chemical to chemical association @@ -24,9 +24,9 @@ chemical to chemical association->association - + -is_a +is_a @@ -37,9 +37,9 @@ chemical to chemical association->chemical to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ chemical to chemical association->id - - -id + + +id @@ -63,9 +63,9 @@ chemical to chemical association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ chemical to chemical association->name - - -name + + +name @@ -89,9 +89,9 @@ chemical to chemical association->description - - -description + + +description @@ -102,9 +102,9 @@ chemical to chemical association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ chemical to chemical association->subject - - -subject + + +subject @@ -128,9 +128,9 @@ chemical to chemical association->predicate - - -predicate + + +predicate @@ -141,9 +141,9 @@ chemical to chemical association->negated - - -negated + + +negated @@ -154,9 +154,9 @@ chemical to chemical association->qualifiers - - -qualifiers + + +qualifiers @@ -167,9 +167,9 @@ chemical to chemical association->publications - - -publications + + +publications @@ -180,269 +180,269 @@ chemical to chemical association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string chemical to chemical association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string chemical to chemical association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string chemical to chemical association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type chemical to chemical association->timepoint - - -timepoint + + +timepoint original subject - -string + +string chemical to chemical association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie chemical to chemical association->original predicate - - -original predicate + + +original predicate original object - -string + +string chemical to chemical association->original object - - -original object + + +original object subject category - -ontology class + +ontology class chemical to chemical association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class chemical to chemical association->object category - - -object category + + +object category subject closure - -string + +string chemical to chemical association->subject closure - - -subject closure + + +subject closure object closure - -string + +string chemical to chemical association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class chemical to chemical association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class chemical to chemical association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string chemical to chemical association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string chemical to chemical association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string chemical to chemical association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string chemical to chemical association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source chemical to chemical association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type chemical to chemical association->type - - -type + + +type category - -category + +category chemical to chemical association->category - - -category + + +category @@ -453,9 +453,9 @@ chemical to chemical association->object - - -object + + +object @@ -479,14 +479,14 @@ association_type - -string + +string association_category - -category type + +category type @@ -497,8 +497,8 @@ chemical to chemical association_object - -chemical entity + +chemical entity diff --git a/graphviz/chemical_to_chemical_derivation_association.gv b/graphviz/chemical_to_chemical_derivation_association.gv index ba262d2315..6e27f9c45d 100644 --- a/graphviz/chemical_to_chemical_derivation_association.gv +++ b/graphviz/chemical_to_chemical_derivation_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,5134.1,283"]; + graph [bb="0,0,4949.1,283"]; node [label="\N"]; "chemical to chemical derivation association" [height=0.5, label="chemical to chemical derivation association", - pos="2731.5,265", + pos="2546.5,265", width=5.9036]; "chemical to chemical association" [height=0.5, pos="162.49,178", width=4.5135]; "chemical to chemical derivation association" -> "chemical to chemical association" [label=is_a, lp="480.49,221.5", - pos="e,235.5,194.12 2518.6,264.72 2034.1,265.71 860.52,264.25 466.49,229 391.17,222.26 306.32,207.72 245.44,196.04"]; + pos="e,235.51,194.09 2333.7,264.37 1878.7,264.51 823.72,261.21 466.49,229 391.17,222.21 306.33,207.67 245.45,196.01"]; id [color=blue, height=0.5, label=string, @@ -19,7 +19,7 @@ digraph { "chemical to chemical derivation association" -> id [color=blue, label=id, lp="595.49,221.5", - pos="e,410.47,189.98 2520.4,262.81 2017.5,259.66 776.46,249.85 588.49,229 516.75,221.04 498.99,215.43 429.49,196 426.38,195.13 423.18,\ + pos="e,410.47,189.98 2335.9,262.46 1865.7,258.7 758.06,247.94 588.49,229 516.76,220.99 498.99,215.43 429.49,196 426.38,195.13 423.18,\ 194.17 419.98,193.15", style=solid]; iri [color=blue, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "chemical to chemical derivation association" -> iri [color=blue, label=iri, - lp="708.49,221.5", - pos="e,515.4,190.19 2520.8,262.52 2037.6,258.82 877.39,248.06 700.49,229 626.13,220.99 607.87,214.78 535.49,196 532.11,195.12 528.63,\ -194.16 525.15,193.14", + lp="701.49,221.5", + pos="e,515.41,190.15 2336.3,262.25 1885.3,258.16 852.65,246.96 693.49,229 622.2,220.95 604.85,214.31 535.49,196 532.11,195.11 528.64,\ +194.13 525.16,193.11", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "chemical to chemical derivation association" -> name [color=blue, label=name, - lp="815.49,221.5", - pos="e,639.24,191.54 2520.2,262.97 2053.4,260.3 962.3,251.68 795.49,229 744.71,222.09 688.12,206.58 649.23,194.65", + lp="804.49,221.5", + pos="e,638.07,191.87 2335.5,262.73 1900.9,259.69 933.96,250.57 784.49,229 737.11,222.16 684.54,206.98 647.95,195.12", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "chemical to chemical derivation association" -> description [color=blue, label=description, - lp="935.99,221.5", - pos="e,785.29,194.15 2519.2,263.7 2070,262.53 1051.3,256.81 895.49,229 860.65,222.78 822.91,209.42 794.81,198.07", + lp="917.99,221.5", + pos="e,781.61,194.51 2334.2,263.76 1916.5,262.67 1016.3,257.05 877.49,229 847.35,222.91 815.15,210.01 790.85,198.84", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "chemical to chemical derivation association" -> "has attribute" [color=blue, label="has attribute", - lp="1081.5,221.5", - pos="e,926.11,192.95 2519.3,263.49 2096.4,261.91 1176.5,255.44 1034.5,229 1000,222.58 962.73,208.62 935.62,197.07", + lp="1052.5,221.5", + pos="e,921.42,194.01 2334.2,263.95 1941.7,263.15 1131.2,257.95 1005.5,229 978.98,222.89 951.13,210 930.22,198.83", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "chemical to chemical derivation association" -> negated [color=blue, label=negated, - lp="1236.5,221.5", - pos="e,1047.3,190.46 2519,264.63 2161.4,264.76 1454.4,260.78 1207.5,229 1154.9,222.23 1096.2,205.81 1057.3,193.62", + lp="1190.5,221.5", + pos="e,1043.1,191.97 2336.3,262.16 1977.3,258.5 1273.6,248.88 1161.5,229 1123.5,222.26 1081.9,207.54 1052.6,195.81", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "chemical to chemical derivation association" -> qualifiers [color=blue, label=qualifiers, - lp="1375,221.5", - pos="e,1196.2,193.2 2518.7,264.77 2187,264.94 1562,260.8 1341.5,229 1294.8,222.26 1243,207.87 1205.8,196.25", + lp="1301,221.5", + pos="e,1182.2,194.94 2335.5,262.69 1999,259.93 1368.3,251.76 1267.5,229 1240.9,222.99 1212.8,210.61 1191.3,199.68", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "chemical to chemical derivation association" -> publications [color=blue, label=publications, - lp="1520.5,221.5", - pos="e,1347.2,192.85 2518.7,264.89 2214.5,265 1670.6,260.53 1476.5,229 1435.1,222.28 1389.6,207.95 1356.9,196.35", + lp="1401.5,221.5", + pos="e,1321.7,195.78 2336.5,262.03 2007,258.35 1401.1,248.91 1357.5,229 1345.7,223.62 1335.6,213.65 1327.8,204.03", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,288 +100,288 @@ digraph { width=2.0943]; "chemical to chemical derivation association" -> "has evidence" [color=blue, label="has evidence", - lp="1679,221.5", - pos="e,1505.5,193.63 2519.4,263.84 2249.1,262.49 1797.1,256.07 1632.5,229 1592.1,222.35 1547.7,208.52 1515.2,197.09", + lp="1500,221.5", + pos="e,1455.5,195.85 2333.8,264.69 2024.4,264.64 1483.6,260.06 1453.5,229 1447.2,222.53 1448,213.5 1451.2,204.89", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1669.5,178", - width=3.015]; + label=string, + pos="1599.5,178", + width=1.0652]; "chemical to chemical derivation association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1834,221.5", - pos="e,1695,195.61 2523.7,261.12 2262.7,256.78 1840.2,247.06 1769.5,229 1746.4,223.1 1722.4,211.34 1703.7,200.71", + lp="1619,221.5", + pos="e,1575.1,191.97 2334,263.92 2050.6,262.74 1581.1,256.6 1554.5,229 1544.8,218.94 1554,207.35 1566.6,197.86", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1904.5,178", - width=3.015]; + label=string, + pos="1694.5,178", + width=1.0652]; "chemical to chemical derivation association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2005.5,221.5", - pos="e,1901.5,196.33 2522.3,261.76 2286.4,258.25 1932.7,249.57 1910.5,229 1904.4,223.32 1902,214.91 1901.4,206.59", + lp="1788.5,221.5", + pos="e,1688.6,196.04 2335.7,262.56 2090.3,259.83 1715.5,251.91 1693.5,229 1687.7,222.94 1686.4,214.33 1687.1,205.95", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2139.5,178", - width=3.015]; + label=string, + pos="1869.5,178", + width=1.0652]; "chemical to chemical derivation association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2214,221.5", - pos="e,2117.7,195.87 2529.8,259.28 2353.1,254.12 2122.1,244.46 2107.5,229 2100.3,221.43 2103.8,212.05 2110.6,203.46", + lp="2009,221.5", + pos="e,1875.9,196.03 2336.9,261.94 2163.5,258.69 1939.7,250.36 1902.5,229 1893,223.57 1885.8,214.18 1880.5,204.99", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2321.5,178", + pos="2095.5,178", width=1.5346]; "chemical to chemical derivation association" -> timepoint [color=blue, label=timepoint, - lp="2368.5,221.5", - pos="e,2320.9,196.43 2540.3,257.11 2446.5,251.95 2350,243.25 2333.5,229 2326.9,223.36 2323.6,214.85 2322,206.44", + lp="2171.5,221.5", + pos="e,2104.5,195.99 2339,261.04 2256.3,256.83 2172.2,247.8 2136.5,229 2125.8,223.39 2116.9,213.72 2110.1,204.36", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2433.5,178", + pos="2207.5,178", width=1.0652]; "chemical to chemical derivation association" -> "original subject" [color=blue, label="original subject", - lp="2466.5,221.5", - pos="e,2417.7,194.82 2556.4,254.76 2487.1,249.28 2421.2,241 2410.5,229 2403.8,221.56 2406.4,211.86 2411.9,202.98", + lp="2275.5,221.5", + pos="e,2206.9,196.38 2375.8,254.22 2303.2,248.49 2232.2,240.17 2219.5,229 2213,223.3 2209.7,214.78 2208.1,206.37", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2547.5,178", + pos="2333.5,178", width=1.5887]; "chemical to chemical derivation association" -> "original predicate" [color=blue, label="original predicate", - lp="2593,221.5", - pos="e,2533.7,195.8 2585.7,251.87 2559.8,246.73 2538.3,239.42 2529.5,229 2523.6,222.05 2524.9,213.06 2528.8,204.62", + lp="2406,221.5", + pos="e,2332,196.09 2404.8,251.57 2376.7,246.43 2352.8,239.19 2342.5,229 2336.5,223.06 2333.7,214.58 2332.6,206.29", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2661.5,178", + pos="2467.5,178", width=1.0652]; "chemical to chemical derivation association" -> "original object" [color=blue, label="original object", - lp="2717,221.5", - pos="e,2658.9,196.07 2685.2,247.23 2677.5,242.47 2670.4,236.48 2665.5,229 2661.1,222.32 2659.3,214 2658.9,206.08", + lp="2532,221.5", + pos="e,2468.5,196.29 2502.5,247.3 2494.2,242.47 2486.4,236.43 2480.5,229 2475.4,222.54 2472.3,214.29 2470.4,206.35", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2794.5,178", + pos="2600.5,178", width=2.1304]; "chemical to chemical derivation association" -> "subject category" [color=blue, label="subject category", - lp="2841,221.5", - pos="e,2789.1,196.22 2754.9,247.1 2761.2,241.81 2767.6,235.61 2772.5,229 2777.7,221.97 2782,213.49 2785.4,205.54", + lp="2654,221.5", + pos="e,2598.6,196.23 2571.5,246.86 2577.5,241.72 2583.3,235.66 2587.5,229 2591.8,222.13 2594.7,213.88 2596.6,206.07", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2965.5,178", + pos="2771.5,178", width=2.1304]; "chemical to chemical derivation association" -> "object category" [color=blue, label="object category", - lp="2984,221.5", - pos="e,2949.4,195.91 2843.4,249.66 2864.3,244.69 2885.5,238 2904.5,229 2918.1,222.54 2931.3,212.41 2941.9,202.94", + lp="2795,221.5", + pos="e,2757.6,195.94 2660.3,249.76 2680,244.79 2699.8,238.07 2717.5,229 2729.9,222.64 2741.5,212.65 2750.7,203.26", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3098.5,178", + pos="2904.5,178", width=1.0652]; "chemical to chemical derivation association" -> "subject closure" [color=blue, label="subject closure", - lp="3121,221.5", - pos="e,3085.4,195.42 2876.4,251.81 2950.2,244.87 3027.7,236.16 3043.5,229 3056.7,223.04 3068.8,212.72 3078.4,203", + lp="2930,221.5", + pos="e,2892.9,195.41 2691.9,251.83 2764.1,244.99 2839.2,236.38 2854.5,229 2866.8,223.09 2877.8,212.91 2886.3,203.27", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3198.5,178", + pos="3012.5,178", width=1.0652]; "chemical to chemical derivation association" -> "object closure" [color=blue, label="object closure", - lp="3241.5,221.5", - pos="e,3196.6,196.18 2883.1,252.39 3012.8,242.42 3178.7,229.57 3179.5,229 3186.9,223.48 3191.4,214.73 3194.1,206.08", + lp="3051.5,221.5", + pos="e,3008.9,196.29 2698.5,252.4 2825.8,242.62 2987,230.05 2988.5,229 2996.4,223.54 3001.9,214.69 3005.5,205.94", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3331.5,178", + pos="3145.5,178", width=2.1304]; "chemical to chemical derivation association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3400,221.5", - pos="e,3324.1,196.07 2880.1,252.13 2904.6,250.31 2929.8,248.53 2953.5,247 2991.5,244.55 3262.1,247.23 3295.5,229 3305.3,223.62 3313.2,\ -214.24 3319,205.05", + lp="3211,221.5", + pos="e,3136.8,196.11 2695.4,252.12 2719.8,250.31 2744.9,248.54 2768.5,247 2805.9,244.57 3072.1,246.14 3105.5,229 3116.1,223.55 3124.8,\ +213.9 3131.4,204.52", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3523.5,178", + pos="3338.5,178", width=2.1304]; "chemical to chemical derivation association" -> "object category closure" [color=blue, label="object category closure", - lp="3591,221.5", - pos="e,3517.5,196.1 2877.7,251.91 2903,250.07 2929,248.35 2953.5,247 2983.3,245.36 3465.5,243.79 3491.5,229 3500.9,223.65 3508,214.27 \ -3513,205.08", + lp="3403,221.5", + pos="e,3331.1,196.15 2692.7,251.91 2718,250.08 2744,248.35 2768.5,247 2798.1,245.37 3276.3,242.98 3302.5,229 3312.5,223.66 3320.4,214.15 \ +3326.2,204.86", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3713.5,178", + pos="3528.5,178", width=1.0652]; "chemical to chemical derivation association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3763.5,221.5", - pos="e,3706.5,196.17 2876.5,251.81 2902.1,249.97 2928.6,248.26 2953.5,247 2993.7,244.96 3643,248.05 3678.5,229 3688.3,223.74 3695.9,214.38 \ -3701.6,205.18", + lp="3575.5,221.5", + pos="e,3520.8,195.72 2691.5,251.81 2717.1,249.97 2743.6,248.26 2768.5,247 2808.6,244.97 3454.8,247.28 3490.5,229 3500.9,223.66 3509.3,\ +213.97 3515.5,204.54", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3872.5,178", + pos="3687.5,178", width=1.0652]; "chemical to chemical derivation association" -> "object namespace" [color=blue, label="object namespace", - lp="3916.5,221.5", - pos="e,3865.1,195.73 2875.9,251.76 2901.7,249.91 2928.4,248.22 2953.5,247 3002.4,244.63 3791.9,251.5 3835.5,229 3845.8,223.66 3854,213.98 \ -3860,204.54", + lp="3729.5,221.5", + pos="e,3679.2,195.76 2690.9,251.76 2716.7,249.91 2743.4,248.22 2768.5,247 2817.3,244.63 3603.7,250.61 3647.5,229 3658.3,223.65 3667.2,\ +213.83 3673.8,204.3", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4023.5,178", + pos="3838.5,178", width=1.0652]; "chemical to chemical derivation association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4076.5,221.5", - pos="e,4015.5,195.76 2875.3,251.74 2901.3,249.88 2928.2,248.19 2953.5,247 3010.7,244.31 3933.2,254.58 3984.5,229 3995.2,223.66 4003.8,\ -213.83 4010.2,204.3", + lp="3889.5,221.5", + pos="e,3829.9,195.78 2690.3,251.74 2716.3,249.88 2743.2,248.19 2768.5,247 2825.6,244.32 3746,253.91 3797.5,229 3808.5,223.68 3817.5,213.86 \ +3824.3,204.33", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4194.5,178", + pos="4009.5,178", width=1.0652]; "chemical to chemical derivation association" -> "object label closure" [color=blue, label="object label closure", - lp="4242,221.5", - pos="e,4186.2,195.78 2875,251.71 2901.1,249.85 2928.1,248.16 2953.5,247 2986.8,245.48 4124.5,243.68 4154.5,229 4165.3,223.68 4174.2,213.86 \ -4180.8,204.33", + lp="4057,221.5", + pos="e,4000.6,195.8 2690,251.71 2716.1,249.85 2743.1,248.16 2768.5,247 2801.8,245.48 3937.4,243.3 3967.5,229 3978.6,223.71 3987.9,213.9 \ +3994.8,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4338.5,178", + pos="4153.5,178", width=2.347]; "chemical to chemical derivation association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4398,221.5", - pos="e,4335.5,196 2874.7,251.7 2900.9,249.83 2928,248.14 2953.5,247 2991.3,245.3 4283.8,249.62 4315.5,229 4323.6,223.7 4328.9,214.72 \ -4332.4,205.82", + lp="4213,221.5", + pos="e,4150.5,196 2689.7,251.7 2715.9,249.83 2743,248.14 2768.5,247 2806.3,245.3 4098.8,249.62 4130.5,229 4138.6,223.7 4143.9,214.72 \ +4147.4,205.82", style=solid]; type [height=0.5, - pos="4472.5,178", + pos="4287.5,178", width=0.86659]; "chemical to chemical derivation association" -> type [color=blue, label=type, - lp="4494.5,221.5", - pos="e,4477.6,196.18 2874.7,251.67 2900.9,249.8 2928,248.13 2953.5,247 2974.5,246.07 4456.5,243.85 4471.5,229 4477.4,223.09 4479,214.51 \ -4478.7,206.12", + lp="4309.5,221.5", + pos="e,4292.6,196.18 2689.7,251.67 2715.9,249.8 2743,248.13 2768.5,247 2789.5,246.07 4271.5,243.85 4286.5,229 4292.4,223.09 4294,214.51 \ +4293.7,206.12", style=solid]; category [height=0.5, - pos="4573.5,178", + pos="4388.5,178", width=1.4263]; "chemical to chemical derivation association" -> category [color=blue, label=category, - lp="4572,221.5", - pos="e,4559.9,195.45 2874.7,251.66 2900.9,249.79 2928,248.12 2953.5,247 2996.8,245.09 4473.9,244.17 4514.5,229 4529.1,223.56 4542.5,212.8 \ -4552.9,202.65", + lp="4387,221.5", + pos="e,4374.9,195.45 2689.7,251.66 2715.9,249.79 2743,248.12 2768.5,247 2811.8,245.09 4288.9,244.17 4329.5,229 4344.1,223.56 4357.5,212.8 \ +4367.9,202.65", style=solid]; "catalyst qualifier" [height=0.5, - pos="4731.5,178", + pos="4546.5,178", width=2.4734]; "chemical to chemical derivation association" -> "catalyst qualifier" [color=blue, label="catalyst qualifier", - lp="4718,221.5", - pos="e,4701.1,194.96 2874.4,251.67 2900.7,249.8 2927.9,248.12 2953.5,247 3045.3,242.99 4517.4,246.99 4607.5,229 4636.9,223.12 4668.3,\ -210.42 4692.1,199.29", + lp="4533,221.5", + pos="e,4516.1,194.96 2689.4,251.67 2715.7,249.8 2742.9,248.12 2768.5,247 2860.3,242.99 4332.4,246.99 4422.5,229 4451.9,223.12 4483.3,\ +210.42 4507.1,199.29", style=solid]; subject [height=0.5, - pos="4882.5,178", + pos="4697.5,178", width=1.2277]; "chemical to chemical derivation association" -> subject [color=blue, label=subject, - lp="4849.5,221.5", - pos="e,4860.2,193.86 2874.4,251.65 2900.7,249.78 2927.9,248.1 2953.5,247 3055,242.62 4683.7,252.83 4782.5,229 4807,223.09 4832.3,210.33 \ -4851.4,199.17", + lp="4664.5,221.5", + pos="e,4675.2,193.86 2689.4,251.65 2715.7,249.78 2742.9,248.1 2768.5,247 2870,242.62 4498.7,252.83 4597.5,229 4622,223.09 4647.3,210.33 \ +4666.4,199.17", style=solid]; object [height=0.5, - pos="4925.5,91", + pos="4740.5,91", width=1.0832]; "chemical to chemical derivation association" -> object [color=blue, label=object, - lp="4975.5,178", - pos="e,4938.9,108.09 2874.4,251.64 2900.7,249.77 2927.9,248.1 2953.5,247 3006.9,244.71 4827.9,243.32 4879.5,229 4907.3,221.27 4918.3,\ -219.22 4935.5,196 4954.1,170.92 4957.4,156.9 4948.5,127 4947.5,123.55 4946,120.13 4944.2,116.85", + lp="4790.5,178", + pos="e,4753.9,108.09 2689.4,251.64 2715.7,249.77 2742.9,248.1 2768.5,247 2821.9,244.71 4642.9,243.32 4694.5,229 4722.3,221.27 4733.3,\ +219.22 4750.5,196 4769.1,170.92 4772.4,156.9 4763.5,127 4762.5,123.55 4761,120.13 4759.2,116.85", style=solid]; predicate [height=0.5, - pos="5079.5,178", + pos="4894.5,178", width=1.5165]; "chemical to chemical derivation association" -> predicate [color=blue, label=predicate, - lp="5052.5,221.5", - pos="e,5055.7,194.36 2874.1,251.65 2900.5,249.77 2927.8,248.1 2953.5,247 3065.8,242.21 4867.1,254.67 4976.5,229 5001.4,223.16 5027.3,\ -210.57 5046.9,199.48", + lp="4867.5,221.5", + pos="e,4870.7,194.36 2689.1,251.65 2715.5,249.77 2742.8,248.1 2768.5,247 2880.8,242.21 4682.1,254.67 4791.5,229 4816.4,223.16 4842.3,\ +210.57 4861.9,199.48", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3000.5,265", + pos="2815.5,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3131.5,265", + pos="2946.5,265", width=2.0762]; "chemical to chemical derivation association_catalyst qualifier" [color=blue, height=0.5, label="macromolecular machine mixin", - pos="3380.5,265", + pos="3195.5,265", width=4.3329]; subject -> object [label=relation, - lp="4920.5,134.5", - pos="e,4907.6,107.23 4883.6,159.55 4884.8,149.57 4887.3,137.07 4892.5,127 4894.7,122.68 4897.6,118.52 4900.8,114.66"]; + lp="4735.5,134.5", + pos="e,4722.6,107.23 4698.6,159.55 4699.8,149.57 4702.3,137.07 4707.5,127 4709.7,122.68 4712.6,118.52 4715.8,114.66"]; relation [height=0.5, - pos="4870.5,18", + pos="4685.5,18", width=1.2999]; - subject -> relation [pos="e,4871.8,36.188 4881.2,159.79 4879.1,132.48 4875,78.994 4872.6,46.38", + subject -> relation [pos="e,4686.8,36.188 4696.2,159.79 4694.1,132.48 4690,78.994 4687.6,46.38", style=dotted]; "chemical to chemical derivation association_subject" [color=blue, height=0.5, label="chemical entity", - pos="3636.5,265", + pos="3451.5,265", width=2.2748]; - object -> relation [pos="e,4883.3,35.54 4913,73.889 4906.1,64.939 4897.3,53.617 4889.5,43.584", + object -> relation [pos="e,4698.3,35.54 4728,73.889 4721.1,64.939 4712.3,53.617 4704.5,43.584", style=dotted]; "chemical to chemical derivation association_object" [color=blue, height=0.5, label="chemical entity", - pos="3818.5,265", + pos="3633.5,265", width=2.2748]; "chemical to chemical derivation association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3996.5,265", + pos="3811.5,265", width=2.1665]; } diff --git a/graphviz/chemical_to_chemical_derivation_association.svg b/graphviz/chemical_to_chemical_derivation_association.svg index 80dbbef40c..2bf97433c1 100644 --- a/graphviz/chemical_to_chemical_derivation_association.svg +++ b/graphviz/chemical_to_chemical_derivation_association.svg @@ -4,16 +4,16 @@ - + %3 - + chemical to chemical derivation association - -chemical to chemical derivation association + +chemical to chemical derivation association @@ -24,8 +24,8 @@ chemical to chemical derivation association->chemical to chemical association - - + + is_a @@ -37,7 +37,7 @@ chemical to chemical derivation association->id - + id @@ -50,9 +50,9 @@ chemical to chemical derivation association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ chemical to chemical derivation association->name - - -name + + +name @@ -76,9 +76,9 @@ chemical to chemical derivation association->description - - -description + + +description @@ -89,9 +89,9 @@ chemical to chemical derivation association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ chemical to chemical derivation association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ chemical to chemical derivation association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ chemical to chemical derivation association->publications - - -publications + + +publications @@ -141,382 +141,382 @@ chemical to chemical derivation association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string chemical to chemical derivation association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string chemical to chemical derivation association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string chemical to chemical derivation association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type chemical to chemical derivation association->timepoint - - -timepoint + + +timepoint original subject - -string + +string chemical to chemical derivation association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie chemical to chemical derivation association->original predicate - - -original predicate + + +original predicate original object - -string + +string chemical to chemical derivation association->original object - - -original object + + +original object subject category - -ontology class + +ontology class chemical to chemical derivation association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class chemical to chemical derivation association->object category - - -object category + + +object category subject closure - -string + +string chemical to chemical derivation association->subject closure - - -subject closure + + +subject closure object closure - -string + +string chemical to chemical derivation association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class chemical to chemical derivation association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class chemical to chemical derivation association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string chemical to chemical derivation association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string chemical to chemical derivation association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string chemical to chemical derivation association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string chemical to chemical derivation association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source chemical to chemical derivation association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type chemical to chemical derivation association->type - - -type + + +type category - -category + +category chemical to chemical derivation association->category - - -category + + +category catalyst qualifier - -catalyst qualifier + +catalyst qualifier chemical to chemical derivation association->catalyst qualifier - - -catalyst qualifier + + +catalyst qualifier subject - -subject + +subject chemical to chemical derivation association->subject - - -subject + + +subject object - -object + +object chemical to chemical derivation association->object - - -object + + +object predicate - -predicate + +predicate chemical to chemical derivation association->predicate - - -predicate + + +predicate association_type - -string + +string association_category - -category type + +category type chemical to chemical derivation association_catalyst qualifier - -macromolecular machine mixin + +macromolecular machine mixin subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + chemical to chemical derivation association_subject - -chemical entity + +chemical entity object->relation - - + + chemical to chemical derivation association_object - -chemical entity + +chemical entity chemical to chemical derivation association_predicate - -predicate type + +predicate type diff --git a/graphviz/chemical_to_disease_or_phenotypic_feature_association.gv b/graphviz/chemical_to_disease_or_phenotypic_feature_association.gv index ba7c5ffcf3..b578362b60 100644 --- a/graphviz/chemical_to_disease_or_phenotypic_feature_association.gv +++ b/graphviz/chemical_to_disease_or_phenotypic_feature_association.gv @@ -1,30 +1,30 @@ digraph { - graph [bb="0,0,5769.4,283"]; + graph [bb="0,0,5504.4,283"]; node [label="\N"]; "chemical to disease or phenotypic feature association" [height=0.5, label="chemical to disease or phenotypic feature association", - pos="3355.4,265", + pos="3090.4,265", width=7.2035]; association [height=0.5, pos="62.394,178", width=1.7332]; "chemical to disease or phenotypic feature association" -> association [label=is_a, lp="728.39,221.5", - pos="e,106.71,190.75 3096.2,264.31 2622.9,264.04 1587.1,259.6 714.39,229 456.36,219.95 389.9,233.14 134.39,196 128.61,195.16 122.61,194.08 \ -116.66,192.88"]; + pos="e,106.71,190.75 2831.4,263.75 2394.7,262.53 1484.1,256.55 714.39,229 456.37,219.76 389.9,233.14 134.39,196 128.61,195.16 122.61,\ +194.08 116.66,192.88"]; "chemical to entity association mixin" [height=0.5, pos="320.39,178", width=4.9287]; "chemical to disease or phenotypic feature association" -> "chemical to entity association mixin" [label=uses, lp="1034.9,221.5", - pos="e,445.34,190.82 3095.9,264.31 2664.5,263.87 1772.5,258.98 1018.4,229 790.99,219.96 734.29,213.64 507.39,196 490.62,194.7 473,193.23 \ + pos="e,445.34,190.82 2831.9,263.58 2439.6,262.05 1670.8,255.56 1018.4,229 791,219.74 734.29,213.64 507.39,196 490.62,194.7 473,193.23 \ 455.57,191.71"]; "entity to disease or phenotypic feature association mixin" [height=0.5, pos="790.39,178", width=7.6188]; "chemical to disease or phenotypic feature association" -> "entity to disease or phenotypic feature association mixin" [label=uses, - lp="1219.9,221.5", - pos="e,894.92,194.71 3097.2,263.17 2608.3,261.05 1563.9,253.69 1203.4,229 1102.1,222.07 987.58,207.68 904.85,196.11"]; + lp="1218.9,221.5", + pos="e,895.1,194.71 2833.2,262.49 2392.7,259.36 1511.3,250.55 1202.4,229 1101.7,221.97 987.73,207.65 905.25,196.13"]; id [color=blue, height=0.5, label=string, @@ -32,9 +32,9 @@ digraph { width=1.0652]; "chemical to disease or phenotypic feature association" -> id [color=blue, label=id, - lp="1340.4,221.5", - pos="e,1150.4,190.01 3099,262.16 2593.9,258.16 1504,247.49 1333.4,229 1259.5,220.99 1241.1,215.79 1169.4,196 1166.3,195.14 1163.1,194.18 \ -1159.9,193.17", + lp="1338.4,221.5", + pos="e,1150.4,190 2831.1,264.6 2414.4,264.6 1613.7,260.3 1331.4,229 1258.4,220.9 1240.2,215.65 1169.4,196 1166.3,195.14 1163.1,194.17 \ +1159.9,193.16", style=solid]; iri [color=blue, height=0.5, @@ -43,9 +43,9 @@ digraph { width=1.2277]; "chemical to disease or phenotypic feature association" -> iri [color=blue, label=iri, - lp="1460.4,221.5", - pos="e,1255,190.17 3096,264.56 2651.7,264.61 1763,260.59 1452.4,229 1372.8,220.9 1353,215.59 1275.4,196 1272,195.13 1268.4,194.17 1264.9,\ -193.15", + lp="1454.4,221.5", + pos="e,1255.3,190.23 2831.4,263.83 2437.6,262.67 1706.7,256.68 1446.4,229 1369.4,220.81 1350.4,215.19 1275.4,196 1272,195.14 1268.5,194.18 \ +1265.1,193.17", style=solid]; name [color=blue, height=0.5, @@ -54,8 +54,8 @@ digraph { width=1.5707]; "chemical to disease or phenotypic feature association" -> name [color=blue, label=name, - lp="1574.4,221.5", - pos="e,1381,191.06 3099.7,261.88 2638.9,257.65 1703.2,246.96 1554.4,229 1497.5,222.13 1433.7,205.99 1390.8,193.89", + lp="1564.4,221.5", + pos="e,1380.2,191.31 2830.9,264.83 2457,264.87 1785.1,260.34 1544.4,229 1490.7,222.01 1430.6,206.18 1389.9,194.19", style=solid]; description [color=blue, height=0.5, @@ -64,8 +64,8 @@ digraph { width=2.0943]; "chemical to disease or phenotypic feature association" -> description [color=blue, label=description, - lp="1706.9,221.5", - pos="e,1530.7,193.39 3098.8,262.32 2661,258.91 1803.6,249.67 1666.4,229 1623,222.47 1575.2,208.32 1540.6,196.74", + lp="1690.9,221.5", + pos="e,1528.3,193.84 2835.4,261.68 2453,257.6 1763.5,247.77 1650.4,229 1611.6,222.57 1569.2,208.89 1538,197.46", style=solid]; "has attribute" [color=blue, height=0.5, @@ -74,8 +74,8 @@ digraph { width=1.4443]; "chemical to disease or phenotypic feature association" -> "has attribute" [color=blue, label="has attribute", - lp="1871.4,221.5", - pos="e,1671.9,191.22 3101.2,261.4 2698.5,256.8 1946.8,246.06 1824.4,229 1774.7,222.06 1719.3,206.31 1681.6,194.33", + lp="1844.4,221.5", + pos="e,1669.1,192.05 2837.8,260.88 2490.4,256.01 1896.6,245.43 1797.4,229 1756,222.15 1710.6,207.32 1678.5,195.58", style=solid]; subject [color=blue, height=0.5, @@ -84,8 +84,8 @@ digraph { width=1.9318]; "chemical to disease or phenotypic feature association" -> subject [color=blue, label=subject, - lp="2030.4,221.5", - pos="e,1821.8,191.63 3097.1,263.15 2765.5,261.03 2208.3,253.78 2004.4,229 1944.6,221.74 1877.4,206.06 1831.6,194.18", + lp="1988.4,221.5", + pos="e,1816.8,192.78 2832.7,262.91 2552.7,260.49 2123.8,252.87 1962.4,229 1915.5,222.06 1863.5,207.47 1826.4,195.83", style=solid]; predicate [color=blue, height=0.5, @@ -94,8 +94,8 @@ digraph { width=2.1665]; "chemical to disease or phenotypic feature association" -> predicate [color=blue, label=predicate, - lp="2168.4,221.5", - pos="e,1985.3,193.15 3097,263.44 2794.8,261.57 2313.2,254.51 2134.4,229 2086.5,222.17 2033.4,207.78 1995.2,196.19", + lp="2101.4,221.5", + pos="e,1972.8,194.63 2841.1,259.96 2562.5,254.74 2140.8,244.45 2067.4,229 2037.7,222.76 2006,209.99 1981.9,198.93", style=solid]; negated [color=blue, height=0.5, @@ -104,8 +104,8 @@ digraph { width=1.2999]; "chemical to disease or phenotypic feature association" -> negated [color=blue, label=negated, - lp="2312.4,221.5", - pos="e,2120,190.37 3101.3,261.38 2835.2,257.63 2435.4,248.83 2283.4,229 2229.6,221.98 2169.4,205.49 2129.6,193.35", + lp="2204.4,221.5", + pos="e,2106.3,194.38 2839.7,260.39 2590.9,255.84 2237.7,246.43 2175.4,229 2153.9,222.99 2132,210.95 2115.1,200.18", style=solid]; qualifiers [color=blue, height=0.5, @@ -114,8 +114,8 @@ digraph { width=2.1304]; "chemical to disease or phenotypic feature association" -> qualifiers [color=blue, label=qualifiers, - lp="2444.9,221.5", - pos="e,2268.1,193.18 3102.1,261.07 2868.5,257.19 2539.4,248.41 2411.4,229 2365.5,222.05 2314.8,207.84 2278,196.34", + lp="2282.9,221.5", + pos="e,2229.6,196.4 2841.5,259.93 2602.4,255.07 2273.9,245.43 2249.4,229 2241.4,223.66 2236.2,214.84 2232.7,206.08", style=solid]; publications [color=blue, height=0.5, @@ -124,8 +124,8 @@ digraph { width=1.7332]; "chemical to disease or phenotypic feature association" -> publications [color=blue, label=publications, - lp="2582.4,221.5", - pos="e,2417.8,193.06 3103.6,260.6 2904.4,256.54 2642.9,247.75 2538.4,229 2500,222.11 2457.9,208.11 2427.3,196.67", + lp="2368.4,221.5", + pos="e,2348.3,192.96 2838.2,260.72 2622,256.63 2342.3,247.74 2324.4,229 2313.9,217.96 2324.3,206.87 2339.2,197.94", style=solid]; "has evidence" [color=blue, height=0.5, @@ -134,226 +134,228 @@ digraph { width=2.0943]; "chemical to disease or phenotypic feature association" -> "has evidence" [color=blue, label="has evidence", - lp="2727.9,221.5", - pos="e,2573.6,194.18 3112.2,258.66 2953.5,253.77 2761.4,244.81 2681.4,229 2647.4,222.29 2610.6,209.15 2583,198.02", + lp="2465.9,221.5", + pos="e,2480.4,189.32 2845.5,259.05 2660,254.06 2434.4,244.78 2419.4,229 2414.8,224.16 2415.4,219.33 2419.4,214 2426.2,204.89 2447.6,197.36 \ +2470.5,191.65", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2741.4,178", - width=3.015]; + label=string, + pos="2671.4,178", + width=1.0652]; "chemical to disease or phenotypic feature association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2866.9,221.5", - pos="e,2756.6,196.17 3097.7,262.73 2980.5,259.11 2856,250.09 2802.4,229 2788,223.35 2774.5,212.99 2763.9,203.16", + lp="2595.9,221.5", + pos="e,2642.7,189.94 2860,256.7 2711.2,250.82 2543.1,241.48 2531.4,229 2484.1,178.66 2457.1,241.46 2623.4,196 2626.5,195.14 2629.8,194.17 \ +2633,193.14", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2976.4,178", - width=3.015]; + label=string, + pos="2766.4,178", + width=1.0652]; "chemical to disease or phenotypic feature association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="3033.4,221.5", - pos="e,2951.1,195.6 3120.2,257.4 3033.2,252.49 2952.1,243.92 2938.4,229 2930.8,220.79 2935.4,211.15 2943.6,202.54", + lp="2762.4,221.5", + pos="e,2736.7,189.52 2853.3,257.68 2764.5,252.81 2681.4,244.21 2667.4,229 2662.9,224.1 2663.5,219.44 2667.4,214 2681.3,194.38 2695.7,\ +204.01 2718.4,196 2721.3,194.99 2724.2,193.94 2727.2,192.88", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="3211.4,178", - width=3.015]; + label=string, + pos="2861.4,178", + width=1.0652]; "chemical to disease or phenotypic feature association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="3242.9,221.5", - pos="e,3160.6,194.03 3188.3,251.21 3164.3,246.1 3144.9,238.96 3136.4,229 3126,216.84 3135.9,206.43 3151.4,198.31", + lp="2974.9,221.5", + pos="e,2859.1,196.06 2925.4,251.06 2899.5,245.97 2878.1,238.88 2868.4,229 2862.5,223.02 2860.1,214.53 2859.3,206.24", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="3393.4,178", + pos="3080.4,178", width=1.5346]; "chemical to disease or phenotypic feature association" -> timepoint [color=blue, label=timepoint, - lp="3391.4,221.5", - pos="e,3371.3,194.53 3352.5,246.62 3351.6,236.66 3351.9,224.16 3356.4,214 3358.3,209.58 3361.2,205.46 3364.4,201.7", + lp="3121.4,221.5", + pos="e,3082.4,196.18 3088.4,246.8 3087,235.16 3085.2,219.55 3083.6,206.24", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="3505.4,178", + pos="3192.4,178", width=1.0652]; "chemical to disease or phenotypic feature association" -> "original subject" [color=blue, label="original subject", - lp="3505.4,221.5", - pos="e,3483.3,192.7 3392,247.02 3403.2,241.54 3415.4,235.26 3426.4,229 3437,222.96 3439.1,220.57 3449.4,214 3457.6,208.79 3466.4,203.21 \ -3474.7,198.07", + lp="3229.4,221.5", + pos="e,3184.5,195.95 3133.1,247.24 3142.7,242.26 3152.4,236.18 3160.4,229 3167.9,222.22 3174.4,213.26 3179.5,204.8", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3619.4,178", + pos="3318.4,178", width=1.5887]; "chemical to disease or phenotypic feature association" -> "original predicate" [color=blue, label="original predicate", - lp="3644.9,221.5", - pos="e,3602.4,195.43 3498.9,249.98 3520.5,244.94 3541.9,238.15 3561.4,229 3568.9,225.48 3582.7,213.61 3595,202.31", + lp="3366.9,221.5", + pos="e,3312.8,196.02 3221.8,249.44 3251.1,244.26 3277.2,237.54 3289.4,229 3297.7,223.18 3304,214.13 3308.6,205.32", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3733.4,178", + pos="3452.4,178", width=1.0652]; "chemical to disease or phenotypic feature association" -> "original object" [color=blue, label="original object", - lp="3775.9,221.5", - pos="e,3730.4,196.18 3550.7,253.11 3625.8,247.36 3697.2,239.32 3711.4,229 3719.1,223.42 3724.1,214.54 3727.4,205.8", + lp="3496.9,221.5", + pos="e,3450.8,196.08 3283.3,252.94 3354.6,247.24 3421.2,239.28 3434.4,229 3441.6,223.37 3445.9,214.59 3448.5,205.96", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3866.4,178", + pos="3585.4,178", width=2.1304]; "chemical to disease or phenotypic feature association" -> "subject category" [color=blue, label="subject category", - lp="3906.9,221.5", - pos="e,3859.3,195.98 3539.2,252.28 3670.4,243.63 3824.8,232.74 3831.4,229 3841.1,223.5 3848.7,214.1 3854.3,204.93", + lp="3627.9,221.5", + pos="e,3578.9,195.95 3271.4,252.09 3398.2,243.47 3546.1,232.7 3552.4,229 3561.8,223.46 3569.1,214.06 3574.3,204.89", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="4037.4,178", + pos="3756.4,178", width=2.1304]; "chemical to disease or phenotypic feature association" -> "object category" [color=blue, label="object category", - lp="4052.9,221.5", - pos="e,4020.9,195.75 3538.1,252.18 3566.9,250.39 3596.5,248.61 3624.4,247 3701.3,242.57 3898,255.15 3970.4,229 3986.1,223.31 4001.3,212.6 \ -4013.2,202.54", + lp="3772.9,221.5", + pos="e,3740.5,195.74 3273.4,252.21 3302.2,250.42 3331.6,248.63 3359.4,247 3433.2,242.67 3622.1,254.68 3691.4,229 3706.8,223.29 3721.5,\ +212.57 3733,202.52", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="4170.4,178", + pos="3889.4,178", width=1.0652]; "chemical to disease or phenotypic feature association" -> "subject closure" [color=blue, label="subject closure", - lp="4188.9,221.5", - pos="e,4154.6,194.71 3535.1,251.98 3564.9,250.18 3595.5,248.44 3624.4,247 3678.6,244.29 4061.9,248.83 4112.4,229 4120.3,225.9 4134.7,\ -213.48 4147.2,201.8", + lp="3911.9,221.5", + pos="e,3876.3,195.31 3270.1,252.01 3299.9,250.21 3330.5,248.46 3359.4,247 3411.9,244.34 3783.5,248.46 3832.4,229 3846.4,223.41 3859.3,\ +212.79 3869.3,202.76", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="4266.4,178", + pos="3997.4,178", width=1.0652]; "chemical to disease or phenotypic feature association" -> "object closure" [color=blue, label="object closure", - lp="4308.4,221.5", - pos="e,4264,196.39 3533.3,251.9 3563.7,250.08 3594.9,248.36 3624.4,247 3658.9,245.41 4216.9,248.52 4245.4,229 4253.2,223.66 4258.1,214.83 \ -4261.2,206.07", + lp="4034.4,221.5", + pos="e,3993,196.03 3268.7,251.89 3298.9,250.07 3330.1,248.36 3359.4,247 3393.3,245.43 3941.5,246.82 3970.4,229 3979,223.68 3985.1,214.56 \ +3989.2,205.57", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="4399.4,178", + pos="4130.4,178", width=2.1304]; "chemical to disease or phenotypic feature association" -> "subject category closure" [color=blue, label="subject category closure", - lp="4466.9,221.5", - pos="e,4391.8,196.2 3532.6,251.82 3563.2,250 3594.7,248.3 3624.4,247 3665.4,245.21 4326,247.9 4362.4,229 4372.6,223.72 4380.7,214.23 \ -4386.7,204.92", + lp="4194.9,221.5", + pos="e,4121.1,196.26 3267.6,251.83 3298.2,250.01 3329.7,248.3 3359.4,247 3399.9,245.22 4051.9,246.56 4088.4,229 4099.3,223.73 4108.5,\ +214.11 4115.4,204.7", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="4588.4,178", + pos="4323.4,178", width=2.1304]; "chemical to disease or phenotypic feature association" -> "object category closure" [color=blue, label="object category closure", - lp="4656.9,221.5", - pos="e,4583.1,196.12 3531.5,251.76 3562.4,249.93 3594.4,248.24 3624.4,247 3650.3,245.93 4535.9,242 4558.4,229 4567.5,223.73 4574.2,214.5 \ -4578.8,205.39", + lp="4386.9,221.5", + pos="e,4315.8,196.22 3266.5,251.76 3297.4,249.93 3329.4,248.24 3359.4,247 3410.9,244.88 4240.6,252.63 4286.4,229 4296.6,223.74 4304.7,\ +214.26 4310.7,204.95", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4778.4,178", + pos="4513.4,178", width=1.0652]; "chemical to disease or phenotypic feature association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4828.4,221.5", - pos="e,4771.7,196.2 3530.8,251.72 3561.9,249.88 3594.1,248.2 3624.4,247 3655.5,245.77 4717,243.78 4744.4,229 4754.1,223.77 4761.6,214.41 \ -4767,205.2", + lp="4560.4,221.5", + pos="e,4505.4,195.77 3265.8,251.72 3296.9,249.88 3329.1,248.2 3359.4,247 3390.3,245.77 4446.7,242.81 4474.4,229 4485.1,223.66 4493.8,\ +213.84 4500.2,204.31", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4937.4,178", + pos="4672.4,178", width=1.0652]; "chemical to disease or phenotypic feature association" -> "object namespace" [color=blue, label="object namespace", - lp="4981.4,221.5", - pos="e,4930,195.75 3530.4,251.69 3561.7,249.85 3594,248.17 3624.4,247 3659.8,245.63 4868.9,245.18 4900.4,229 4910.7,223.7 4918.9,214.02 \ -4924.9,204.58", + lp="4714.4,221.5", + pos="e,4664.1,195.79 3265.4,251.69 3296.7,249.85 3329,248.17 3359.4,247 3394.7,245.63 4600.6,244.54 4632.4,229 4643.3,223.69 4652.1,213.87 \ +4658.7,204.33", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="5088.4,178", + pos="4823.4,178", width=1.0652]; "chemical to disease or phenotypic feature association" -> "subject label closure" [color=blue, label="subject label closure", - lp="5141.4,221.5", - pos="e,5080.4,195.78 3530.1,251.68 3561.4,249.83 3593.9,248.16 3624.4,247 3664,245.5 5013.9,246.59 5049.4,229 5060.1,223.68 5068.8,213.86 \ -5075.2,204.32", + lp="4876.4,221.5", + pos="e,4814.8,195.8 3265.1,251.68 3296.4,249.83 3328.9,248.16 3359.4,247 3398.9,245.5 4746.8,246.13 4782.4,229 4793.4,223.71 4802.4,213.9 \ +4809.2,204.35", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="5259.4,178", + pos="4994.4,178", width=1.0652]; "chemical to disease or phenotypic feature association" -> "object label closure" [color=blue, label="object label closure", - lp="5307.9,221.5", - pos="e,5251.1,195.8 3529.7,251.66 3561.2,249.81 3593.8,248.14 3624.4,247 3668.7,245.35 5179.6,248.42 5219.4,229 5230.3,223.7 5239.1,213.89 \ -5245.7,204.35", + lp="5042.9,221.5", + pos="e,4986.1,195.8 3264.7,251.66 3296.2,249.81 3328.8,248.14 3359.4,247 3403.7,245.35 4914.6,248.42 4954.4,229 4965.3,223.7 4974.1,213.89 \ +4980.7,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="5421.4,178", + pos="5156.4,178", width=2.347]; "chemical to disease or phenotypic feature association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="5469.9,221.5", - pos="e,5412.8,196.3 3529.7,251.64 3561.2,249.79 3593.8,248.12 3624.4,247 3673.2,245.21 5337.5,250.37 5381.4,229 5392.1,223.78 5400.9,\ -214.17 5407.4,204.76", + lp="5204.9,221.5", + pos="e,5147.8,196.3 3264.7,251.64 3296.2,249.79 3328.8,248.12 3359.4,247 3408.2,245.21 5072.5,250.37 5116.4,229 5127.1,223.78 5135.9,\ +214.17 5142.4,204.76", style=solid]; type [height=0.5, - pos="5555.4,178", + pos="5290.4,178", width=0.86659]; "chemical to disease or phenotypic feature association" -> type [color=blue, label=type, - lp="5569.4,221.5", - pos="e,5556.2,196.19 3529.3,251.64 3560.9,249.78 3593.6,248.11 3624.4,247 3651,246.03 5522.5,245.6 5543.4,229 5550.2,223.55 5553.6,214.93 \ -5555.2,206.37", + lp="5304.4,221.5", + pos="e,5291.2,196.19 3264.3,251.64 3295.9,249.78 3328.6,248.11 3359.4,247 3386,246.03 5257.5,245.6 5278.4,229 5285.2,223.55 5288.6,214.93 \ +5290.2,206.37", style=solid]; category [height=0.5, - pos="5656.4,178", + pos="5391.4,178", width=1.4263]; "chemical to disease or phenotypic feature association" -> category [color=blue, label=category, - lp="5648.9,221.5", - pos="e,5640.8,195.26 3529.3,251.63 3560.9,249.77 3593.6,248.11 3624.4,247 3678.9,245.03 5537.7,246.44 5589.4,229 5605.6,223.54 5621.1,\ -212.51 5633.1,202.2", + lp="5383.9,221.5", + pos="e,5375.8,195.26 3264.3,251.63 3295.9,249.77 3328.6,248.11 3359.4,247 3413.9,245.03 5272.7,246.44 5324.4,229 5340.6,223.54 5356.1,\ +212.51 5368.1,202.2", style=solid]; object [height=0.5, pos="1843.4,91", width=1.0832]; "chemical to disease or phenotypic feature association" -> object [color=blue, label=object, - lp="5747.4,178", - pos="e,1882.5,91.926 3529.3,251.62 3560.9,249.76 3593.6,248.11 3624.4,247 3681.6,244.94 5631.8,251.53 5684.4,229 5715.5,215.69 5740.1,\ -184.11 5716.4,160 5646.1,88.423 2338.3,91.209 1892.8,91.91", + lp="5482.4,178", + pos="e,1882.5,91.978 3264.3,251.62 3295.9,249.76 3328.6,248.11 3359.4,247 3416.6,244.94 5366.8,251.53 5419.4,229 5450.5,215.69 5475.1,\ +184.13 5451.4,160 5386.1,93.449 2320.4,91.871 1892.7,91.975", style=solid]; subject -> object [label=relation, lp="1842.4,134.5", @@ -366,18 +368,18 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="3671.4,265", + pos="3406.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3802.4,265", + pos="3537.4,265", width=2.0762]; object -> relation [pos="e,1801.2,35.54 1830.9,73.889 1824,64.939 1815.2,53.617 1807.4,43.584", style=dotted]; "chemical to disease or phenotypic feature association_object" [color=blue, height=0.5, label="disease or phenotypic feature", - pos="4044.4,265", + pos="3779.4,265", width=4.1344]; } diff --git a/graphviz/chemical_to_disease_or_phenotypic_feature_association.svg b/graphviz/chemical_to_disease_or_phenotypic_feature_association.svg index 0fa717a9f3..13658b33e4 100644 --- a/graphviz/chemical_to_disease_or_phenotypic_feature_association.svg +++ b/graphviz/chemical_to_disease_or_phenotypic_feature_association.svg @@ -4,16 +4,16 @@ - + %3 - + chemical to disease or phenotypic feature association - -chemical to disease or phenotypic feature association + +chemical to disease or phenotypic feature association @@ -24,7 +24,7 @@ chemical to disease or phenotypic feature association->association - + is_a @@ -37,7 +37,7 @@ chemical to disease or phenotypic feature association->chemical to entity association mixin - + uses @@ -50,9 +50,9 @@ chemical to disease or phenotypic feature association->entity to disease or phenotypic feature association mixin - - -uses + + +uses @@ -63,9 +63,9 @@ chemical to disease or phenotypic feature association->id - - -id + + +id @@ -76,9 +76,9 @@ chemical to disease or phenotypic feature association->iri - - -iri + + +iri @@ -89,9 +89,9 @@ chemical to disease or phenotypic feature association->name - - -name + + +name @@ -102,9 +102,9 @@ chemical to disease or phenotypic feature association->description - - -description + + +description @@ -115,9 +115,9 @@ chemical to disease or phenotypic feature association->has attribute - - -has attribute + + +has attribute @@ -128,9 +128,9 @@ chemical to disease or phenotypic feature association->subject - - -subject + + +subject @@ -141,9 +141,9 @@ chemical to disease or phenotypic feature association->predicate - - -predicate + + +predicate @@ -154,9 +154,9 @@ chemical to disease or phenotypic feature association->negated - - -negated + + +negated @@ -167,9 +167,9 @@ chemical to disease or phenotypic feature association->qualifiers - - -qualifiers + + +qualifiers @@ -180,9 +180,9 @@ chemical to disease or phenotypic feature association->publications - - -publications + + +publications @@ -193,269 +193,269 @@ chemical to disease or phenotypic feature association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string chemical to disease or phenotypic feature association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string chemical to disease or phenotypic feature association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string chemical to disease or phenotypic feature association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type chemical to disease or phenotypic feature association->timepoint - - -timepoint + + +timepoint original subject - -string + +string chemical to disease or phenotypic feature association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie chemical to disease or phenotypic feature association->original predicate - - -original predicate + + +original predicate original object - -string + +string chemical to disease or phenotypic feature association->original object - - -original object + + +original object subject category - -ontology class + +ontology class chemical to disease or phenotypic feature association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class chemical to disease or phenotypic feature association->object category - - -object category + + +object category subject closure - -string + +string chemical to disease or phenotypic feature association->subject closure - - -subject closure + + +subject closure object closure - -string + +string chemical to disease or phenotypic feature association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class chemical to disease or phenotypic feature association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class chemical to disease or phenotypic feature association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string chemical to disease or phenotypic feature association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string chemical to disease or phenotypic feature association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string chemical to disease or phenotypic feature association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string chemical to disease or phenotypic feature association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source chemical to disease or phenotypic feature association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type chemical to disease or phenotypic feature association->type - - -type + + +type category - -category + +category chemical to disease or phenotypic feature association->category - - -category + + +category @@ -466,9 +466,9 @@ chemical to disease or phenotypic feature association->object - - -object + + +object @@ -492,14 +492,14 @@ association_type - -string + +string association_category - -category type + +category type @@ -510,8 +510,8 @@ chemical to disease or phenotypic feature association_object - -disease or phenotypic feature + +disease or phenotypic feature diff --git a/graphviz/chemical_to_pathway_association.gv b/graphviz/chemical_to_pathway_association.gv index 0e131e6df9..ac691bc404 100644 --- a/graphviz/chemical_to_pathway_association.gv +++ b/graphviz/chemical_to_pathway_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,5161.4,283"]; + graph [bb="0,0,4943.4,283"]; node [label="\N"]; "chemical to pathway association" [height=0.5, label="chemical to pathway association", - pos="2797.4,265", + pos="2579.4,265", width=4.4774]; association [height=0.5, pos="62.394,178", width=1.7332]; "chemical to pathway association" -> association [label=is_a, - lp="496.39,221.5", - pos="e,107.14,190.57 2636.8,263.23 2184,260.81 902.56,252.06 482.39,229 327.27,220.49 287.69,221.24 134.39,196 128.71,195.06 122.81,193.93 \ + lp="495.39,221.5", + pos="e,107.14,190.57 2419.2,262.95 1996.5,259.92 857.73,250 481.39,229 326.72,220.37 287.25,221.19 134.39,196 128.71,195.06 122.81,193.93 \ 116.94,192.71"]; "chemical to entity association mixin" [height=0.5, pos="320.39,178", width=4.9287]; "chemical to pathway association" -> "chemical to entity association mixin" [label=uses, - lp="651.89,221.5", - pos="e,397.05,194.27 2636.2,264.34 2203.5,264.79 1023.5,262.77 635.39,229 557.64,222.23 470.01,207.76 406.95,196.12"]; + lp="650.89,221.5", + pos="e,397.12,194.3 2418.2,264 2016.5,263.55 978.81,259.37 634.39,229 557.02,222.18 469.83,207.75 406.99,196.13"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "chemical to pathway association" -> id [color=blue, label=id, - lp="771.39,221.5", - pos="e,583.38,190 2637.1,262.94 2189.7,259.73 947.96,249.1 764.39,229 691.35,221 673.2,215.65 602.39,196 599.29,195.14 596.09,194.17 \ -592.89,193.16", + lp="769.39,221.5", + pos="e,583.38,189.98 2418.2,264.7 2035.5,265.74 1080.5,264.56 762.39,229 690.24,220.93 672.34,215.5 602.39,196 599.29,195.13 596.09,194.17 \ +592.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,9 @@ digraph { width=1.2277]; "chemical to pathway association" -> iri [color=blue, label=iri, - lp="888.39,221.5", - pos="e,688.29,190.23 2636.2,264.61 2238.6,265.54 1218.7,264.28 880.39,229 802.98,220.93 783.81,215.26 708.39,196 705.02,195.14 701.54,\ -194.18 698.05,193.17", + lp="882.39,221.5", + pos="e,688.3,190.2 2418.1,264.3 2052.6,264.41 1170.2,261.19 874.39,229 799.61,220.86 781.22,214.85 708.39,196 705.02,195.13 701.54,194.16 \ +698.06,193.15", style=solid]; name [color=blue, height=0.5, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "chemical to pathway association" -> name [color=blue, label=name, - lp="1000.4,221.5", - pos="e,813.39,191.26 2637.2,262.86 2223.8,259.64 1141.9,249.36 980.39,229 925.75,222.11 864.59,206.19 823.21,194.15", + lp="990.39,221.5", + pos="e,812.19,191.4 2419.5,262.58 2040.9,258.93 1110.9,248.11 970.39,229 918.75,221.98 861.11,206.29 821.78,194.35", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "chemical to pathway association" -> description [color=blue, label=description, - lp="1128.9,221.5", - pos="e,961.8,193.64 2636.6,263.23 2240.5,260.96 1238.3,252.92 1088.4,229 1048,222.56 1003.8,208.65 971.45,197.13", + lp="1111.9,221.5", + pos="e,958.95,194.11 2419.1,263.03 2057.8,260.46 1201,251.99 1071.4,229 1035.7,222.68 997.04,209.22 968.29,197.87", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "chemical to pathway association" -> "has attribute" [color=blue, label="has attribute", - lp="1286.4,221.5", - pos="e,1103,191.74 2637.4,262.79 2267.5,259.66 1374.5,250.01 1239.4,229 1195.3,222.14 1146.5,206.98 1112.6,195.14", + lp="1258.4,221.5", + pos="e,1099.7,192.78 2419.3,262.71 2083.6,259.6 1327.2,250.31 1211.4,229 1175.8,222.44 1137.1,208.32 1109.1,196.75", style=solid]; predicate [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=2.1665]; "chemical to pathway association" -> predicate [color=blue, label=predicate, - lp="1446.4,221.5", - pos="e,1260.6,193.08 2636.1,264.49 2323.2,264.68 1644.1,261.21 1412.4,229 1363.6,222.22 1309.5,207.75 1270.6,196.12", + lp="1402.4,221.5", + pos="e,1252.9,194.04 2420.4,261.98 2115.4,257.72 1469.1,246.73 1368.4,229 1331.9,222.57 1292.1,209.12 1262.6,197.79", style=solid]; negated [color=blue, height=0.5, @@ -87,8 +87,8 @@ digraph { width=1.2999]; "chemical to pathway association" -> negated [color=blue, label=negated, - lp="1591.4,221.5", - pos="e,1395,190.21 2636.9,263.29 2351.2,261.39 1765.3,254.41 1562.4,229 1507.1,222.07 1445.1,205.34 1404.5,193.13", + lp="1520.4,221.5", + pos="e,1388,192.62 2420.6,261.8 2140.5,257.49 1579.7,246.76 1491.4,229 1458.5,222.38 1423,208.39 1397.3,196.89", style=solid]; qualifiers [color=blue, height=0.5, @@ -97,8 +97,8 @@ digraph { width=2.1304]; "chemical to pathway association" -> qualifiers [color=blue, label=qualifiers, - lp="1726.9,221.5", - pos="e,1543.9,193 2636.9,263.31 2375.8,261.44 1870.4,254.53 1693.4,229 1645.4,222.07 1592,207.62 1553.8,196.03", + lp="1621.9,221.5", + pos="e,1522.9,195.38 2419.6,262.57 2159.6,259.61 1665.8,251.14 1588.4,229 1568,223.18 1547.4,211.62 1531.4,201.08", style=solid]; publications [color=blue, height=0.5, @@ -107,8 +107,8 @@ digraph { width=1.7332]; "chemical to pathway association" -> publications [color=blue, label=publications, - lp="1867.4,221.5", - pos="e,1694.1,192.76 2636.9,263.25 2401.7,261.29 1975,254.25 1823.4,229 1782.1,222.11 1736.6,207.8 1703.9,196.25", + lp="1712.4,221.5", + pos="e,1656.9,196.02 2419.1,262.94 2165.2,260.54 1696.4,252.89 1668.4,229 1661.8,223.37 1658.8,214.71 1657.6,206.17", style=solid]; "has evidence" [color=blue, height=0.5, @@ -117,263 +117,264 @@ digraph { width=2.0943]; "chemical to pathway association" -> "has evidence" [color=blue, label="has evidence", - lp="2018.9,221.5", - pos="e,1851.4,193.77 2638.1,262.23 2435.1,259.11 2095.8,250.74 1972.4,229 1934,222.24 1892.1,208.65 1861,197.35", + lp="1810.9,221.5", + pos="e,1783,194.37 2419.1,262.74 2188.1,260.12 1786.7,252.23 1764.4,229 1755.2,219.42 1762.7,209.02 1774.4,200.2", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2016.4,178", - width=3.015]; + label=string, + pos="1946.4,178", + width=1.0652]; "chemical to pathway association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2164.9,221.5", - pos="e,2037.8,195.77 2636,264.86 2461.9,264.19 2196.8,258.14 2100.4,229 2081.1,223.17 2061.6,212 2046.3,201.69", + lp="1928.9,221.5", + pos="e,1917.1,189.71 2420.8,261.72 2216,257.97 1883.3,248.86 1864.4,229 1859.8,224.17 1860.7,219.56 1864.4,214 1867.1,209.87 1887.6,201.11 \ +1907.5,193.39", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2251.4,178", - width=3.015]; + label=string, + pos="2041.4,178", + width=1.0652]; "chemical to pathway association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2332.4,221.5", - pos="e,2239.3,196.25 2643.6,259.53 2482.6,254.07 2251.2,243.73 2237.4,229 2231.4,222.6 2232,213.84 2235,205.44", + lp="2095.4,221.5", + pos="e,2018.4,192.58 2424.8,259.85 2258.3,254.6 2014.8,244.35 2000.4,229 1991.4,219.44 1999.2,208.17 2010.3,198.76", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2486.4,178", - width=3.015]; + label=string, + pos="2183.4,178", + width=1.0652]; "chemical to pathway association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2540.9,221.5", - pos="e,2452.3,195.1 2646,258.83 2553,254.04 2449.1,245.14 2434.4,229 2425.6,219.36 2432.6,209.3 2443.9,200.75", + lp="2312.9,221.5", + pos="e,2186.7,196.22 2433.8,257.26 2337.3,251.61 2225.2,242.32 2206.4,229 2198.6,223.46 2193.4,214.59 2189.9,205.85", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2668.4,178", + pos="2409.4,178", width=1.5346]; "chemical to pathway association" -> timepoint [color=blue, label=timepoint, - lp="2690.4,221.5", - pos="e,2657.3,195.8 2704.6,250.28 2682.1,244.99 2662.4,237.99 2655.4,229 2650.1,222.2 2650.6,213.44 2653.3,205.16", + lp="2471.4,221.5", + pos="e,2414.6,196.25 2479.1,250.86 2463.8,245.74 2448.9,238.69 2436.4,229 2428.7,223.04 2422.9,214.23 2418.7,205.66", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2780.4,178", + pos="2521.4,178", width=1.0652]; "chemical to pathway association" -> "original subject" [color=blue, label="original subject", - lp="2787.4,221.5", - pos="e,2754.3,191.31 2750.9,247.74 2743.1,242.92 2736.1,236.78 2731.4,229 2724.1,216.95 2733.5,205.59 2745.8,196.74", + lp="2569.4,221.5", + pos="e,2513.4,195.83 2532.9,247.74 2525.1,242.92 2518.1,236.78 2513.4,229 2509.2,222.01 2509.1,213.51 2510.7,205.53", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2894.4,178", + pos="2647.4,178", width=1.5887]; "chemical to pathway association" -> "original predicate" [color=blue, label="original predicate", - lp="2922.9,221.5", - pos="e,2878.4,195.75 2820.8,247.1 2828.2,241.53 2836.3,235.17 2843.4,229 2852.8,220.85 2862.7,211.38 2871.2,202.9", + lp="2697.9,221.5", + pos="e,2642.2,196.38 2606.2,247.16 2613.1,241.95 2620.1,235.78 2625.4,229 2630.8,222.12 2635.2,213.69 2638.6,205.72", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3008.4,178", + pos="2781.4,178", width=1.0652]; "chemical to pathway association" -> "original object" [color=blue, label="original object", - lp="3052.9,221.5", - pos="e,3006.6,196.32 2914.2,252.53 2947.3,247.2 2977.9,239.61 2990.4,229 2997.2,223.24 3001.4,214.7 3004.1,206.3", + lp="2827.9,221.5", + pos="e,2780.3,196.25 2693.2,252.23 2724.8,246.9 2753.6,239.39 2765.4,229 2772,223.17 2775.9,214.61 2778.2,206.21", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3141.4,178", + pos="2914.4,178", width=2.1304]; "chemical to pathway association" -> "subject category" [color=blue, label="subject category", - lp="3183.9,221.5", - pos="e,3134.6,196.3 2911.8,252.24 2998.7,243.14 3104.1,231.65 3108.4,229 3117.5,223.43 3124.6,214.32 3129.8,205.38", + lp="2957.9,221.5", + pos="e,2908.3,196.26 2692.6,252.11 2777.3,243.03 2879.2,231.65 2883.4,229 2892.2,223.4 2899,214.27 2903.8,205.34", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3312.4,178", + pos="3085.4,178", width=2.1304]; "chemical to pathway association" -> "object category" [color=blue, label="object category", - lp="3328.9,221.5", - pos="e,3296.5,195.68 2910.9,252.16 2930.1,250.32 2949.8,248.52 2968.4,247 3030.3,241.93 3189.2,250.89 3247.4,229 3262.8,223.21 3277.5,\ -212.49 3289,202.45", + lp="3102.9,221.5", + pos="e,3069.8,195.67 2692.9,252.19 2712.1,250.34 2731.8,248.54 2750.4,247 2810.5,242.01 2965,250.53 3021.4,229 3036.4,223.25 3050.8,212.67 \ +3062.1,202.72", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3445.4,178", + pos="3218.4,178", width=1.0652]; "chemical to pathway association" -> "subject closure" [color=blue, label="subject closure", - lp="3465.9,221.5", - pos="e,3432.3,195.28 2909.1,251.98 2928.8,250.12 2949.2,248.36 2968.4,247 3015,243.69 3345,246.39 3388.4,229 3402.4,223.38 3415.3,212.75 \ -3425.3,202.73", + lp="3239.9,221.5", + pos="e,3205.6,195.28 2691.1,252 2710.8,250.13 2731.2,248.37 2750.4,247 2796.1,243.73 3119.9,246.26 3162.4,229 3176.2,223.37 3188.9,212.74 \ +3198.7,202.72", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3545.4,178", + pos="3326.4,178", width=1.0652]; "chemical to pathway association" -> "object closure" [color=blue, label="object closure", - lp="3587.4,221.5", - pos="e,3542.9,196.38 2908.1,251.9 2928.2,250.02 2948.9,248.28 2968.4,247 2999.2,244.97 3498.9,246.52 3524.4,229 3532.2,223.65 3537.1,\ -214.82 3540.2,206.06", + lp="3362.4,221.5", + pos="e,3321.7,196.04 2690.1,251.91 2710.2,250.03 2730.9,248.29 2750.4,247 2780.8,244.99 3272.4,244.83 3298.4,229 3307.2,223.63 3313.5,\ +214.38 3317.8,205.29", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3678.4,178", + pos="3459.4,178", width=2.1304]; "chemical to pathway association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3745.9,221.5", - pos="e,3670.7,196.19 2907.7,251.85 2927.9,249.97 2948.7,248.24 2968.4,247 3005.7,244.65 3608.2,246.28 3641.4,229 3651.6,223.71 3659.6,\ -214.21 3665.6,204.91", + lp="3522.9,221.5", + pos="e,3449.8,196.26 2689.7,251.86 2709.9,249.97 2730.7,248.24 2750.4,247 2787.3,244.67 3383,244.89 3416.4,229 3427.5,223.73 3436.8,214.11 \ +3443.9,204.7", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3870.4,178", + pos="3652.4,178", width=2.1304]; "chemical to pathway association" -> "object category closure" [color=blue, label="object category closure", - lp="3936.9,221.5", - pos="e,3864.1,196.16 2907.2,251.8 2927.5,249.91 2948.6,248.19 2968.4,247 3016.6,244.11 3795.1,252.32 3837.4,229 3847,223.73 3854.2,214.37 \ -3859.5,205.16", + lp="3714.9,221.5", + pos="e,3644.4,196.23 2689.2,251.8 2709.5,249.91 2730.6,248.19 2750.4,247 2798.3,244.12 3571.6,250.78 3614.4,229 3624.7,223.75 3633,214.27 \ +3639.2,204.96", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4060.4,178", + pos="3842.4,178", width=1.0652]; "chemical to pathway association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4109.4,221.5", - pos="e,4053.3,195.73 2907.2,251.74 2927.5,249.85 2948.6,248.15 2968.4,247 2997.7,245.3 3998.4,242.6 4024.4,229 4034.6,223.67 4042.6,213.98 \ -4048.4,204.55", + lp="3888.4,221.5", + pos="e,3834.1,195.77 2689.2,251.74 2709.5,249.85 2730.6,248.15 2750.4,247 2808.7,243.61 3749.9,254.77 3802.4,229 3813.2,223.67 3822.1,\ +213.85 3828.7,204.32", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4219.4,178", + pos="4001.4,178", width=1.0652]; "chemical to pathway association" -> "object namespace" [color=blue, label="object namespace", - lp="4263.4,221.5", - pos="e,4211.7,195.76 2906.8,251.74 2927.2,249.84 2948.4,248.14 2968.4,247 3002,245.08 4151.3,244.2 4181.4,229 4191.9,223.71 4200.2,214.03 \ -4206.4,204.59", + lp="4042.4,221.5", + pos="e,3992.8,195.79 2688.8,251.75 2709.2,249.85 2730.4,248.14 2750.4,247 2784,245.09 3930.1,243.6 3960.4,229 3971.4,223.7 3980.4,213.88 \ +3987.2,204.34", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4370.4,178", + pos="4152.4,178", width=1.0652]; "chemical to pathway association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4423.4,221.5", - pos="e,4362.4,195.78 2906.8,251.72 2927.2,249.82 2948.4,248.12 2968.4,247 3006.2,244.88 4297.5,245.84 4331.4,229 4342.1,223.68 4350.8,\ -213.86 4357.2,204.32", + lp="4204.4,221.5", + pos="e,4143.5,195.81 2688.8,251.72 2709.2,249.82 2730.4,248.12 2750.4,247 2788.1,244.88 4076.3,245.18 4110.4,229 4121.5,223.72 4130.8,\ +213.91 4137.7,204.36", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4541.4,178", + pos="4323.4,178", width=1.0652]; "chemical to pathway association" -> "object label closure" [color=blue, label="object label closure", - lp="4589.9,221.5", - pos="e,4533.1,195.8 2906.8,251.69 2927.2,249.8 2948.4,248.11 2968.4,247 3010.9,244.64 4463.1,247.67 4501.4,229 4512.3,223.7 4521.1,213.88 \ -4527.7,204.34", + lp="4371.9,221.5", + pos="e,4314.8,195.81 2688.8,251.69 2709.2,249.8 2730.4,248.11 2750.4,247 2792.9,244.64 4244,247.43 4282.4,229 4293.4,223.71 4302.4,213.9 \ +4309.2,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4703.4,178", + pos="4485.4,178", width=2.347]; "chemical to pathway association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4751.9,221.5", - pos="e,4694.8,196.3 2906.3,251.72 2926.9,249.81 2948.3,248.1 2968.4,247 3015.4,244.42 4621.1,249.62 4663.4,229 4674.1,223.78 4682.9,214.17 \ -4689.4,204.75", + lp="4533.9,221.5", + pos="e,4476.8,196.3 2688.3,251.72 2708.9,249.81 2730.3,248.1 2750.4,247 2797.4,244.42 4403.1,249.62 4445.4,229 4456.1,223.78 4464.9,214.17 \ +4471.4,204.75", style=solid]; type [height=0.5, - pos="4837.4,178", + pos="4619.4,178", width=0.86659]; "chemical to pathway association" -> type [color=blue, label=type, - lp="4851.4,221.5", - pos="e,4838.2,196.18 2906.3,251.7 2926.9,249.79 2948.3,248.09 2968.4,247 2994.1,245.6 4805.2,245.07 4825.4,229 4832.2,223.54 4835.6,214.93 \ -4837.1,206.37", + lp="4633.4,221.5", + pos="e,4620.2,196.18 2688.3,251.7 2708.9,249.79 2730.3,248.09 2750.4,247 2776.1,245.6 4587.2,245.07 4607.4,229 4614.2,223.54 4617.6,214.93 \ +4619.1,206.37", style=solid]; category [height=0.5, - pos="4938.4,178", + pos="4720.4,178", width=1.4263]; "chemical to pathway association" -> category [color=blue, label=category, - lp="4931.9,221.5", - pos="e,4922.8,195.26 2906.3,251.7 2926.9,249.79 2948.3,248.09 2968.4,247 3021.2,244.13 4821.3,245.89 4871.4,229 4887.6,223.54 4903.1,\ -212.51 4915.1,202.2", + lp="4713.9,221.5", + pos="e,4704.8,195.26 2688.3,251.7 2708.9,249.79 2730.3,248.09 2750.4,247 2803.2,244.13 4603.3,245.89 4653.4,229 4669.6,223.54 4685.1,\ +212.51 4697.1,202.2", style=solid]; subject [height=0.5, - pos="5052.4,178", + pos="4834.4,178", width=1.2277]; "chemical to pathway association" -> subject [color=blue, label=subject, - lp="5028.4,221.5", - pos="e,5033.1,194.33 2906.3,251.69 2926.9,249.78 2948.3,248.09 2968.4,247 3079.3,241 4860.4,258.66 4967.4,229 4988.1,223.25 5009,211.09 \ -5024.9,200.2", + lp="4810.4,221.5", + pos="e,4815.1,194.33 2688.3,251.69 2708.9,249.78 2730.3,248.09 2750.4,247 2861.3,241 4642.4,258.66 4749.4,229 4770.1,223.25 4791,211.09 \ +4806.9,200.2", style=solid]; object [height=0.5, - pos="5095.4,91", + pos="4877.4,91", width=1.0832]; "chemical to pathway association" -> object [color=blue, label=object, - lp="5139.4,178", - pos="e,5108.8,108.09 2906.3,251.69 2926.9,249.78 2948.3,248.08 2968.4,247 3026.4,243.88 5003.1,246.73 5058.4,229 5082.7,221.2 5091,217.1 \ -5105.4,196 5119.3,175.59 5115.5,166.51 5118.4,142 5119.2,135.38 5120.3,133.39 5118.4,127 5117.4,123.55 5115.9,120.13 5114.1,116.85", + lp="4921.4,178", + pos="e,4890.8,108.09 2688.3,251.69 2708.9,249.78 2730.3,248.08 2750.4,247 2808.4,243.88 4785.1,246.73 4840.4,229 4864.7,221.2 4873,217.1 \ +4887.4,196 4901.3,175.59 4897.5,166.51 4900.4,142 4901.2,135.38 4902.3,133.39 4900.4,127 4899.4,123.55 4897.9,120.13 4896.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3015.4,265", + pos="2797.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3146.4,265", + pos="2928.4,265", width=2.0762]; subject -> object [label=relation, - lp="5090.4,134.5", - pos="e,5077.5,107.23 5053.5,159.55 5054.7,149.57 5057.2,137.07 5062.4,127 5064.6,122.68 5067.5,118.52 5070.7,114.66"]; + lp="4872.4,134.5", + pos="e,4859.5,107.23 4835.5,159.55 4836.7,149.57 4839.2,137.07 4844.4,127 4846.6,122.68 4849.5,118.52 4852.7,114.66"]; relation [height=0.5, - pos="5040.4,18", + pos="4822.4,18", width=1.2999]; - subject -> relation [pos="e,5041.7,36.188 5051.1,159.79 5049,132.48 5045,78.994 5042.5,46.38", + subject -> relation [pos="e,4823.7,36.188 4833.1,159.79 4831,132.48 4827,78.994 4824.5,46.38", style=dotted]; "chemical to pathway association_subject" [color=blue, height=0.5, label="chemical entity", - pos="3321.4,265", + pos="3103.4,265", width=2.2748]; - object -> relation [pos="e,5053.2,35.54 5082.9,73.889 5076,64.939 5067.2,53.617 5059.4,43.584", + object -> relation [pos="e,4835.2,35.54 4864.9,73.889 4858,64.939 4849.2,53.617 4841.4,43.584", style=dotted]; "chemical to pathway association_object" [color=blue, height=0.5, label=pathway, - pos="3471.4,265", + pos="3253.4,265", width=1.3902]; } diff --git a/graphviz/chemical_to_pathway_association.svg b/graphviz/chemical_to_pathway_association.svg index 2ba11e1ebd..a8ea89bf60 100644 --- a/graphviz/chemical_to_pathway_association.svg +++ b/graphviz/chemical_to_pathway_association.svg @@ -4,16 +4,16 @@ - + %3 - + chemical to pathway association - -chemical to pathway association + +chemical to pathway association @@ -24,9 +24,9 @@ chemical to pathway association->association - + -is_a +is_a @@ -37,9 +37,9 @@ chemical to pathway association->chemical to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ chemical to pathway association->id - - -id + + +id @@ -63,9 +63,9 @@ chemical to pathway association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ chemical to pathway association->name - - -name + + +name @@ -89,9 +89,9 @@ chemical to pathway association->description - - -description + + +description @@ -102,9 +102,9 @@ chemical to pathway association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ chemical to pathway association->predicate - - -predicate + + +predicate @@ -128,9 +128,9 @@ chemical to pathway association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ chemical to pathway association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ chemical to pathway association->publications - - -publications + + +publications @@ -167,344 +167,344 @@ chemical to pathway association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string chemical to pathway association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string chemical to pathway association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string chemical to pathway association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type chemical to pathway association->timepoint - - -timepoint + + +timepoint original subject - -string + +string chemical to pathway association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie chemical to pathway association->original predicate - - -original predicate + + +original predicate original object - -string + +string chemical to pathway association->original object - - -original object + + +original object subject category - -ontology class + +ontology class chemical to pathway association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class chemical to pathway association->object category - - -object category + + +object category subject closure - -string + +string chemical to pathway association->subject closure - - -subject closure + + +subject closure object closure - -string + +string chemical to pathway association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class chemical to pathway association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class chemical to pathway association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string chemical to pathway association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string chemical to pathway association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string chemical to pathway association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string chemical to pathway association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source chemical to pathway association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type chemical to pathway association->type - - -type + + +type category - -category + +category chemical to pathway association->category - - -category + + +category subject - -subject + +subject chemical to pathway association->subject - - -subject + + +subject object - -object + +object chemical to pathway association->object - - -object + + +object association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + chemical to pathway association_subject - -chemical entity + +chemical entity object->relation - - + + chemical to pathway association_object - -pathway + +pathway diff --git a/graphviz/contributor_association.gv b/graphviz/contributor_association.gv index 57abed7a72..7bc9233658 100644 --- a/graphviz/contributor_association.gv +++ b/graphviz/contributor_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4715.3,283"]; + graph [bb="0,0,4543.3,283"]; node [label="\N"]; "contributor association" [height=0.5, label="contributor association", - pos="2444.4,265", + pos="2272.4,265", width=3.2858]; association [height=0.5, pos="62.394,178", width=1.7332]; "contributor association" -> association [label=is_a, - lp="280.39,221.5", - pos="e,102.91,191.79 2326.4,263.65 1902.4,262.18 470.51,255.32 266.39,229 213.1,222.13 153.57,206.6 112.64,194.66"]; + lp="278.39,221.5", + pos="e,102.89,191.89 2154.3,263.49 1752.3,261.55 451.08,253.41 264.39,229 211.77,222.12 153.04,206.67 112.52,194.76"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "contributor association" -> id [color=blue, label=id, - lp="396.39,221.5", - pos="e,210.38,189.98 2326.4,263.27 1918.4,260.59 581.35,250.24 389.39,229 317.23,221.01 299.34,215.5 229.39,196 226.29,195.13 223.09,\ -194.17 219.89,193.15", + lp="392.39,221.5", + pos="e,210.39,189.96 2154.5,263.12 1768.9,260.04 560.12,248.92 385.39,229 314.98,220.97 297.61,215.2 229.39,196 226.29,195.13 223.09,\ +194.15 219.89,193.13", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "contributor association" -> iri [color=blue, label=iri, - lp="504.39,221.5", - pos="e,315.31,190.17 2326.5,263.15 1932.6,260.12 677.42,249.01 496.39,229 423.79,220.98 406.05,214.52 335.39,196 332.02,195.12 328.54,\ -194.14 325.06,193.12", + lp="494.39,221.5", + pos="e,315.33,190.1 2154.7,263.03 1783.2,259.78 650.79,248.39 486.39,229 418.17,220.96 401.73,213.84 335.39,196 332.03,195.09 328.55,\ +194.11 325.08,193.08", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "contributor association" -> name [color=blue, label=name, - lp="609.39,221.5", - pos="e,438.3,191.65 2326.4,263.43 1945.1,261.34 760.3,252.98 589.39,229 540.27,222.11 485.63,206.67 447.98,194.75", + lp="593.39,221.5", + pos="e,436.69,192.22 2154.4,263.36 1794.8,261.15 728.19,252.67 573.39,229 529.33,222.26 480.68,207.39 446.4,195.61", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "contributor association" -> description [color=blue, label=description, - lp="725.89,221.5", - pos="e,583.28,194.39 2326,263.95 1957.4,263.47 845.21,259.49 685.39,229 653.14,222.85 618.44,209.7 592.44,198.44", + lp="700.89,221.5", + pos="e,578.07,194.99 2154.1,264.2 1806.7,264.41 804.35,262.08 660.39,229 634.7,223.1 607.76,210.8 587.09,199.88", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "contributor association" -> "has attribute" [color=blue, label="has attribute", - lp="865.39,221.5", - pos="e,723.57,193.54 2326.1,263.95 1976.7,263.46 964.38,259.39 818.39,229 788.46,222.77 756.54,209.42 732.86,198.09", + lp="825.39,221.5", + pos="e,715.86,194.96 2154.7,262.91 1813.5,259.52 843.96,248.24 778.39,229 758.87,223.27 739.32,211.64 724.21,201.04", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "contributor association" -> negated [color=blue, label=negated, - lp="1011.4,221.5", - pos="e,845.52,191.31 2326.7,262.94 2002.8,259.78 1113.3,249.33 982.39,229 937.95,222.1 888.83,206.64 855.05,194.72", + lp="946.39,221.5", + pos="e,836.69,193.75 2154.4,263.78 1846.7,262.82 1035.6,257.56 917.39,229 892.01,222.87 865.51,210.02 845.61,198.88", style=solid]; publications [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.7332]; "contributor association" -> publications [color=blue, label=publications, - lp="1154.4,221.5", - pos="e,976.9,192.74 2327,262.66 2023.6,258.96 1228.5,247.59 1110.4,229 1067.5,222.25 1020.3,207.76 986.5,196.1", + lp="1051.4,221.5", + pos="e,956.57,195.64 2155.1,262.67 1851.7,258.98 1061,247.62 1007.4,229 991.47,223.47 976.19,212.66 964.26,202.5", style=solid]; "has evidence" [color=blue, height=0.5, @@ -90,289 +90,289 @@ digraph { width=2.0943]; "contributor association" -> "has evidence" [color=blue, label="has evidence", - lp="1315.9,221.5", - pos="e,1135.6,193.41 2325.9,264.25 2069.5,264.16 1470.1,260.48 1269.4,229 1226.7,222.3 1179.6,208.24 1145.4,196.73", + lp="1154.9,221.5", + pos="e,1095.6,196.12 2154.1,264.28 1866,264.45 1148.5,261.57 1108.4,229 1101.6,223.47 1098.2,214.84 1096.7,206.29", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1298.4,178", - width=3.015]; + label=string, + pos="1228.4,178", + width=1.0652]; "contributor association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1474.9,221.5", - pos="e,1326.8,195.38 2326.9,262.56 2074.7,259.11 1497.5,249.11 1410.4,229 1384.4,222.99 1357,210.87 1335.8,200.06", + lp="1273.9,221.5", + pos="e,1214.3,195.21 2154,264.46 1883.7,264.92 1241.8,262.47 1209.4,229 1202.7,222.09 1204.5,212.6 1209.1,203.74", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1533.4,178", - width=3.015]; + label=string, + pos="1323.4,178", + width=1.0652]; "contributor association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1650.4,221.5", - pos="e,1536.2,196.38 2326.8,262.66 2092.5,259.52 1586.7,250.33 1555.4,229 1547.5,223.65 1542.5,214.82 1539.2,206.06", + lp="1453.4,221.5", + pos="e,1330.4,196.12 2155.1,262.27 1916.1,258.37 1392.7,247.73 1358.4,229 1348.6,223.67 1341,214.31 1335.4,205.11", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1768.4,178", - width=3.015]; + label=string, + pos="1532.4,178", + width=1.0652]; "contributor association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="1859.9,221.5", - pos="e,1755.7,196.25 2327.4,262.22 2135.4,258.72 1772.8,249.43 1753.4,229 1747.3,222.61 1748,213.84 1751.2,205.44", + lp="1674.9,221.5", + pos="e,1539.8,196.09 2154.1,263.68 1966.9,262.34 1618.3,256.17 1568.4,229 1558.5,223.63 1550.7,214.26 1544.9,205.06", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="1950.4,178", + pos="1758.4,178", width=1.5346]; "contributor association" -> timepoint [color=blue, label=timepoint, - lp="2020.4,221.5", - pos="e,1957.5,195.97 2329.9,260.35 2203.7,255.53 2014.6,245.65 1985.4,229 1975.7,223.49 1968.1,214.09 1962.5,204.92", + lp="1839.4,221.5", + pos="e,1769,196.06 2158.9,259.87 2030.6,254.51 1835.5,244.04 1804.4,229 1792.9,223.43 1782.9,213.63 1775.2,204.17", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2062.4,178", + pos="1870.4,178", width=1.0652]; "contributor association" -> "original subject" [color=blue, label="original subject", - lp="2121.4,221.5", - pos="e,2058.3,196.06 2329.3,260.82 2224.6,256.74 2083.6,247.81 2065.4,229 2059.6,223.03 2057.7,214.54 2057.6,206.25", + lp="1944.4,221.5", + pos="e,1871.9,196.11 2158.8,259.79 2053.4,254.89 1909.5,245.33 1888.4,229 1881.2,223.4 1876.8,214.64 1874.2,206", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2176.4,178", + pos="1996.4,178", width=1.5887]; "contributor association" -> "original predicate" [color=blue, label="original predicate", - lp="2254.9,221.5", - pos="e,2177,196.37 2330.3,260.08 2273.5,255.83 2212.5,247.07 2191.4,229 2184.7,223.3 2181,214.77 2178.9,206.37", + lp="2077.9,221.5", + pos="e,1998.1,196.46 2158.5,260.02 2100.1,255.77 2036.7,247.01 2014.4,229 2007.4,223.33 2003.1,214.7 2000.5,206.2", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2304.4,178", + pos="2125.4,178", width=1.0652]; "contributor association" -> "original object" [color=blue, label="original object", - lp="2385.9,221.5", - pos="e,2310.9,196.03 2375.2,250.34 2360.7,245.28 2346.3,238.39 2334.4,229 2326.5,222.73 2320.2,213.74 2315.4,205.11", + lp="2209.9,221.5", + pos="e,2132.9,196.07 2201.6,250.51 2186.4,245.44 2171.1,238.49 2158.4,229 2150,222.71 2143.1,213.6 2137.8,204.89", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2437.4,178", + pos="2258.4,178", width=2.1304]; "contributor association" -> "subject category" [color=blue, label="subject category", - lp="2500.9,221.5", - pos="e,2438.8,196.18 2443,246.8 2442,235.16 2440.7,219.55 2439.6,206.24", + lp="2325.9,221.5", + pos="e,2261.2,196.18 2269.6,246.8 2267.6,235.16 2265.1,219.55 2262.9,206.24", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2608.4,178", + pos="2429.4,178", width=2.1304]; "contributor association" -> "object category" [color=blue, label="object category", - lp="2636.9,221.5", - pos="e,2597.2,196.1 2515.2,250.52 2532.1,245.4 2549.6,238.43 2564.4,229 2574.6,222.54 2583.7,213.06 2591,204.09", + lp="2460.9,221.5", + pos="e,2419.5,196.09 2342.6,250.47 2358.8,245.37 2375.4,238.42 2389.4,229 2398.9,222.59 2407.2,213.24 2413.8,204.35", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="2741.4,178", + pos="2562.4,178", width=1.0652]; "contributor association" -> "subject closure" [color=blue, label="subject closure", - lp="2769.9,221.5", - pos="e,2730.9,195.77 2529.9,252.47 2602.2,242.66 2694.5,230 2696.4,229 2707.6,223.07 2717.3,213.21 2724.9,203.81", + lp="2592.9,221.5", + pos="e,2552.9,195.75 2358.4,252.59 2428.6,243.16 2516.8,231.02 2520.4,229 2531,223.11 2540.1,213.39 2547.1,204.07", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="2847.4,178", + pos="2675.4,178", width=1.0652]; "contributor association" -> "object closure" [color=blue, label="object closure", - lp="2890.4,221.5", - pos="e,2845.6,196.21 2527.6,252.19 2542.5,250.29 2557.9,248.47 2572.4,247 2600.8,244.12 2805.5,246 2828.4,229 2835.8,223.51 2840.3,214.77 \ -2843.1,206.12", + lp="2714.4,221.5", + pos="e,2671.8,196.31 2355.6,252.2 2370.5,250.31 2385.9,248.48 2400.4,247 2428.2,244.16 2628.3,244.73 2651.4,229 2659.4,223.57 2664.8,\ +214.72 2668.4,205.97", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="2980.4,178", + pos="2808.4,178", width=2.1304]; "contributor association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3048.9,221.5", - pos="e,2973,196.09 2526.9,252.01 2542,250.11 2557.7,248.33 2572.4,247 2613.6,243.27 2908,248.75 2944.4,229 2954.4,223.58 2962.3,214.07 \ -2968.1,204.78", + lp="2873.9,221.5", + pos="e,2799.7,196.13 2354.9,252.02 2370,250.11 2385.7,248.34 2400.4,247 2441.2,243.3 2731.9,247.63 2768.4,229 2779,223.58 2787.7,213.93 \ +2794.3,204.55", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3173.4,178", + pos="3001.4,178", width=2.1304]; "contributor association" -> "object category closure" [color=blue, label="object category closure", - lp="3239.9,221.5", - pos="e,3167,196.12 2525.9,251.93 2541.3,250 2557.3,248.24 2572.4,247 2603.9,244.42 3112.8,244.4 3140.4,229 3149.9,223.67 3157.2,214.3 \ -3162.4,205.11", + lp="3065.9,221.5", + pos="e,2994.1,196.16 2353.9,251.94 2369.3,250.01 2385.3,248.24 2400.4,247 2431.7,244.43 2937.7,243.76 2965.4,229 2975.4,223.67 2983.3,\ +214.17 2989.1,204.87", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3363.4,178", + pos="3191.4,178", width=1.0652]; "contributor association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3412.4,221.5", - pos="e,3356.3,195.7 2525.5,251.88 2541,249.94 2557.2,248.19 2572.4,247 2614.2,243.73 3290.3,248.57 3327.4,229 3337.6,223.63 3345.6,213.94 \ -3351.4,204.51", + lp="3238.4,221.5", + pos="e,3183.7,195.72 2353.5,251.88 2369,249.94 2385.2,248.19 2400.4,247 2442.1,243.74 3116.1,248.04 3153.4,229 3163.8,223.66 3172.2,213.98 \ +3178.4,204.54", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3522.4,178", + pos="3350.4,178", width=1.0652]; "contributor association" -> "object namespace" [color=blue, label="object namespace", - lp="3565.4,221.5", - pos="e,3514.7,195.74 2525.5,251.83 2541,249.9 2557.2,248.16 2572.4,247 2622.9,243.16 3439.2,251.97 3484.4,229 3494.9,223.68 3503.2,214 \ -3509.4,204.56", + lp="3392.4,221.5", + pos="e,3342.1,195.76 2353.5,251.83 2369,249.9 2385.2,248.16 2400.4,247 2450.8,243.17 3265,251.35 3310.4,229 3321.2,223.66 3330.1,213.83 \ +3336.7,204.3", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3673.4,178", + pos="3501.4,178", width=1.0652]; "contributor association" -> "subject label closure" [color=blue, label="subject label closure", - lp="3725.4,221.5", - pos="e,3665.1,195.78 2525.2,251.84 2540.8,249.89 2557.1,248.14 2572.4,247 2631.2,242.61 3580.5,254.99 3633.4,229 3644.2,223.67 3653.1,\ -213.85 3659.7,204.32", + lp="3552.4,221.5", + pos="e,3492.8,195.79 2353.2,251.84 2368.8,249.89 2385.1,248.14 2400.4,247 2459.1,242.62 3407.4,254.64 3460.4,229 3471.4,223.69 3480.4,\ +213.87 3487.2,204.33", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="3844.4,178", + pos="3672.4,178", width=1.0652]; "contributor association" -> "object label closure" [color=blue, label="object label closure", - lp="3890.9,221.5", - pos="e,3835.8,195.8 2525.2,251.81 2540.8,249.87 2557.1,248.13 2572.4,247 2606.5,244.49 3772.6,243.85 3803.4,229 3814.4,223.7 3823.4,213.88 \ -3830.2,204.34", + lp="3719.9,221.5", + pos="e,3663.5,195.81 2353.2,251.81 2368.8,249.87 2385.1,248.13 2400.4,247 2434.5,244.5 3599.5,243.66 3630.4,229 3641.5,223.71 3650.8,\ +213.9 3657.7,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="3988.4,178", + pos="3816.4,178", width=2.347]; "contributor association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4046.9,221.5", - pos="e,3985.1,196.03 2525.2,251.79 2540.8,249.85 2557.1,248.11 2572.4,247 2611,244.2 3931.8,249.81 3964.4,229 3972.7,223.67 3978.3,214.56 \ -3981.9,205.56", + lp="3875.9,221.5", + pos="e,3813.4,196 2353.2,251.79 2368.8,249.85 2385.1,248.11 2400.4,247 2439,244.2 3760.9,250.09 3793.4,229 3801.5,223.7 3806.8,214.72 \ +3810.3,205.82", style=solid]; type [height=0.5, - pos="4122.4,178", + pos="3950.4,178", width=0.86659]; "contributor association" -> type [color=blue, label=type, - lp="4143.4,221.5", - pos="e,4127.1,196.23 2525.2,251.77 2540.8,249.83 2557.1,248.1 2572.4,247 2593.8,245.46 4105,243.99 4120.4,229 4126.4,223.15 4128.2,214.58 \ -4128,206.19", + lp="3972.4,221.5", + pos="e,3955.5,196.18 2353.2,251.77 2368.8,249.83 2385.1,248.1 2400.4,247 2421.9,245.46 3934.1,244.15 3949.4,229 3955.4,223.09 3957,214.51 \ +3956.6,206.12", style=solid]; category [height=0.5, - pos="4223.4,178", + pos="4051.4,178", width=1.4263]; "contributor association" -> category [color=blue, label=category, - lp="4220.9,221.5", - pos="e,4209.5,195.46 2525.2,251.77 2540.8,249.83 2557.1,248.1 2572.4,247 2616.5,243.83 4121.9,244.28 4163.4,229 4178.1,223.57 4191.8,\ -212.81 4202.4,202.66", + lp="4049.9,221.5", + pos="e,4037.8,195.46 2353.2,251.77 2368.8,249.83 2385.1,248.1 2400.4,247 2444.5,243.83 3951,244.46 3992.4,229 4007,223.56 4020.4,212.8 \ +4030.8,202.65", style=solid]; subject [height=0.5, - pos="4337.4,178", + pos="4165.4,178", width=1.2277]; "contributor association" -> subject [color=blue, label=subject, - lp="4316.4,221.5", - pos="e,4318.9,194.56 2525.2,251.76 2540.8,249.82 2557.1,248.09 2572.4,247 2665.7,240.33 4166.5,255.02 4256.4,229 4276,223.31 4295.6,211.45 \ -4310.6,200.7", + lp="4144.4,221.5", + pos="e,4147.1,194.55 2353.2,251.76 2368.8,249.82 2385.1,248.09 2400.4,247 2493.8,240.33 3995.5,255.29 4085.4,229 4104.8,223.31 4124.2,\ +211.44 4139,200.7", style=solid]; predicate [height=0.5, - pos="4454.4,178", + pos="4282.4,178", width=1.5165]; "contributor association" -> predicate [color=blue, label=predicate, - lp="4424.4,221.5", - pos="e,4429.7,194.11 2524.8,251.8 2540.6,249.84 2557,248.1 2572.4,247 2670.7,240 4250.2,250.69 4346.4,229 4372.6,223.09 4400.1,210.27 \ -4420.7,199.1", + lp="4252.4,221.5", + pos="e,4257.7,194.11 2352.8,251.8 2368.6,249.84 2385,248.1 2400.4,247 2498.7,240 4078.2,250.69 4174.4,229 4200.6,223.09 4228.1,210.27 \ +4248.7,199.1", style=solid]; object [height=0.5, - pos="4404.4,91", + pos="4232.4,91", width=1.0832]; "contributor association" -> object [color=blue, label=object, - lp="4546.4,178", - pos="e,4434.2,102.71 2524.8,251.79 2540.6,249.83 2557,248.09 2572.4,247 2677.1,239.57 4361.2,257.11 4462.4,229 4490.2,221.27 4504.1,221.08 \ -4518.4,196 4540.7,156.94 4484.7,124.38 4443.5,106.59", + lp="4373.4,178", + pos="e,4262.2,102.71 2352.8,251.79 2368.6,249.83 2385,248.09 2400.4,247 2505.1,239.57 4189.2,257.11 4290.4,229 4318.2,221.27 4332.1,221.08 \ +4346.4,196 4368.7,156.94 4312.7,124.38 4271.5,106.59", style=solid]; qualifiers [height=0.5, - pos="4661.4,178", + pos="4489.4,178", width=1.4985]; "contributor association" -> qualifiers [color=blue, label=qualifiers, - lp="4632.9,221.5", - pos="e,4637.8,194.36 2524.8,251.78 2540.6,249.83 2557,248.09 2572.4,247 2682.5,239.22 4452,254.43 4559.4,229 4584.1,223.16 4609.7,210.56 \ -4629.1,199.48", + lp="4460.9,221.5", + pos="e,4465.8,194.36 2352.8,251.78 2368.6,249.83 2385,248.09 2400.4,247 2510.5,239.22 4280,254.43 4387.4,229 4412.1,223.16 4437.7,210.56 \ +4457.1,199.48", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2619.4,265", + pos="2447.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2750.4,265", + pos="2578.4,265", width=2.0762]; subject -> object [label=relation, - lp="4403.4,134.5", - pos="e,4391.7,108.05 4350.3,160.61 4360.3,147.95 4374.3,130.24 4385.5,115.98"]; + lp="4231.4,134.5", + pos="e,4219.7,108.05 4178.3,160.61 4188.3,147.95 4202.3,130.24 4213.5,115.98"]; relation [height=0.5, - pos="4349.4,18", + pos="4177.4,18", width=1.2999]; - subject -> relation [pos="e,4348.1,36.188 4338.7,159.79 4340.8,132.48 4344.8,78.994 4347.3,46.38", + subject -> relation [pos="e,4176.1,36.188 4166.7,159.79 4168.8,132.48 4172.8,78.994 4175.3,46.38", style=dotted]; "contributor association_subject" [color=blue, height=0.5, label="information content entity", - pos="2976.4,265", + pos="2804.4,265", width=3.7011]; "contributor association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3205.4,265", + pos="3033.4,265", width=2.1665]; - object -> relation [pos="e,4362.2,35.54 4391.9,73.889 4385,64.939 4376.2,53.617 4368.4,43.584", + object -> relation [pos="e,4190.2,35.54 4219.9,73.889 4213,64.939 4204.2,53.617 4196.4,43.584", style=dotted]; "contributor association_object" [color=blue, height=0.5, label=agent, - pos="3338.4,265", + pos="3166.4,265", width=1.0291]; "contributor association_qualifiers" [color=blue, height=0.5, label="ontology class", - pos="3470.4,265", + pos="3298.4,265", width=2.1304]; } diff --git a/graphviz/contributor_association.svg b/graphviz/contributor_association.svg index be5993866b..5778d88b1f 100644 --- a/graphviz/contributor_association.svg +++ b/graphviz/contributor_association.svg @@ -4,16 +4,16 @@ - + %3 - + contributor association - -contributor association + +contributor association @@ -24,9 +24,9 @@ contributor association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ contributor association->id - - -id + + +id @@ -50,9 +50,9 @@ contributor association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ contributor association->name - - -name + + +name @@ -76,9 +76,9 @@ contributor association->description - - -description + + +description @@ -89,9 +89,9 @@ contributor association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ contributor association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ contributor association->publications - - -publications + + +publications @@ -128,382 +128,382 @@ contributor association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string contributor association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string contributor association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string contributor association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type contributor association->timepoint - - -timepoint + + +timepoint original subject - -string + +string contributor association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie contributor association->original predicate - - -original predicate + + +original predicate original object - -string + +string contributor association->original object - - -original object + + +original object subject category - -ontology class + +ontology class contributor association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class contributor association->object category - - -object category + + +object category subject closure - -string + +string contributor association->subject closure - - -subject closure + + +subject closure object closure - -string + +string contributor association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class contributor association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class contributor association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string contributor association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string contributor association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string contributor association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string contributor association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source contributor association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type contributor association->type - - -type + + +type category - -category + +category contributor association->category - - -category + + +category subject - -subject + +subject contributor association->subject - - -subject + + +subject predicate - -predicate + +predicate contributor association->predicate - - -predicate + + +predicate object - -object + +object contributor association->object - - -object + + +object qualifiers - -qualifiers + +qualifiers contributor association->qualifiers - - -qualifiers + + +qualifiers association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + contributor association_subject - -information content entity + +information content entity contributor association_predicate - -predicate type + +predicate type object->relation - - + + contributor association_object - -agent + +agent contributor association_qualifiers - -ontology class + +ontology class diff --git a/graphviz/correlated_gene_to_disease_association.gv b/graphviz/correlated_gene_to_disease_association.gv new file mode 100644 index 0000000000..004bc51f93 --- /dev/null +++ b/graphviz/correlated_gene_to_disease_association.gv @@ -0,0 +1,501 @@ +digraph { + graph [bb="0,0,6813.8,283"]; + node [label="\N"]; + "correlated gene to disease association" [height=0.5, + label="correlated gene to disease association", + pos="3631.8,265", + width=5.2356]; + "gene to disease association" [height=0.5, + pos="137.79,178", + width=3.8274]; + "correlated gene to disease association" -> "gene to disease association" [label=is_a, + lp="762.79,221.5", + pos="e,234.98,190.85 3444.3,263.17 2891.9,260.49 1276.3,250.94 748.79,229 542.22,220.41 490.64,215.21 284.79,196 271.95,194.8 258.49,\ +193.42 245.15,191.97"]; + "entity to disease association mixin" [height=0.5, + pos="464.79,178", + width=4.7482]; + "correlated gene to disease association" -> "entity to disease association mixin" [label=uses, + lp="973.29,221.5", + pos="e,569.19,192.31 3443.4,263.7 2917.6,262.51 1441.3,256.74 956.79,229 827.1,221.58 678.84,205.46 579.27,193.52"]; + "gene to entity association mixin" [height=0.5, + pos="812.79,178", + width=4.4232]; + "correlated gene to disease association" -> "gene to entity association mixin" [label=uses, + lp="1124.3,221.5", + pos="e,883.62,194.16 3444.2,263.07 2898.7,260.12 1337.7,249.95 1107.8,229 1034.8,222.35 952.66,207.84 893.63,196.16"]; + id [color=blue, + height=0.5, + label=string, + pos="1028.8,178", + width=1.0652]; + "correlated gene to disease association" -> id [color=blue, + label=id, + lp="1241.8,221.5", + pos="e,1057.8,189.97 3443.8,263.33 2917,261.14 1451.3,252.97 1234.8,229 1163.5,221.11 1145.9,215.35 1076.8,196 1073.7,195.13 1070.5,194.16 \ +1067.3,193.14", + style=solid]; + iri [color=blue, + height=0.5, + label="iri type", + pos="1129.8,178", + width=1.2277]; + "correlated gene to disease association" -> iri [color=blue, + label=iri, + lp="1346.8,221.5", + pos="e,1162.7,190.13 3444.2,263.22 2933.8,260.8 1544.8,252.15 1338.8,229 1268.4,221.09 1251.3,214.18 1182.8,196 1179.4,195.11 1175.9,\ +194.12 1172.5,193.1", + style=solid]; + name [color=blue, + height=0.5, + label="label type", + pos="1248.8,178", + width=1.5707]; + "correlated gene to disease association" -> name [color=blue, + label=name, + lp="1448.8,221.5", + pos="e,1284.7,191.92 3443.4,263.76 2946.6,262.72 1624.9,257.32 1428.8,229 1382.1,222.26 1330.4,207.06 1294.5,195.18", + style=solid]; + description [color=blue, + height=0.5, + label="narrative text", + pos="1398.8,178", + width=2.0943]; + "correlated gene to disease association" -> description [color=blue, + label=description, + lp="1561.3,221.5", + pos="e,1428.4,194.79 3444.6,262.78 2945.4,259.27 1614,248.16 1520.8,229 1491.8,223.04 1461,210.36 1437.6,199.27", + style=solid]; + "has attribute" [color=blue, + height=0.5, + label=attribute, + pos="1543.8,178", + width=1.4443]; + "correlated gene to disease association" -> "has attribute" [color=blue, + label="has attribute", + lp="1693.8,221.5", + pos="e,1567.6,194.29 3444.5,262.88 2966.6,259.73 1733.1,249.65 1646.8,229 1621.9,223.05 1596,210.46 1576.4,199.4", + style=solid]; + negated [color=blue, + height=0.5, + label=boolean, + pos="1660.8,178", + width=1.2999]; + "correlated gene to disease association" -> negated [color=blue, + label=negated, + lp="1826.8,221.5", + pos="e,1689.1,192.49 3443.3,263.92 3007.7,263.25 1956,258.52 1797.8,229 1763.1,222.53 1725.6,208.28 1698.6,196.64", + style=solid]; + qualifiers [color=blue, + height=0.5, + label="ontology class", + pos="1801.8,178", + width=2.1304]; + "correlated gene to disease association" -> qualifiers [color=blue, + label=qualifiers, + lp="1931.3,221.5", + pos="e,1825.4,195.24 3444.7,262.52 3011.7,258.77 1971.6,247.85 1897.8,229 1875.3,223.26 1852.2,211.42 1834.3,200.71", + style=solid]; + publications [color=blue, + height=0.5, + label=publication, + pos="1958.8,178", + width=1.7332]; + "correlated gene to disease association" -> publications [color=blue, + label=publications, + lp="2024.8,221.5", + pos="e,1961.6,196.44 3444.8,262.66 3018.9,259.25 2010.9,249.08 1980.8,229 1972.9,223.72 1967.8,214.91 1964.5,206.14", + style=solid]; + "has evidence" [color=blue, + height=0.5, + label="evidence type", + pos="2114.8,178", + width=2.0943]; + "correlated gene to disease association" -> "has evidence" [color=blue, + label="has evidence", + lp="2123.3,221.5", + pos="e,2090.2,195.13 3444.1,263.17 3035.6,260.92 2100.4,253.13 2076.8,229 2068.7,220.76 2073.8,210.79 2082.5,201.94", + style=solid]; + "knowledge source" [color=blue, + height=0.5, + label=string, + pos="2246.8,178", + width=1.0652]; + "correlated gene to disease association" -> "knowledge source" [color=blue, + label="knowledge source", + lp="2241.3,221.5", + pos="e,2217.9,189.84 3444.6,262.87 3056.5,260.07 2198.6,251.37 2176.8,229 2172.1,224.23 2173.3,219.67 2176.8,214 2180.7,207.6 2194.4,\ +200.19 2208.6,193.84", + style=solid]; + "primary knowledge source" [color=blue, + height=0.5, + label=string, + pos="2341.8,178", + width=1.0652]; + "correlated gene to disease association" -> "primary knowledge source" [color=blue, + label="primary knowledge source", + lp="2408.8,221.5", + pos="e,2323.8,194.35 3445.2,262.38 3086.3,258.81 2333.2,248.97 2313.8,229 2306.3,221.28 2310.1,211.15 2317.1,202.02", + style=solid]; + "aggregator knowledge source" [color=blue, + height=0.5, + label=string, + pos="2483.8,178", + width=1.0652]; + "correlated gene to disease association" -> "aggregator knowledge source" [color=blue, + label="aggregator knowledge source", + lp="2631.3,221.5", + pos="e,2492.4,195.72 3445.7,262.11 3141,258.45 2565.2,248.93 2524.8,229 2513.8,223.61 2504.8,213.78 2498,204.25", + style=solid]; + timepoint [color=blue, + height=0.5, + label="time type", + pos="2710.8,178", + width=1.5346]; + "correlated gene to disease association" -> timepoint [color=blue, + label=timepoint, + lp="2797.8,221.5", + pos="e,2722.8,195.77 3443.8,263.48 3207.1,261.75 2823.5,254.9 2762.8,229 2749.9,223.5 2738.3,213.23 2729.4,203.43", + style=solid]; + "original subject" [color=blue, + height=0.5, + label=string, + pos="2822.8,178", + width=1.0652]; + "correlated gene to disease association" -> "original subject" [color=blue, + label="original subject", + lp="2905.8,221.5", + pos="e,2827.2,195.97 3449.2,260.34 3226.1,255.2 2874.8,244.68 2849.8,229 2841.2,223.61 2835.1,214.49 2831,205.49", + style=solid]; + "original predicate" [color=blue, + height=0.5, + label=uriorcurie, + pos="2947.8,178", + width=1.5887]; + "correlated gene to disease association" -> "original predicate" [color=blue, + label="original predicate", + lp="3044.3,221.5", + pos="e,2954.2,196.03 3444.9,262.47 3266.8,259.64 3020.2,251.62 2980.8,229 2971.3,223.57 2964.1,214.18 2958.8,205", + style=solid]; + "original object" [color=blue, + height=0.5, + label=string, + pos="3076.8,178", + width=1.0652]; + "correlated gene to disease association" -> "original object" [color=blue, + label="original object", + lp="3186.3,221.5", + pos="e,3090.2,195.15 3444.3,262.96 3327.5,259.98 3189.5,251.53 3134.8,229 3120.7,223.19 3107.6,212.54 3097.4,202.56", + style=solid]; + "subject category" [color=blue, + height=0.5, + label="ontology class", + pos="3209.8,178", + width=2.1304]; + "correlated gene to disease association" -> "subject category" [color=blue, + label="subject category", + lp="3322.3,221.5", + pos="e,3222.6,195.99 3456.8,258.17 3379.2,253.4 3297.5,244.74 3262.8,229 3250.1,223.23 3238.4,213.13 3229.4,203.51", + style=solid]; + "object category" [color=blue, + height=0.5, + label="ontology class", + pos="3380.8,178", + width=2.1304]; + "correlated gene to disease association" -> "object category" [color=blue, + label="object category", + lp="3451.3,221.5", + pos="e,3381.4,196.34 3480.3,254.28 3443.1,249.1 3409.8,241.16 3395.8,229 3389.2,223.27 3385.4,214.73 3383.3,206.33", + style=solid]; + "subject closure" [color=blue, + height=0.5, + label=string, + pos="3513.8,178", + width=1.0652]; + "correlated gene to disease association" -> "subject closure" [color=blue, + label="subject closure", + lp="3571.3,221.5", + pos="e,3510.3,196.01 3542.2,249.12 3532.4,244.15 3523.6,237.6 3516.8,229 3511.8,222.64 3510,214.28 3509.8,206.23", + style=solid]; + "object closure" [color=blue, + height=0.5, + label=string, + pos="3626.8,178", + width=1.0652]; + "correlated gene to disease association" -> "object closure" [color=blue, + label="object closure", + lp="3679.8,221.5", + pos="e,3627.8,196.18 3630.8,246.8 3630.1,235.16 3629.2,219.55 3628.4,206.24", + style=solid]; + "subject category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3759.8,178", + width=2.1304]; + "correlated gene to disease association" -> "subject category closure" [color=blue, + label="subject category closure", + lp="3832.3,221.5", + pos="e,3754.1,196.41 3699.9,248.21 3711.7,243.38 3723.2,237.11 3732.8,229 3740.1,222.78 3745.8,214.06 3750,205.64", + style=solid]; + "object category closure" [color=blue, + height=0.5, + label="ontology class", + pos="3952.8,178", + width=2.1304]; + "correlated gene to disease association" -> "object category closure" [color=blue, + label="object category closure", + lp="4022.3,221.5", + pos="e,3947.4,196.22 3771.6,252.85 3840,246.39 3910.4,237.81 3923.8,229 3932.3,223.41 3938.6,214.41 3943.1,205.57", + style=solid]; + "subject namespace" [color=blue, + height=0.5, + label=string, + pos="4142.8,178", + width=1.0652]; + "correlated gene to disease association" -> "subject namespace" [color=blue, + label="subject namespace", + lp="4193.8,221.5", + pos="e,4136.4,195.99 3764.6,252.2 3786.4,250.38 3808.7,248.58 3829.8,247 3860.9,244.67 4082.8,244.65 4109.8,229 4119.2,223.52 4126.5,\ +214.12 4131.7,204.94", + style=solid]; + "object namespace" [color=blue, + height=0.5, + label=string, + pos="4301.8,178", + width=1.0652]; + "correlated gene to disease association" -> "object namespace" [color=blue, + label="object namespace", + lp="4346.8,221.5", + pos="e,4294.4,196.12 3762.2,251.98 3784.7,250.14 3807.9,248.39 3829.8,247 3878.2,243.93 4223.1,251.99 4265.8,229 4275.8,223.62 4283.7,\ +214.11 4289.5,204.82", + style=solid]; + "subject label closure" [color=blue, + height=0.5, + label=string, + pos="4412.8,178", + width=1.0652]; + "correlated gene to disease association" -> "subject label closure" [color=blue, + label="subject label closure", + lp="4495.8,221.5", + pos="e,4419.1,196.07 3761.1,251.87 3784,250.02 3807.6,248.29 3829.8,247 3862.2,245.11 4392.2,252.34 4414.8,229 4420.6,222.97 4421.8,214.36 \ +4420.9,205.98", + style=solid]; + "object label closure" [color=blue, + height=0.5, + label=string, + pos="4507.8,178", + width=1.0652]; + "correlated gene to disease association" -> "object label closure" [color=blue, + label="object label closure", + lp="4648.3,221.5", + pos="e,4538.2,188.94 3760.3,251.81 3783.4,249.95 3807.3,248.24 3829.8,247 3850.4,245.87 4559.3,243.79 4573.8,229 4587.3,215.2 4568.5,\ +202.13 4547.6,192.82", + style=solid]; + "retrieval source ids" [color=blue, + height=0.5, + label="retrieval source", + pos="4648.8,178", + width=2.347]; + "correlated gene to disease association" -> "retrieval source ids" [color=blue, + label="retrieval source ids", + lp="4796.3,221.5", + pos="e,4694.8,193.15 3759.8,251.78 3783.1,249.9 3807.1,248.2 3829.8,247 3854.5,245.69 4704.4,246.7 4721.8,229 4733.6,216.9 4721.7,205.95 \ +4704.3,197.4", + style=solid]; + type [height=0.5, + pos="4782.8,178", + width=0.86659]; + "correlated gene to disease association" -> type [color=blue, + label=type, + lp="4889.8,221.5", + pos="e,4807.5,189.33 3759.5,251.74 3782.9,249.87 3807,248.17 3829.8,247 3858.6,245.51 4849.5,249.61 4869.8,229 4874.5,224.25 4873.5,219.51 \ +4869.8,214 4857.4,195.87 4844.2,204.2 4823.8,196 4821.6,195.1 4819.3,194.17 4816.9,193.22", + style=solid]; + category [height=0.5, + pos="4883.8,178", + width=1.4263]; + "correlated gene to disease association" -> category [color=blue, + label=category, + lp="4946.3,221.5", + pos="e,4901.3,194.94 3759.5,251.73 3782.9,249.86 3807,248.16 3829.8,247 3859.8,245.47 4888.7,250.39 4909.8,229 4917,221.63 4913.9,211.83 \ +4907.7,202.85", + style=solid]; + "subject aspect qualifier" [height=0.5, + pos="5071.8,178", + width=3.3039]; + "correlated gene to disease association" -> "subject aspect qualifier" [color=blue, + label="subject aspect qualifier", + lp="5102.3,221.5", + pos="e,5049.1,195.77 3759.2,251.73 3782.7,249.85 3807,248.16 3829.8,247 3893.7,243.76 4920,245.54 4981.8,229 5002.6,223.43 5023.8,212 \ +5040.4,201.48", + style=solid]; + "object direction qualifier" [height=0.5, + pos="5333.8,178", + width=3.4664]; + "correlated gene to disease association" -> "object direction qualifier" [color=blue, + label="object direction qualifier", + lp="5334.8,221.5", + pos="e,5297.4,195.31 3759,251.71 3782.5,249.83 3806.9,248.13 3829.8,247 3980.7,239.53 5040.9,255.12 5189.8,229 5223.6,223.07 5260.1,210.31 \ +5287.9,199.17", + style=solid]; + predicate [height=0.5, + pos="5530.8,178", + width=1.5165]; + "correlated gene to disease association" -> predicate [color=blue, + label=predicate, + lp="5502.8,221.5", + pos="e,5506.7,194.34 3759,251.67 3782.5,249.79 3806.9,248.11 3829.8,247 3918.4,242.7 5340.4,249.2 5426.8,229 5451.9,223.13 5478,210.54 \ +5497.8,199.46", + style=solid]; + "frequency qualifier" [color=blue, + height=0.5, + label="frequency value", + pos="5688.8,178", + width=2.3651]; + "correlated gene to disease association" -> "frequency qualifier" [color=blue, + label="frequency qualifier", + lp="5667.8,221.5", + pos="e,5653.4,194.48 3758.7,251.68 3782.3,249.79 3806.8,248.11 3829.8,247 4019.7,237.86 5353.3,260.82 5540.8,229 5576.5,222.94 5615.2,\ +209.62 5644,198.25", + style=solid]; + "severity qualifier" [color=blue, + height=0.5, + label="severity value", + pos="5867.8,178", + width=2.1123]; + "correlated gene to disease association" -> "severity qualifier" [color=blue, + label="severity qualifier", + lp="5851.8,221.5", + pos="e,5837.2,194.61 3758.7,251.66 3782.3,249.77 3806.8,248.09 3829.8,247 3935.8,241.96 5635.6,249.14 5739.8,229 5770.4,223.09 5803.1,\ +210.18 5827.8,198.97", + style=solid]; + "onset qualifier" [color=blue, + height=0.5, + label=onset, + pos="5997.8,178", + width=1.011]; + "correlated gene to disease association" -> "onset qualifier" [color=blue, + label="onset qualifier", + lp="6002.3,221.5", + pos="e,5980.2,193.84 3758.4,251.66 3782.1,249.77 3806.7,248.09 3829.8,247 3887.7,244.27 5861.1,245.07 5916.8,229 5936.8,223.22 5956.8,\ +210.98 5971.9,200.06", + style=solid]; + "sex qualifier" [color=blue, + height=0.5, + label="biological sex", + pos="6125.8,178", + width=2.0401]; + "correlated gene to disease association" -> "sex qualifier" [color=blue, + label="sex qualifier", + lp="6130.8,221.5", + pos="e,6109.4,195.76 3758.4,251.65 3782.1,249.76 3806.7,248.08 3829.8,247 3891.6,244.1 5999.1,248.53 6057.8,229 6073.9,223.63 6089.4,\ +212.83 6101.6,202.64", + style=solid]; + "has count" [color=blue, + height=0.5, + label=integer, + pos="6261.8,178", + width=1.2277]; + "correlated gene to disease association" -> "has count" [color=blue, + label="has count", + lp="6247.8,221.5", + pos="e,6243.1,194.34 3758.4,251.65 3782.1,249.76 3806.7,248.08 3829.8,247 3895,243.96 6116,246.71 6178.8,229 6199,223.31 6219.1,211.32 \ +6234.6,200.51", + style=solid]; + "has total" [color=blue, + height=0.5, + label=integer, + pos="6367.8,178", + width=1.2277]; + "correlated gene to disease association" -> "has total" [color=blue, + label="has total", + lp="6352.3,221.5", + pos="e,6349.3,194.58 3758.4,251.64 3782.1,249.75 3806.7,248.07 3829.8,247 3898,243.83 6221.2,247.87 6286.8,229 6306.4,223.35 6326,211.48 \ +6341,200.73", + style=solid]; + "has quotient" [color=blue, + height=0.5, + label=double, + pos="6471.8,178", + width=1.1735]; + "correlated gene to disease association" -> "has quotient" [color=blue, + label="has quotient", + lp="6467.8,221.5", + pos="e,6452.8,194.34 3758.4,251.63 3782.1,249.75 3806.7,248.07 3829.8,247 3900.8,243.71 6319.3,248.09 6387.8,229 6408.3,223.27 6429,211.11 \ +6444.6,200.21", + style=solid]; + "has percentage" [color=blue, + height=0.5, + label=double, + pos="6573.8,178", + width=1.1735]; + "correlated gene to disease association" -> "has percentage" [color=blue, + label="has percentage", + lp="6596.8,221.5", + pos="e,6560.8,195.47 3758.4,251.63 3782.1,249.74 3806.7,248.07 3829.8,247 3904.3,243.55 6447,255.53 6516.8,229 6530.9,223.63 6543.8,213.03 \ +6553.8,202.96", + style=solid]; + subject [height=0.5, + pos="6695.8,178", + width=1.2277]; + "correlated gene to disease association" -> subject [color=blue, + label=subject, + lp="6700.8,221.5", + pos="e,6687.5,195.82 3758.2,251.64 3781.9,249.75 3806.6,248.07 3829.8,247 3869,245.19 6620.5,246.12 6655.8,229 6666.7,223.73 6675.5,213.92 \ +6682.1,204.37", + style=solid]; + object [height=0.5, + pos="6738.8,91", + width=1.0832]; + "correlated gene to disease association" -> object [color=blue, + label=object, + lp="6791.8,178", + pos="e,6752.2,108.09 3758.2,251.64 3781.9,249.74 3806.6,248.07 3829.8,247 3870,245.15 6696.2,249.68 6730.8,229 6771.5,204.69 6775.4,172.39 \ +6761.8,127 6760.8,123.55 6759.3,120.13 6757.5,116.85", + style=solid]; + association_type [color=blue, + height=0.5, + label=string, + pos="3876.8,265", + width=1.0652]; + association_category [color=blue, + height=0.5, + label="category type", + pos="4007.8,265", + width=2.0762]; + "gene to disease or phenotypic feature association_subject aspect qualifier" [color=blue, + height=0.5, + label=GeneOrGeneProductOrChemicalEntityAspectEnum, + pos="4349.8,265", + width=6.9147]; + "gene to disease or phenotypic feature association_object direction qualifier" [color=blue, + height=0.5, + label=DirectionQualifierEnum, + pos="4737.8,265", + width=3.358]; + "gene to disease or phenotypic feature association_predicate" [color=blue, + height=0.5, + label="predicate type", + pos="4954.8,265", + width=2.1665]; + subject -> object [label=relation, + lp="6733.8,134.5", + pos="e,6720.9,107.23 6696.9,159.55 6698.1,149.57 6700.6,137.07 6705.8,127 6708,122.68 6710.9,118.52 6714.1,114.66"]; + relation [height=0.5, + pos="6683.8,18", + width=1.2999]; + subject -> relation [pos="e,6685.1,36.188 6694.5,159.79 6692.4,132.48 6688.3,78.994 6685.9,46.38", + style=dotted]; + "correlated gene to disease association_subject" [color=blue, + height=0.5, + label="gene or gene product", + pos="5160.8,265", + width=3.0692]; + object -> relation [pos="e,6696.6,35.54 6726.3,73.889 6719.4,64.939 6710.6,53.617 6702.8,43.584", + style=dotted]; + "correlated gene to disease association_object" [color=blue, + height=0.5, + label=disease, + pos="5334.8,265", + width=1.2638]; +} diff --git a/graphviz/correlated_gene_to_disease_association.svg b/graphviz/correlated_gene_to_disease_association.svg new file mode 100644 index 0000000000..7ef42cb85e --- /dev/null +++ b/graphviz/correlated_gene_to_disease_association.svg @@ -0,0 +1,671 @@ + + + + + + +%3 + + + +correlated gene to disease association + +correlated gene to disease association + + + +gene to disease association + +gene to disease association + + + +correlated gene to disease association->gene to disease association + + +is_a + + + +entity to disease association mixin + +entity to disease association mixin + + + +correlated gene to disease association->entity to disease association mixin + + +uses + + + +gene to entity association mixin + +gene to entity association mixin + + + +correlated gene to disease association->gene to entity association mixin + + +uses + + + +id + +string + + + +correlated gene to disease association->id + + +id + + + +iri + +iri type + + + +correlated gene to disease association->iri + + +iri + + + +name + +label type + + + +correlated gene to disease association->name + + +name + + + +description + +narrative text + + + +correlated gene to disease association->description + + +description + + + +has attribute + +attribute + + + +correlated gene to disease association->has attribute + + +has attribute + + + +negated + +boolean + + + +correlated gene to disease association->negated + + +negated + + + +qualifiers + +ontology class + + + +correlated gene to disease association->qualifiers + + +qualifiers + + + +publications + +publication + + + +correlated gene to disease association->publications + + +publications + + + +has evidence + +evidence type + + + +correlated gene to disease association->has evidence + + +has evidence + + + +knowledge source + +string + + + +correlated gene to disease association->knowledge source + + +knowledge source + + + +primary knowledge source + +string + + + +correlated gene to disease association->primary knowledge source + + +primary knowledge source + + + +aggregator knowledge source + +string + + + +correlated gene to disease association->aggregator knowledge source + + +aggregator knowledge source + + + +timepoint + +time type + + + +correlated gene to disease association->timepoint + + +timepoint + + + +original subject + +string + + + +correlated gene to disease association->original subject + + +original subject + + + +original predicate + +uriorcurie + + + +correlated gene to disease association->original predicate + + +original predicate + + + +original object + +string + + + +correlated gene to disease association->original object + + +original object + + + +subject category + +ontology class + + + +correlated gene to disease association->subject category + + +subject category + + + +object category + +ontology class + + + +correlated gene to disease association->object category + + +object category + + + +subject closure + +string + + + +correlated gene to disease association->subject closure + + +subject closure + + + +object closure + +string + + + +correlated gene to disease association->object closure + + +object closure + + + +subject category closure + +ontology class + + + +correlated gene to disease association->subject category closure + + +subject category closure + + + +object category closure + +ontology class + + + +correlated gene to disease association->object category closure + + +object category closure + + + +subject namespace + +string + + + +correlated gene to disease association->subject namespace + + +subject namespace + + + +object namespace + +string + + + +correlated gene to disease association->object namespace + + +object namespace + + + +subject label closure + +string + + + +correlated gene to disease association->subject label closure + + +subject label closure + + + +object label closure + +string + + + +correlated gene to disease association->object label closure + + +object label closure + + + +retrieval source ids + +retrieval source + + + +correlated gene to disease association->retrieval source ids + + +retrieval source ids + + + +type + +type + + + +correlated gene to disease association->type + + +type + + + +category + +category + + + +correlated gene to disease association->category + + +category + + + +subject aspect qualifier + +subject aspect qualifier + + + +correlated gene to disease association->subject aspect qualifier + + +subject aspect qualifier + + + +object direction qualifier + +object direction qualifier + + + +correlated gene to disease association->object direction qualifier + + +object direction qualifier + + + +predicate + +predicate + + + +correlated gene to disease association->predicate + + +predicate + + + +frequency qualifier + +frequency value + + + +correlated gene to disease association->frequency qualifier + + +frequency qualifier + + + +severity qualifier + +severity value + + + +correlated gene to disease association->severity qualifier + + +severity qualifier + + + +onset qualifier + +onset + + + +correlated gene to disease association->onset qualifier + + +onset qualifier + + + +sex qualifier + +biological sex + + + +correlated gene to disease association->sex qualifier + + +sex qualifier + + + +has count + +integer + + + +correlated gene to disease association->has count + + +has count + + + +has total + +integer + + + +correlated gene to disease association->has total + + +has total + + + +has quotient + +double + + + +correlated gene to disease association->has quotient + + +has quotient + + + +has percentage + +double + + + +correlated gene to disease association->has percentage + + +has percentage + + + +subject + +subject + + + +correlated gene to disease association->subject + + +subject + + + +object + +object + + + +correlated gene to disease association->object + + +object + + + +association_type + +string + + + +association_category + +category type + + + +gene to disease or phenotypic feature association_subject aspect qualifier + +GeneOrGeneProductOrChemicalEntityAspectEnum + + + +gene to disease or phenotypic feature association_object direction qualifier + +DirectionQualifierEnum + + + +gene to disease or phenotypic feature association_predicate + +predicate type + + + +subject->object + + +relation + + + +relation + +relation + + + +subject->relation + + + + + +correlated gene to disease association_subject + +gene or gene product + + + +object->relation + + + + + +correlated gene to disease association_object + +disease + + + diff --git a/graphviz/disease_or_phenotypic_feature_to_genetic_inheritance_association.gv b/graphviz/disease_or_phenotypic_feature_to_genetic_inheritance_association.gv index dff5eb113d..ee81a57c89 100644 --- a/graphviz/disease_or_phenotypic_feature_to_genetic_inheritance_association.gv +++ b/graphviz/disease_or_phenotypic_feature_to_genetic_inheritance_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,5342.4,283"]; + graph [bb="0,0,5104.4,283"]; node [label="\N"]; "disease or phenotypic feature to genetic inheritance association" [height=0.5, label="disease or phenotypic feature to genetic inheritance association", - pos="2970.4,265", + pos="2732.4,265", width=8.5576]; association [height=0.5, pos="62.394,178", width=1.7332]; "disease or phenotypic feature to genetic inheritance association" -> association [label=is_a, - lp="664.39,221.5", - pos="e,106.72,190.7 2662.5,264.13 2218.1,263.23 1370.9,257.46 650.39,229 420.77,219.93 361.69,229.86 134.39,196 128.62,195.14 122.62,\ -194.05 116.66,192.83"]; + lp="663.39,221.5", + pos="e,106.72,190.7 2425.2,263.37 2018.8,261.49 1280,254.49 649.39,229 420.22,219.74 361.25,229.8 134.39,196 128.62,195.14 122.62,194.05 \ +116.66,192.83"]; "disease or phenotypic feature to entity association mixin" [height=0.5, pos="417.39,178", width=7.6188]; "disease or phenotypic feature to genetic inheritance association" -> "disease or phenotypic feature to entity association mixin" [label=uses, - lp="845.89,221.5", - pos="e,521.67,194.71 2664.2,262.94 2160,260.52 1176.4,252.83 829.39,229 728.37,222.06 614.1,207.67 531.57,196.11"]; + lp="844.89,221.5", + pos="e,521.85,194.71 2428,262.21 1971.1,258.88 1129.8,250.05 828.39,229 727.9,221.98 614.25,207.66 531.97,196.14"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "disease or phenotypic feature to genetic inheritance association" -> id [color=blue, label=id, - lp="965.39,221.5", - pos="e,777.38,190 2667.2,261.79 2146.7,257.55 1122.9,247.04 958.39,229 885.35,220.99 867.2,215.65 796.39,196 793.29,195.14 790.09,194.17 \ -786.89,193.16", + lp="962.39,221.5", + pos="e,777.38,189.98 2424,264.8 1992.5,264.73 1230.4,259.98 955.39,229 883.68,220.92 865.9,215.43 796.39,196 793.29,195.13 790.09,194.17 \ +786.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,9 @@ digraph { width=1.2277]; "disease or phenotypic feature to genetic inheritance association" -> iri [color=blue, label=iri, - lp="1081.4,221.5", - pos="e,882.3,190.23 2662.2,264.76 2205.7,264.78 1371.7,260.3 1073.4,229 996.41,220.92 977.38,215.19 902.39,196 899.02,195.14 895.54,194.18 \ -892.05,193.17", + lp="1074.4,221.5", + pos="e,882.31,190.19 2424.5,264.07 2016.9,263.02 1320.3,256.99 1066.4,229 992.49,220.85 974.35,214.72 902.39,196 899.02,195.12 895.54,\ +194.15 892.06,193.14", style=solid]; name [color=blue, height=0.5, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "disease or phenotypic feature to genetic inheritance association" -> name [color=blue, label=name, - lp="1192.4,221.5", - pos="e,1007,191.24 2667.7,261.66 2193.8,257.46 1315.9,247.33 1172.4,229 1118.3,222.08 1057.7,206.16 1016.7,194.13", + lp="1181.4,221.5", + pos="e,1006,191.5 2431.8,261.04 2010.8,256.33 1283,245.88 1161.4,229 1110.9,221.99 1054.6,206.49 1015.9,194.59", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "disease or phenotypic feature to genetic inheritance association" -> description [color=blue, label=description, - lp="1319.9,221.5", - pos="e,1155.4,193.76 2665.4,262.31 2215.3,259.12 1411.7,250.47 1279.4,229 1239.9,222.58 1196.6,208.74 1164.9,197.24", + lp="1300.9,221.5", + pos="e,1152,194.23 2428.9,261.87 2031.3,258.29 1371.5,249.36 1260.4,229 1226.1,222.72 1189.1,209.43 1161.4,198.13", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "disease or phenotypic feature to genetic inheritance association" -> "has attribute" [color=blue, label="has attribute", - lp="1475.4,221.5", - pos="e,1296.6,191.98 2667.9,261.54 2253.5,257.49 1546.7,247.91 1428.4,229 1385.9,222.22 1339.2,207.3 1306.3,195.52", + lp="1444.4,221.5", + pos="e,1292.4,193.02 2430.7,261.34 2068,257.32 1495.6,248.05 1397.4,229 1364,222.51 1327.9,208.62 1301.6,197.13", style=solid]; subject [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=1.9318]; "disease or phenotypic feature to genetic inheritance association" -> subject [color=blue, label=subject, - lp="1630.4,221.5", - pos="e,1445.6,192.36 2662.6,263.9 2323.7,262.41 1801,255.64 1604.4,229 1552.9,222.02 1495.4,206.97 1455.2,195.2", + lp="1579.4,221.5", + pos="e,1437.8,193.68 2437.7,259.72 2116.9,254.36 1637.9,244 1553.4,229 1516.7,222.49 1476.8,208.84 1447.4,197.44", style=solid]; negated [color=blue, height=0.5, @@ -87,8 +87,8 @@ digraph { width=1.2999]; "disease or phenotypic feature to genetic inheritance association" -> negated [color=blue, label=negated, - lp="1767.4,221.5", - pos="e,1572.1,190.32 2666.1,262.1 2360.5,258.97 1910.8,250.73 1738.4,229 1683.6,222.1 1622.3,205.5 1581.9,193.31", + lp="1684.4,221.5", + pos="e,1563.2,193.22 2436.4,259.95 2143.9,255.04 1729.6,245.34 1655.4,229 1626.2,222.57 1595.1,209.1 1572.2,197.76", style=solid]; qualifiers [color=blue, height=0.5, @@ -97,8 +97,8 @@ digraph { width=2.1304]; "disease or phenotypic feature to genetic inheritance association" -> qualifiers [color=blue, label=qualifiers, - lp="1901.9,221.5", - pos="e,1720.8,193.12 2666.6,262.01 2394.5,258.83 2016.4,250.55 1868.4,229 1821,222.1 1768.4,207.72 1730.6,196.15", + lp="1778.9,221.5", + pos="e,1694.6,195.6 2427.8,262.32 2161.8,259.35 1808.5,251.21 1745.4,229 1729.5,223.4 1714.2,212.59 1702.3,202.44", style=solid]; publications [color=blue, height=0.5, @@ -107,8 +107,8 @@ digraph { width=1.7332]; "disease or phenotypic feature to genetic inheritance association" -> publications [color=blue, label=publications, - lp="2042.4,221.5", - pos="e,1871,192.88 2667.3,261.71 2430.9,258.3 2122.3,249.87 1998.4,229 1957.7,222.14 1912.9,207.9 1880.6,196.36", + lp="1864.4,221.5", + pos="e,1823,195.81 2427.9,262.28 2171,259.27 1841.7,251.1 1820.4,229 1814.1,222.48 1815,213.43 1818.5,204.83", style=solid]; "has evidence" [color=blue, height=0.5, @@ -117,232 +117,233 @@ digraph { width=2.0943]; "disease or phenotypic feature to genetic inheritance association" -> "has evidence" [color=blue, label="has evidence", - lp="2192.9,221.5", - pos="e,2027.9,193.89 2675.4,259.8 2481,255.44 2244.8,246.63 2146.4,229 2108.8,222.27 2067.8,208.75 2037.4,197.47", + lp="1962.9,221.5", + pos="e,1945.6,192.33 2432.9,260.75 2207.6,256.78 1934.6,248.05 1916.4,229 1904.1,216.12 1917.6,204.8 1936.4,196.21", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2193.4,178", - width=3.015]; + label=string, + pos="2123.4,178", + width=1.0652]; "disease or phenotypic feature to genetic inheritance association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2337.9,221.5", - pos="e,2213.7,195.77 2696.2,256.8 2518.9,251 2313.9,241.72 2273.4,229 2254.8,223.17 2236.3,212 2221.7,201.69", + lp="2080.9,221.5", + pos="e,2094,189.64 2442.5,258.89 2250.6,254.03 2031.6,245.01 2016.4,229 2011.8,224.17 2012.4,219.36 2016.4,214 2032.7,191.97 2049.4,204.58 \ +2075.4,196 2078.3,195.04 2081.3,194.02 2084.4,192.98", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2428.4,178", - width=3.015]; + label=string, + pos="2218.4,178", + width=1.0652]; "disease or phenotypic feature to genetic inheritance association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2505.4,221.5", - pos="e,2414.3,196.1 2708.9,255.46 2568.3,249.55 2421.3,240.65 2410.4,229 2404.2,222.38 2405.4,213.47 2409.3,204.99", + lp="2248.4,221.5", + pos="e,2188,189.07 2466.1,255.9 2319.5,250.09 2164.8,241.14 2153.4,229 2140.4,215.25 2158.4,202.32 2178.7,193.05", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2663.4,178", - width=3.015]; + label=string, + pos="2336.4,178", + width=1.0652]; "disease or phenotypic feature to genetic inheritance association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2714.9,221.5", - pos="e,2627.2,195.05 2735.9,253.3 2672.6,248.03 2618.6,240.28 2608.4,229 2599.4,219.14 2606.6,209.11 2618.4,200.64", + lp="2465.9,221.5", + pos="e,2339.7,196.22 2513.3,252.34 2440.1,246.72 2373.5,238.99 2359.4,229 2351.6,223.46 2346.4,214.59 2342.9,205.85", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2845.4,178", + pos="2562.4,178", width=1.5346]; "disease or phenotypic feature to genetic inheritance association" -> timepoint [color=blue, label=timepoint, - lp="2863.4,221.5", - pos="e,2832.3,195.65 2868.4,247.98 2849.9,243.01 2834.5,236.74 2828.4,229 2822.9,221.97 2824,213.06 2827.6,204.71", + lp="2624.4,221.5", + pos="e,2567.6,196.25 2624.4,248.09 2611.8,243.27 2599.8,237.05 2589.4,229 2581.7,223.04 2575.9,214.23 2571.7,205.66", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2957.4,178", + pos="2674.4,178", width=1.0652]; "disease or phenotypic feature to genetic inheritance association" -> "original subject" [color=blue, label="original subject", - lp="2960.4,221.5", - pos="e,2929.7,190.76 2922.9,247.11 2915.5,242.39 2908.9,236.45 2904.4,229 2896.7,216.25 2907.3,204.67 2920.9,195.86", + lp="2722.4,221.5", + pos="e,2666.4,195.83 2684.9,247.11 2677.5,242.39 2670.9,236.45 2666.4,229 2662.2,222.01 2662.1,213.51 2663.7,205.53", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3071.4,178", + pos="2800.4,178", width=1.5887]; "disease or phenotypic feature to genetic inheritance association" -> "original predicate" [color=blue, label="original predicate", - lp="3097.9,221.5", - pos="e,3053.9,195.61 2993.6,246.94 3001,241.36 3009.1,235.03 3016.4,229 3026.5,220.62 3037.2,211.01 3046.5,202.48", + lp="2850.9,221.5", + pos="e,2795.2,196.38 2759.7,246.8 2766.4,241.66 2773.2,235.62 2778.4,229 2783.8,222.12 2788.2,213.69 2791.6,205.72", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3185.4,178", + pos="2929.4,178", width=1.0652]; "disease or phenotypic feature to genetic inheritance association" -> "original object" [color=blue, label="original object", - lp="3228.9,221.5", - pos="e,3182.8,196.36 3108,248.87 3133.4,243.87 3155.1,237.37 3165.4,229 3172.5,223.23 3177.1,214.57 3180,206.08", + lp="2978.9,221.5", + pos="e,2930.1,196.11 2868,248.82 2890.7,243.87 2909.7,237.41 2918.4,229 2924.5,223.08 2927.6,214.61 2929,206.32", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3318.4,178", + pos="3062.4,178", width=2.1304]; "disease or phenotypic feature to genetic inheritance association" -> "subject category" [color=blue, label="subject category", - lp="3359.9,221.5", - pos="e,3311.3,196.31 3190.9,252.43 3231.4,247.26 3266.5,239.79 3284.4,229 3293.7,223.39 3301,214.15 3306.5,205.12", + lp="3107.9,221.5", + pos="e,3057.3,196.22 2950.5,252.24 2987.1,247.07 3018.4,239.65 3034.4,229 3042.8,223.41 3048.9,214.41 3053.3,205.57", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3489.4,178", + pos="3233.4,178", width=2.1304]; "disease or phenotypic feature to genetic inheritance association" -> "object category" [color=blue, label="object category", - lp="3504.9,221.5", - pos="e,3473.1,195.61 3191.5,252.46 3295,246.04 3400.7,237.62 3423.4,229 3438.9,223.12 3453.8,212.38 3465.6,202.36", + lp="3251.9,221.5", + pos="e,3217.8,196.08 2950.7,252.29 3049.8,245.92 3149.8,237.6 3171.4,229 3185.9,223.23 3199.6,212.86 3210.5,203.05", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3622.4,178", + pos="3366.4,178", width=1.0652]; "disease or phenotypic feature to genetic inheritance association" -> "subject closure" [color=blue, label="subject closure", - lp="3642.9,221.5", - pos="e,3609,195.21 3185.5,252.11 3353.7,242.7 3559.9,230.83 3564.4,229 3578.5,223.27 3591.6,212.63 3601.8,202.63", + lp="3388.9,221.5", + pos="e,3353.9,195.19 2952.5,252.37 3112.6,243.64 3302.9,232.6 3311.4,229 3325,223.25 3337.5,212.6 3347.1,202.61", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3720.4,178", + pos="3479.4,178", width=1.0652]; "disease or phenotypic feature to genetic inheritance association" -> "object closure" [color=blue, label="object closure", - lp="3762.4,221.5", - pos="e,3718.3,196.32 3186.1,252.14 3220,250.36 3254.6,248.59 3287.4,247 3310.3,245.89 3681.7,242.29 3700.4,229 3708,223.64 3712.7,214.92 \ -3715.6,206.26", + lp="3513.4,221.5", + pos="e,3473.3,196.05 2948.5,252.17 2982.3,250.39 3016.8,248.61 3049.4,247 3093.6,244.81 3409.1,251.12 3447.4,229 3456.7,223.65 3463.7,\ +214.4 3468.8,205.31", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3853.4,178", + pos="3612.4,178", width=2.1304]; "disease or phenotypic feature to genetic inheritance association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3920.9,221.5", - pos="e,3845.7,196.16 3183.5,252 3218.2,250.21 3253.8,248.47 3287.4,247 3316.8,245.71 3790.4,242.68 3816.4,229 3826.5,223.67 3834.6,214.17 \ -3840.6,204.87", + lp="3674.9,221.5", + pos="e,3602.2,196.24 2945.9,252 2980.5,250.21 3015.9,248.48 3049.4,247 3106.9,244.46 3515.2,253.34 3567.4,229 3578.9,223.66 3588.7,213.89 \ +3596.2,204.39", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="4043.4,178", + pos="3805.4,178", width=2.1304]; "disease or phenotypic feature to genetic inheritance association" -> "object category closure" [color=blue, label="object category closure", - lp="4110.9,221.5", - pos="e,4037.7,196.12 3180.9,251.86 3216.5,250.05 3253,248.35 3287.4,247 3327.7,245.42 3977.4,249.03 4012.4,229 4021.6,223.72 4028.4,214.49 \ -4033.3,205.39", + lp="3867.9,221.5", + pos="e,3797.1,196.22 2943.4,251.85 2978.8,250.05 3015.1,248.35 3049.4,247 3089.2,245.43 3730.8,246.93 3766.4,229 3776.8,223.74 3785.3,\ +214.26 3791.7,204.95", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4233.4,178", + pos="3995.4,178", width=1.0652]; "disease or phenotypic feature to genetic inheritance association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4283.4,221.5", - pos="e,4226.4,196.2 3179.7,251.77 3215.6,249.96 3252.6,248.28 3287.4,247 3338,245.14 4153.7,252.82 4198.4,229 4208.2,223.76 4215.9,214.41 \ -4221.5,205.2", + lp="4041.4,221.5", + pos="e,3987.1,195.76 2941.7,251.78 2977.6,249.96 3014.6,248.28 3049.4,247 3099.7,245.15 3910.2,251.26 3955.4,229 3966.2,223.66 3975.1,\ +213.83 3981.7,204.3", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4392.4,178", + pos="4154.4,178", width=1.0652]; "disease or phenotypic feature to genetic inheritance association" -> "object namespace" [color=blue, label="object namespace", - lp="4436.4,221.5", - pos="e,4385,195.74 3178.8,251.73 3215,249.91 3252.3,248.24 3287.4,247 3317,245.96 4329,242.58 4355.4,229 4365.7,223.68 4373.9,214 4379.9,\ -204.56", + lp="4195.4,221.5", + pos="e,4145.8,195.79 2940.8,251.73 2977,249.91 3014.3,248.24 3049.4,247 3078.9,245.96 4086.8,241.87 4113.4,229 4124.4,223.69 4133.4,213.87 \ +4140.2,204.33", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4543.4,178", + pos="4305.4,178", width=1.0652]; "disease or phenotypic feature to genetic inheritance association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4596.4,221.5", - pos="e,4535.4,195.77 3178.4,251.69 3214.7,249.87 3252.1,248.21 3287.4,247 3321.2,245.84 4474.1,244.06 4504.4,229 4515.1,223.67 4523.8,\ -213.85 4530.2,204.31", + lp="4357.4,221.5", + pos="e,4296.5,195.81 2940.4,251.69 2976.7,249.87 3014.1,248.21 3049.4,247 3083.1,245.85 4232.9,243.47 4263.4,229 4274.5,223.71 4283.8,\ +213.9 4290.7,204.35", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4714.4,178", + pos="4476.4,178", width=1.0652]; "disease or phenotypic feature to genetic inheritance association" -> "object label closure" [color=blue, label="object label closure", - lp="4761.9,221.5", - pos="e,4706.1,195.79 3177.9,251.66 3214.4,249.84 3252,248.18 3287.4,247 3325.9,245.72 4639.8,245.92 4674.4,229 4685.3,223.69 4694.1,213.88 \ -4700.7,204.34", + lp="4524.9,221.5", + pos="e,4467.8,195.8 2939.9,251.66 2976.4,249.84 3014,248.18 3049.4,247 3087.9,245.72 4400.7,245.69 4435.4,229 4446.4,223.71 4455.4,213.89 \ +4462.2,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4867.4,178", + pos="4629.4,178", width=2.347]; "disease or phenotypic feature to genetic inheritance association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4920.9,221.5", - pos="e,4861.4,196.18 3177.5,251.64 3214.1,249.81 3251.9,248.16 3287.4,247 3330.4,245.6 4797.8,249.86 4835.4,229 4844.9,223.75 4851.9,\ -214.39 4857,205.19", + lp="4682.9,221.5", + pos="e,4623.7,196.17 2939.5,251.64 2976.1,249.81 3013.9,248.16 3049.4,247 3092.4,245.6 4560.9,250.15 4598.4,229 4607.6,223.78 4614.5,\ +214.57 4619.4,205.45", style=solid]; type [height=0.5, - pos="5001.4,178", + pos="4763.4,178", width=0.86659]; "disease or phenotypic feature to genetic inheritance association" -> type [color=blue, label=type, - lp="5019.4,221.5", - pos="e,5004.1,195.99 3177.1,251.63 3213.8,249.8 3251.7,248.14 3287.4,247 3311.1,246.24 4976.6,244.65 4994.4,229 5000.9,223.32 5003.4,\ -214.65 5004.1,206.12", + lp="4781.4,221.5", + pos="e,4766.1,195.99 2939.1,251.63 2975.8,249.8 3013.7,248.14 3049.4,247 3073.1,246.24 4738.6,244.65 4756.4,229 4762.9,223.32 4765.4,\ +214.65 4766.1,206.12", style=solid]; category [height=0.5, - pos="5102.4,178", + pos="4864.4,178", width=1.4263]; "disease or phenotypic feature to genetic inheritance association" -> category [color=blue, label=category, - lp="5097.9,221.5", - pos="e,5087.7,195.48 3177.1,251.62 3213.8,249.79 3251.7,248.14 3287.4,247 3336,245.45 4993.5,245.26 5039.4,229 5054.6,223.6 5069,212.84 \ -5080.1,202.68", + lp="4859.9,221.5", + pos="e,4849.7,195.48 2939.1,251.62 2975.8,249.79 3013.7,248.14 3049.4,247 3098,245.45 4755.5,245.26 4801.4,229 4816.6,223.6 4831,212.84 \ +4842.1,202.68", style=solid]; predicate [height=0.5, - pos="5226.4,178", + pos="4988.4,178", width=1.5165]; "disease or phenotypic feature to genetic inheritance association" -> predicate [color=blue, label=predicate, - lp="5204.4,221.5", - pos="e,5204.7,194.58 3176.7,251.63 3213.5,249.79 3251.6,248.13 3287.4,247 3389.9,243.75 5034.1,254.53 5133.4,229 5155.8,223.25 5178.7,\ -211.04 5196.1,200.13", + lp="4966.4,221.5", + pos="e,4966.7,194.58 2938.7,251.63 2975.5,249.79 3013.6,248.13 3049.4,247 3151.9,243.75 4796.1,254.53 4895.4,229 4917.8,223.25 4940.7,\ +211.04 4958.1,200.13", style=solid]; object [height=0.5, pos="1470.4,91", width=1.0832]; "disease or phenotypic feature to genetic inheritance association" -> object [color=blue, label=object, - lp="5320.4,178", - pos="e,1509.6,91.936 3176.7,251.61 3213.5,249.77 3251.6,248.12 3287.4,247 3341.7,245.3 5190.6,245.35 5242.4,229 5278,217.76 5316.6,186.65 \ -5290.4,160 5221.1,89.43 1961.9,91.338 1519.8,91.922", + lp="5082.4,178", + pos="e,1509.6,91.983 2938.7,251.61 2975.5,249.77 3013.6,248.12 3049.4,247 3103.7,245.3 4952.6,245.35 5004.4,229 5040,217.76 5078.6,186.66 \ +5052.4,160 4987.6,93.941 1945.5,91.938 1519.7,91.982", style=solid]; subject -> object [label=relation, lp="1469.4,134.5", @@ -355,23 +356,23 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="3334.4,265", + pos="3096.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3465.4,265", + pos="3227.4,265", width=2.0762]; "disease or phenotypic feature to genetic inheritance association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3636.4,265", + pos="3398.4,265", width=2.1665]; object -> relation [pos="e,1428.2,35.54 1457.9,73.889 1451,64.939 1442.2,53.617 1434.4,43.584", style=dotted]; "disease or phenotypic feature to genetic inheritance association_object" [color=blue, height=0.5, label="genetic inheritance", - pos="3833.4,265", + pos="3595.4,265", width=2.7984]; } diff --git a/graphviz/disease_or_phenotypic_feature_to_genetic_inheritance_association.svg b/graphviz/disease_or_phenotypic_feature_to_genetic_inheritance_association.svg index de13a7f003..59eef4e25c 100644 --- a/graphviz/disease_or_phenotypic_feature_to_genetic_inheritance_association.svg +++ b/graphviz/disease_or_phenotypic_feature_to_genetic_inheritance_association.svg @@ -4,16 +4,16 @@ - + %3 - + disease or phenotypic feature to genetic inheritance association - -disease or phenotypic feature to genetic inheritance association + +disease or phenotypic feature to genetic inheritance association @@ -24,9 +24,9 @@ disease or phenotypic feature to genetic inheritance association->association - + -is_a +is_a @@ -37,9 +37,9 @@ disease or phenotypic feature to genetic inheritance association->disease or phenotypic feature to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ disease or phenotypic feature to genetic inheritance association->id - - -id + + +id @@ -63,9 +63,9 @@ disease or phenotypic feature to genetic inheritance association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ disease or phenotypic feature to genetic inheritance association->name - - -name + + +name @@ -89,9 +89,9 @@ disease or phenotypic feature to genetic inheritance association->description - - -description + + +description @@ -102,9 +102,9 @@ disease or phenotypic feature to genetic inheritance association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ disease or phenotypic feature to genetic inheritance association->subject - - -subject + + +subject @@ -128,9 +128,9 @@ disease or phenotypic feature to genetic inheritance association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ disease or phenotypic feature to genetic inheritance association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ disease or phenotypic feature to genetic inheritance association->publications - - -publications + + +publications @@ -167,282 +167,282 @@ disease or phenotypic feature to genetic inheritance association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string disease or phenotypic feature to genetic inheritance association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string disease or phenotypic feature to genetic inheritance association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string disease or phenotypic feature to genetic inheritance association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type disease or phenotypic feature to genetic inheritance association->timepoint - - -timepoint + + +timepoint original subject - -string + +string disease or phenotypic feature to genetic inheritance association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie disease or phenotypic feature to genetic inheritance association->original predicate - - -original predicate + + +original predicate original object - -string + +string disease or phenotypic feature to genetic inheritance association->original object - - -original object + + +original object subject category - -ontology class + +ontology class disease or phenotypic feature to genetic inheritance association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class disease or phenotypic feature to genetic inheritance association->object category - - -object category + + +object category subject closure - -string + +string disease or phenotypic feature to genetic inheritance association->subject closure - - -subject closure + + +subject closure object closure - -string + +string disease or phenotypic feature to genetic inheritance association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class disease or phenotypic feature to genetic inheritance association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class disease or phenotypic feature to genetic inheritance association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string disease or phenotypic feature to genetic inheritance association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string disease or phenotypic feature to genetic inheritance association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string disease or phenotypic feature to genetic inheritance association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string disease or phenotypic feature to genetic inheritance association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source disease or phenotypic feature to genetic inheritance association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type disease or phenotypic feature to genetic inheritance association->type - - -type + + +type category - -category + +category disease or phenotypic feature to genetic inheritance association->category - - -category + + +category predicate - -predicate + +predicate disease or phenotypic feature to genetic inheritance association->predicate - - -predicate + + +predicate @@ -453,9 +453,9 @@ disease or phenotypic feature to genetic inheritance association->object - - -object + + +object @@ -479,20 +479,20 @@ association_type - -string + +string association_category - -category type + +category type disease or phenotypic feature to genetic inheritance association_predicate - -predicate type + +predicate type @@ -503,8 +503,8 @@ disease or phenotypic feature to genetic inheritance association_object - -genetic inheritance + +genetic inheritance diff --git a/graphviz/disease_or_phenotypic_feature_to_location_association.gv b/graphviz/disease_or_phenotypic_feature_to_location_association.gv index 42c751d64d..bf6682fd0d 100644 --- a/graphviz/disease_or_phenotypic_feature_to_location_association.gv +++ b/graphviz/disease_or_phenotypic_feature_to_location_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,5396.4,283"]; + graph [bb="0,0,5138.4,283"]; node [label="\N"]; "disease or phenotypic feature to location association" [height=0.5, label="disease or phenotypic feature to location association", - pos="3028.4,265", + pos="2770.4,265", width=7.0771]; association [height=0.5, pos="62.394,178", width=1.7332]; "disease or phenotypic feature to location association" -> association [label=is_a, - lp="664.39,221.5", - pos="e,106.72,190.7 2773.6,264.35 2338.2,264.04 1423.2,259.38 650.39,229 420.77,219.97 361.69,229.86 134.39,196 128.62,195.14 122.62,\ -194.05 116.66,192.83"]; + lp="663.39,221.5", + pos="e,106.72,190.7 2516,263.7 2117.8,262.35 1323,256.13 649.39,229 420.22,219.77 361.25,229.8 134.39,196 128.62,195.14 122.62,194.05 \ +116.66,192.83"]; "disease or phenotypic feature to entity association mixin" [height=0.5, pos="417.39,178", width=7.6188]; "disease or phenotypic feature to location association" -> "disease or phenotypic feature to entity association mixin" [label=uses, - lp="846.89,221.5", - pos="e,521.5,194.66 2774.3,263.3 2279.2,261.37 1201,254.32 830.39,229 728.95,222.07 614.19,207.64 531.43,196.06"]; + lp="844.89,221.5", + pos="e,521.42,194.66 2517.4,262.68 2068.3,259.81 1148.9,251.32 828.39,229 727.72,221.99 613.86,207.63 531.55,196.09"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "disease or phenotypic feature to location association" -> id [color=blue, label=id, - lp="967.39,221.5", - pos="e,777.37,190.01 2776,262.3 2263.9,258.47 1136,248 960.39,229 886.48,221 868.06,215.79 796.39,196 793.28,195.14 790.08,194.18 786.89,\ -193.17", + lp="964.39,221.5", + pos="e,777.38,189.99 2515.6,264.83 2089.7,265.24 1251.2,261.67 957.39,229 884.8,220.93 866.77,215.57 796.39,196 793.29,195.14 790.09,\ +194.17 786.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,9 @@ digraph { width=1.2277]; "disease or phenotypic feature to location association" -> iri [color=blue, label=iri, - lp="1085.4,221.5", - pos="e,882.01,190.16 2773.6,264.76 2322,265.22 1398.4,261.91 1077.4,229 998.66,220.93 979.11,215.46 902.39,196 898.97,195.13 895.43,194.16 \ -891.9,193.14", + lp="1079.4,221.5", + pos="e,882.3,190.21 2515.9,264.13 2112.3,263.42 1343.3,258.13 1071.4,229 995.3,220.85 976.51,215.05 902.39,196 899.02,195.13 895.54,194.17 \ +892.05,193.16", style=solid]; name [color=blue, height=0.5, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "disease or phenotypic feature to location association" -> name [color=blue, label=name, - lp="1199.4,221.5", - pos="e,1007.6,191.06 2776.9,262.1 2307.9,258.14 1333.3,247.77 1179.4,229 1123,222.12 1059.8,205.98 1017.4,193.88", + lp="1189.4,221.5", + pos="e,1006.8,191.31 2520.2,261.52 2103.3,256.95 1299.1,246.06 1169.4,229 1116.2,222 1056.7,206.18 1016.4,194.19", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "disease or phenotypic feature to location association" -> description [color=blue, label=description, - lp="1330.9,221.5", - pos="e,1157.4,193.52 2775.8,262.58 2329,259.52 1432.8,250.74 1290.4,229 1247.9,222.51 1201.1,208.43 1167,196.86", + lp="1314.9,221.5", + pos="e,1154.5,193.86 2518.7,262.04 2124.3,258.38 1393.1,248.99 1274.4,229 1236.3,222.59 1194.7,208.91 1164.1,197.48", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "disease or phenotypic feature to location association" -> "has attribute" [color=blue, label="has attribute", - lp="1492.4,221.5", - pos="e,1298.4,191.41 2777.2,261.81 2363.9,257.7 1573,247.53 1445.4,229 1397.7,222.07 1344.7,206.59 1308.2,194.67", + lp="1467.4,221.5", + pos="e,1295.5,192.18 2520.6,261.33 2160,256.89 1525.3,246.7 1420.4,229 1380.3,222.24 1336.3,207.57 1305.2,195.87", style=solid]; subject [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=1.9318]; "disease or phenotypic feature to location association" -> subject [color=blue, label=subject, - lp="1657.4,221.5", - pos="e,1448.8,191.65 2774.5,263.44 2433.3,261.69 1845,254.86 1631.4,229 1571.6,221.76 1504.4,206.08 1458.5,194.2", + lp="1616.4,221.5", + pos="e,1443.7,192.68 2516.5,263.34 2224.2,261.36 1762.3,254.19 1590.4,229 1543.1,222.07 1490.6,207.4 1453.3,195.73", style=solid]; predicate [color=blue, height=0.5, @@ -87,8 +87,8 @@ digraph { width=2.1665]; "disease or phenotypic feature to location association" -> predicate [color=blue, label=predicate, - lp="1795.4,221.5", - pos="e,1612.3,193.17 2774,263.79 2461.5,262.34 1949.7,255.77 1761.4,229 1713.5,222.19 1660.4,207.8 1622.2,196.2", + lp="1730.4,221.5", + pos="e,1600.3,194.64 2523.8,260.4 2231.8,255.43 1774.9,245.22 1696.4,229 1666.3,222.78 1634.1,210.01 1609.6,198.94", style=solid]; negated [color=blue, height=0.5, @@ -97,8 +97,8 @@ digraph { width=1.2999]; "disease or phenotypic feature to location association" -> negated [color=blue, label=negated, - lp="1939.4,221.5", - pos="e,1747,190.39 2777.5,261.84 2500.2,258.45 2071.6,249.92 1910.4,229 1856.6,222.02 1796.4,205.52 1756.6,193.37", + lp="1834.4,221.5", + pos="e,1733.7,194.16 2522.5,260.83 2259.5,256.55 1872.6,247.23 1805.4,229 1782.9,222.91 1759.9,210.58 1742.4,199.68", style=solid]; qualifiers [color=blue, height=0.5, @@ -107,8 +107,8 @@ digraph { width=2.1304]; "disease or phenotypic feature to location association" -> qualifiers [color=blue, label=qualifiers, - lp="2072.9,221.5", - pos="e,1895.3,193.2 2778,261.61 2532.6,258.09 2176.3,249.55 2039.4,229 1993.1,222.05 1941.8,207.75 1904.8,196.22", + lp="1913.9,221.5", + pos="e,1857.8,195.99 2524.4,260.29 2270.5,255.56 1907.5,245.9 1880.4,229 1871.8,223.63 1865.7,214.51 1861.6,205.52", style=solid]; publications [color=blue, height=0.5, @@ -117,8 +117,8 @@ digraph { width=1.7332]; "disease or phenotypic feature to location association" -> publications [color=blue, label=publications, - lp="2210.4,221.5", - pos="e,2045,193.08 2778.9,261.31 2567,257.64 2279.6,249.06 2166.4,229 2127.7,222.15 2085.4,208.15 2054.6,196.7", + lp="1999.4,221.5", + pos="e,1977.5,193.31 2520.2,261.55 2288,258 1975,249.44 1955.4,229 1945.3,218.5 1954.8,207.57 1968.5,198.61", style=solid]; "has evidence" [color=blue, height=0.5, @@ -127,225 +127,228 @@ digraph { width=2.0943]; "disease or phenotypic feature to location association" -> "has evidence" [color=blue, label="has evidence", - lp="2356.9,221.5", - pos="e,2200.8,194.09 2785.2,259.53 2613.3,254.97 2398.3,246.04 2310.4,229 2275.9,222.31 2238.4,209.1 2210.3,197.94", + lp="2096.9,221.5", + pos="e,2108.7,189.71 2525,260.03 2322.9,255.52 2067,246.4 2050.4,229 2045.8,224.17 2046.4,219.35 2050.4,214 2056.9,205.25 2077.2,197.84 \ +2099,192.13", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2368.4,178", - width=3.015]; + label=string, + pos="2298.4,178", + width=1.0652]; "disease or phenotypic feature to location association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2495.9,221.5", - pos="e,2384,195.95 2798.8,257.17 2645.4,251.46 2465.8,242.13 2431.4,229 2416.6,223.35 2402.5,212.89 2391.5,202.99", + lp="2227.9,221.5", + pos="e,2269.4,189.98 2536.1,257.87 2370.9,252.36 2176.6,242.96 2163.4,229 2117.8,180.74 2103.1,237.12 2250.4,196 2253.5,195.13 2256.7,\ +194.17 2259.9,193.15", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2603.4,178", - width=3.015]; + label=string, + pos="2393.4,178", + width=1.0652]; "disease or phenotypic feature to location association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2662.4,221.5", - pos="e,2579.2,195.77 2785.3,259.61 2682.9,255.18 2583.5,246.38 2567.4,229 2560,220.97 2564.2,211.37 2572,202.74", + lp="2394.4,221.5", + pos="e,2363.8,189.56 2525.4,260.06 2419.6,255.75 2316,246.93 2299.4,229 2294.9,224.11 2295.6,219.48 2299.4,214 2300.3,212.74 2328.9,202.19 \ +2354.3,193", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2838.4,178", - width=3.015]; + label=string, + pos="2488.4,178", + width=1.0652]; "disease or phenotypic feature to location association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2871.9,221.5", - pos="e,2789.2,194.17 2826.9,253.98 2798.6,248.6 2775.6,240.65 2765.4,229 2755,217.1 2764.7,206.69 2780.1,198.49", + lp="2608.9,221.5", + pos="e,2488.6,196.37 2576.5,253.32 2543.4,248.09 2515.5,240.37 2502.4,229 2495.8,223.29 2492.2,214.77 2490.3,206.36", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="3020.4,178", + pos="2714.4,178", width=1.5346]; "disease or phenotypic feature to location association" -> timepoint [color=blue, label=timepoint, - lp="3018.4,221.5", - pos="e,2997.6,194.47 2998.3,246.83 2992.3,241.89 2986.8,235.93 2983.4,229 2978.7,219.42 2983.1,209.79 2990.4,201.57", + lp="2760.4,221.5", + pos="e,2715.3,196.31 2742.3,246.98 2735.9,241.92 2729.7,235.86 2725.4,229 2721.2,222.28 2718.5,214.16 2716.9,206.44", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="3132.4,178", + pos="2826.4,178", width=1.0652]; "disease or phenotypic feature to location association" -> "original subject" [color=blue, label="original subject", - lp="3132.4,221.5", - pos="e,3108.4,192.24 3043,246.75 3052.1,236.6 3064.3,223.86 3076.4,214 3083.6,208.17 3091.8,202.54 3099.7,197.56", + lp="2861.4,221.5", + pos="e,2816.3,195.84 2783.1,246.71 2787.1,241.11 2791.5,234.84 2795.4,229 2800.7,221.09 2806.2,212.33 2811.1,204.38", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3246.4,178", + pos="2952.4,178", width=1.5887]; "disease or phenotypic feature to location association" -> "original predicate" [color=blue, label="original predicate", - lp="3274.9,221.5", - pos="e,3231.2,195.85 3134.7,248.53 3153.1,243.68 3171.7,237.33 3188.4,229 3201.5,222.46 3214,212.32 3224.1,202.87", + lp="2999.9,221.5", + pos="e,2945.8,196.33 2882.4,248.69 2896.3,243.8 2909.7,237.39 2921.4,229 2929.7,223.06 2936.2,214.14 2941.1,205.48", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3360.4,178", + pos="3086.4,178", width=1.0652]; "disease or phenotypic feature to location association" -> "original object" [color=blue, label="original object", - lp="3402.9,221.5", - pos="e,3357.4,196.13 3242.5,255.23 3284.6,249.97 3321.1,241.76 3338.4,229 3346.1,223.36 3351.1,214.47 3354.4,205.74", + lp="3130.9,221.5", + pos="e,3084.4,196.05 2979.5,254.68 3018.3,249.41 3051.6,241.33 3067.4,229 3074.7,223.33 3079.1,214.55 3081.9,205.92", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3493.4,178", + pos="3219.4,178", width=2.1304]; "disease or phenotypic feature to location association" -> "subject category" [color=blue, label="subject category", - lp="3533.9,221.5", - pos="e,3486.3,195.95 3212.6,252.54 3324.2,245.01 3447.2,235.4 3458.4,229 3468,223.47 3475.7,214.06 3481.3,204.89", + lp="3261.9,221.5", + pos="e,3212.7,196.41 2951.3,252.33 3058.6,244.81 3175.8,235.3 3186.4,229 3195.6,223.56 3202.7,214.47 3207.9,205.52", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3664.4,178", + pos="3390.4,178", width=2.1304]; "disease or phenotypic feature to location association" -> "object category" [color=blue, label="object category", - lp="3679.9,221.5", - pos="e,3647.9,195.71 3208.7,252.26 3236.7,250.47 3265.3,248.67 3292.4,247 3360.2,242.82 3533.6,252.28 3597.4,229 3613.1,223.26 3628.3,\ -212.54 3640.2,202.49", + lp="3406.9,221.5", + pos="e,3374.5,195.69 2951.1,252.3 2979,250.51 3007.5,248.7 3034.4,247 3099.1,242.92 3264.7,251.75 3325.4,229 3340.8,223.23 3355.5,212.51 \ +3367,202.47", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3797.4,178", + pos="3523.4,178", width=1.0652]; "disease or phenotypic feature to location association" -> "subject closure" [color=blue, label="subject closure", - lp="3815.9,221.5", - pos="e,3781.6,194.7 3205.2,252.03 3234.3,250.22 3264.2,248.48 3292.4,247 3342,244.4 3693.2,247.25 3739.4,229 3747.3,225.89 3761.7,213.47 \ -3774.2,201.79", + lp="3543.9,221.5", + pos="e,3510.3,195.29 2947.5,252.04 2976.5,250.24 3006.3,248.49 3034.4,247 3082.4,244.46 3421.8,246.86 3466.4,229 3480.4,223.39 3493.3,\ +212.76 3503.3,202.74", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3893.4,178", + pos="3631.4,178", width=1.0652]; "disease or phenotypic feature to location association" -> "object closure" [color=blue, label="object closure", - lp="3935.4,221.5", - pos="e,3890.9,196.39 3203.4,251.91 3233.1,250.09 3263.6,248.37 3292.4,247 3324.6,245.46 3845.8,247.26 3872.4,229 3880.2,223.65 3885.1,\ -214.82 3888.2,206.06", + lp="3667.4,221.5", + pos="e,3626.4,196.06 2945.7,251.91 2975.3,250.1 3005.7,248.38 3034.4,247 3065.9,245.49 3575.3,245.19 3602.4,229 3611.3,223.65 3617.8,\ +214.41 3622.3,205.31", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="4026.4,178", + pos="3764.4,178", width=2.1304]; "disease or phenotypic feature to location association" -> "subject category closure" [color=blue, label="subject category closure", - lp="4093.9,221.5", - pos="e,4018.7,196.2 3202.7,251.83 3232.6,250.01 3263.4,248.31 3292.4,247 3331.1,245.26 3955,246.88 3989.4,229 3999.6,223.71 4007.7,214.22 \ -4013.6,204.92", + lp="3827.9,221.5", + pos="e,3754.8,196.26 2944.7,251.84 2974.6,250.02 3005.4,248.31 3034.4,247 3072.5,245.27 3686.9,245.38 3721.4,229 3732.5,223.74 3741.8,\ +214.11 3748.9,204.71", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="4215.4,178", + pos="3957.4,178", width=2.1304]; "disease or phenotypic feature to location association" -> "object category closure" [color=blue, label="object category closure", - lp="4283.9,221.5", - pos="e,4210.1,196.12 3201.2,251.77 3231.6,249.94 3262.9,248.25 3292.4,247 3342,244.91 4142.5,253.88 4185.4,229 4194.5,223.73 4201.2,214.5 \ -4205.8,205.39", + lp="4019.9,221.5", + pos="e,3949.4,196.23 2943.6,251.75 2973.8,249.93 3005,248.24 3034.4,247 3083.5,244.92 3875.6,251.3 3919.4,229 3929.7,223.75 3938,214.27 \ +3944.2,204.96", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4405.4,178", + pos="4147.4,178", width=1.0652]; "disease or phenotypic feature to location association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4455.4,221.5", - pos="e,4398.7,196.19 3200.5,251.73 3231.1,249.89 3262.7,248.2 3292.4,247 3322.3,245.79 4345,243.24 4371.4,229 4381.1,223.76 4388.6,214.41 \ -4394,205.2", + lp="4193.4,221.5", + pos="e,4139.1,195.78 2942.9,251.71 2973.4,249.88 3004.8,248.2 3034.4,247 3064.2,245.79 4080.6,242.14 4107.4,229 4118.2,223.67 4127.1,\ +213.85 4133.7,204.32", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4564.4,178", + pos="4306.4,178", width=1.0652]; "disease or phenotypic feature to location association" -> "object namespace" [color=blue, label="object namespace", - lp="4608.4,221.5", - pos="e,4557,195.75 3200.2,251.7 3230.9,249.85 3262.6,248.18 3292.4,247 3326.7,245.65 4496.9,244.66 4527.4,229 4537.7,223.69 4545.9,214.01 \ -4551.9,204.58", + lp="4347.4,221.5", + pos="e,4297.8,195.8 2942.2,251.7 2972.9,249.85 3004.6,248.18 3034.4,247 3068.6,245.65 4234.6,243.85 4265.4,229 4276.4,223.7 4285.4,213.88 \ +4292.2,204.34", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4715.4,178", + pos="4457.4,178", width=1.0652]; "disease or phenotypic feature to location association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4768.4,221.5", - pos="e,4707.4,195.78 3199.8,251.68 3230.6,249.83 3262.4,248.16 3292.4,247 3330.8,245.51 4642,246.09 4676.4,229 4687.1,223.68 4695.8,213.86 \ -4702.2,204.32", + lp="4509.4,221.5", + pos="e,4448.5,195.81 2941.8,251.68 2972.6,249.83 3004.4,248.16 3034.4,247 3072.7,245.52 4380.7,245.43 4415.4,229 4426.5,223.72 4435.8,\ +213.91 4442.7,204.36", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4886.4,178", + pos="4628.4,178", width=1.0652]; "disease or phenotypic feature to location association" -> "object label closure" [color=blue, label="object label closure", - lp="4934.9,221.5", - pos="e,4878.1,195.8 3199.8,251.64 3230.6,249.8 3262.4,248.14 3292.4,247 3335.5,245.36 4807.6,247.93 4846.4,229 4857.3,223.7 4866.1,213.89 \ -4872.7,204.34", + lp="4676.9,221.5", + pos="e,4619.8,195.81 2941.8,251.64 2972.6,249.8 3004.4,248.14 3034.4,247 3077.5,245.36 4548.5,247.68 4587.4,229 4598.4,223.72 4607.4,\ +213.9 4614.2,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="5048.4,178", + pos="4790.4,178", width=2.347]; "disease or phenotypic feature to location association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="5096.9,221.5", - pos="e,5039.8,196.3 3199.5,251.64 3230.4,249.79 3262.3,248.12 3292.4,247 3340,245.22 4965.5,249.87 5008.4,229 5019.1,223.78 5027.9,214.17 \ -5034.4,204.75", + lp="4838.9,221.5", + pos="e,4781.8,196.3 2941.5,251.64 2972.4,249.79 3004.3,248.12 3034.4,247 3082,245.22 4707.5,249.87 4750.4,229 4761.1,223.78 4769.9,214.17 \ +4776.4,204.75", style=solid]; type [height=0.5, - pos="5182.4,178", + pos="4924.4,178", width=0.86659]; "disease or phenotypic feature to location association" -> type [color=blue, label=type, - lp="5196.4,221.5", - pos="e,5183.2,196.19 3199.1,251.64 3230.1,249.78 3262.2,248.12 3292.4,247 3318.5,246.04 5150,245.25 5170.4,229 5177.2,223.54 5180.6,214.93 \ -5182.2,206.37", + lp="4938.4,221.5", + pos="e,4925.2,196.19 2941.1,251.64 2972.1,249.78 3004.2,248.12 3034.4,247 3060.5,246.04 4892,245.25 4912.4,229 4919.2,223.54 4922.6,214.93 \ +4924.2,206.37", style=solid]; category [height=0.5, - pos="5283.4,178", + pos="5025.4,178", width=1.4263]; "disease or phenotypic feature to location association" -> category [color=blue, label=category, - lp="5275.9,221.5", - pos="e,5267.8,195.26 3199.1,251.63 3230.1,249.77 3262.2,248.11 3292.4,247 3345.8,245.03 5165.7,246.08 5216.4,229 5232.6,223.54 5248.1,\ -212.51 5260.1,202.2", + lp="5017.9,221.5", + pos="e,5009.8,195.26 2941.1,251.63 2972.1,249.77 3004.2,248.11 3034.4,247 3087.8,245.03 4907.7,246.08 4958.4,229 4974.6,223.54 4990.1,\ +212.51 5002.1,202.2", style=solid]; object [height=0.5, pos="1470.4,91", width=1.0832]; "disease or phenotypic feature to location association" -> object [color=blue, label=object, - lp="5374.4,178", - pos="e,1509.5,91.926 3199.1,251.62 3230.1,249.76 3262.2,248.11 3292.4,247 3348.4,244.95 5259.8,251.09 5311.4,229 5342.5,215.69 5367.1,\ -184.11 5343.4,160 5273.1,88.423 1965.3,91.209 1519.8,91.91", + lp="5116.4,178", + pos="e,1509.6,91.976 2941.1,251.62 2972.1,249.76 3004.2,248.11 3034.4,247 3090.4,244.95 5001.8,251.09 5053.4,229 5084.5,215.69 5109.1,\ +184.13 5085.4,160 5020,93.321 1948.3,91.853 1519.8,91.973", style=solid]; subject -> object [label=relation, lp="1469.4,134.5", @@ -358,18 +361,18 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="3339.4,265", + pos="3081.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3470.4,265", + pos="3212.4,265", width=2.0762]; object -> relation [pos="e,1428.2,35.54 1457.9,73.889 1451,64.939 1442.2,53.617 1434.4,43.584", style=dotted]; "disease or phenotypic feature to location association_object" [color=blue, height=0.5, label="anatomical entity", - pos="3654.4,265", + pos="3396.4,265", width=2.5456]; } diff --git a/graphviz/disease_or_phenotypic_feature_to_location_association.svg b/graphviz/disease_or_phenotypic_feature_to_location_association.svg index ed94496406..1d731cb0a1 100644 --- a/graphviz/disease_or_phenotypic_feature_to_location_association.svg +++ b/graphviz/disease_or_phenotypic_feature_to_location_association.svg @@ -4,16 +4,16 @@ - + %3 - + disease or phenotypic feature to location association - -disease or phenotypic feature to location association + +disease or phenotypic feature to location association @@ -24,9 +24,9 @@ disease or phenotypic feature to location association->association - + -is_a +is_a @@ -37,9 +37,9 @@ disease or phenotypic feature to location association->disease or phenotypic feature to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ disease or phenotypic feature to location association->id - - -id + + +id @@ -63,9 +63,9 @@ disease or phenotypic feature to location association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ disease or phenotypic feature to location association->name - - -name + + +name @@ -89,9 +89,9 @@ disease or phenotypic feature to location association->description - - -description + + +description @@ -102,9 +102,9 @@ disease or phenotypic feature to location association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ disease or phenotypic feature to location association->subject - - -subject + + +subject @@ -128,9 +128,9 @@ disease or phenotypic feature to location association->predicate - - -predicate + + +predicate @@ -141,9 +141,9 @@ disease or phenotypic feature to location association->negated - - -negated + + +negated @@ -154,9 +154,9 @@ disease or phenotypic feature to location association->qualifiers - - -qualifiers + + +qualifiers @@ -167,9 +167,9 @@ disease or phenotypic feature to location association->publications - - -publications + + +publications @@ -180,269 +180,269 @@ disease or phenotypic feature to location association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string disease or phenotypic feature to location association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string disease or phenotypic feature to location association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string disease or phenotypic feature to location association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type disease or phenotypic feature to location association->timepoint - - -timepoint + + +timepoint original subject - -string + +string disease or phenotypic feature to location association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie disease or phenotypic feature to location association->original predicate - - -original predicate + + +original predicate original object - -string + +string disease or phenotypic feature to location association->original object - - -original object + + +original object subject category - -ontology class + +ontology class disease or phenotypic feature to location association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class disease or phenotypic feature to location association->object category - - -object category + + +object category subject closure - -string + +string disease or phenotypic feature to location association->subject closure - - -subject closure + + +subject closure object closure - -string + +string disease or phenotypic feature to location association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class disease or phenotypic feature to location association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class disease or phenotypic feature to location association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string disease or phenotypic feature to location association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string disease or phenotypic feature to location association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string disease or phenotypic feature to location association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string disease or phenotypic feature to location association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source disease or phenotypic feature to location association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type disease or phenotypic feature to location association->type - - -type + + +type category - -category + +category disease or phenotypic feature to location association->category - - -category + + +category @@ -453,9 +453,9 @@ disease or phenotypic feature to location association->object - - -object + + +object @@ -479,14 +479,14 @@ association_type - -string + +string association_category - -category type + +category type @@ -497,8 +497,8 @@ disease or phenotypic feature to location association_object - -anatomical entity + +anatomical entity diff --git a/graphviz/disease_to_exposure_event_association.gv b/graphviz/disease_to_exposure_event_association.gv index 62be02c51f..a071ddc690 100644 --- a/graphviz/disease_to_exposure_event_association.gv +++ b/graphviz/disease_to_exposure_event_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,5668.7,283"]; + graph [bb="0,0,5403.7,283"]; node [label="\N"]; "disease to exposure event association" [height=0.5, label="disease to exposure event association", - pos="3052.4,265", + pos="2787.4,265", width=5.1815]; association [height=0.5, pos="62.394,178", width=1.7332]; "disease to exposure event association" -> association [label=is_a, lp="669.39,221.5", - pos="e,106.48,190.8 2865.8,264.36 2462.4,264.45 1478.8,261.02 655.39,229 423.11,219.97 363.28,230.53 133.39,196 127.91,195.18 122.23,\ -194.14 116.57,192.98"]; + pos="e,106.48,190.8 2600.9,263.87 2230.1,262.95 1374.1,257.6 655.39,229 423.12,219.76 363.28,230.53 133.39,196 127.91,195.18 122.23,194.14 \ +116.57,192.98"]; "disease to entity association mixin" [height=0.5, pos="313.39,178", width=4.7482]; "disease to exposure event association" -> "disease to entity association mixin" [label=uses, lp="910.89,221.5", - pos="e,428.15,191.38 2867.5,262.57 2417.7,258.84 1275.8,247.77 894.39,229 736.82,221.25 555.8,204.41 438.26,192.41"]; + pos="e,428.43,191.33 2600.9,264.48 2261.2,264.48 1519.2,260.45 894.39,229 736.95,221.07 556.09,204.29 438.54,192.36"]; "entity to exposure event association mixin" [height=0.5, pos="710.39,178", width=5.7773]; "disease to exposure event association" -> "entity to exposure event association mixin" [label=uses, lp="1070.9,221.5", - pos="e,795.58,194.45 2866.3,263.76 2439.9,262.71 1402.7,257.25 1054.4,229 969.83,222.14 874.4,207.74 805.54,196.14"]; + pos="e,795.94,194.45 2601.5,263.17 2217.9,260.96 1350,253.37 1054.4,229 969.98,222.04 874.73,207.68 805.9,196.13"]; id [color=blue, height=0.5, label=string, @@ -32,8 +32,8 @@ digraph { "disease to exposure event association" -> id [color=blue, label=id, lp="1189.4,221.5", - pos="e,1003.4,189.98 2867.4,262.48 2428.1,258.59 1346.3,247.28 1182.4,229 1110.2,220.95 1092.3,215.5 1022.4,196 1019.3,195.13 1016.1,\ -194.17 1012.9,193.15", + pos="e,1003.4,189.98 2601,264.18 2238.8,263.84 1451.8,259.47 1182.4,229 1110.2,220.84 1092.3,215.5 1022.4,196 1019.3,195.13 1016.1,194.17 \ +1012.9,193.15", style=solid]; iri [color=blue, height=0.5, @@ -43,7 +43,7 @@ digraph { "disease to exposure event association" -> iri [color=blue, label=iri, lp="1296.4,221.5", - pos="e,1108.3,190.16 2865.6,264.63 2476.3,265.23 1589.1,262.7 1288.4,229 1216.2,220.91 1198.6,214.45 1128.4,196 1125,195.11 1121.5,194.14 \ + pos="e,1108.3,190.16 2601.1,263.84 2257.6,262.84 1537,257.31 1288.4,229 1216.3,220.79 1198.6,214.45 1128.4,196 1125,195.11 1121.5,194.14 \ 1118.1,193.12", style=solid]; name [color=blue, @@ -54,7 +54,7 @@ digraph { "disease to exposure event association" -> name [color=blue, label=name, lp="1400.4,221.5", - pos="e,1231.3,191.75 2867.2,262.65 2462.6,259.32 1524,249.5 1380.4,229 1331.9,222.08 1278.1,206.72 1240.8,194.84", + pos="e,1231.3,191.7 2600.9,264.85 2273.9,265.42 1610.1,262.25 1380.4,229 1331.9,221.99 1278.1,206.64 1240.8,194.79", style=solid]; description [color=blue, height=0.5, @@ -64,7 +64,7 @@ digraph { "disease to exposure event association" -> description [color=blue, label=description, lp="1516.9,221.5", - pos="e,1375.8,194.37 2866.5,263.41 2478.9,261.66 1609.3,254.86 1476.4,229 1444.7,222.84 1410.7,209.79 1385.1,198.56", + pos="e,1376.1,194.45 2602.7,262.49 2267.4,259.24 1583.6,250.11 1476.4,229 1444.8,222.79 1410.9,209.81 1385.4,198.63", style=solid]; "has attribute" [color=blue, height=0.5, @@ -74,7 +74,7 @@ digraph { "disease to exposure event association" -> "has attribute" [color=blue, label="has attribute", lp="1655.4,221.5", - pos="e,1515.9,193.52 2866.6,263.35 2504.2,261.52 1728,254.62 1608.4,229 1579.1,222.73 1548,209.39 1524.9,198.06", + pos="e,1516.3,193.71 2602.9,262.23 2295.4,258.74 1702.5,249.43 1608.4,229 1579.3,222.69 1548.4,209.49 1525.4,198.23", style=solid]; subject [color=blue, height=0.5, @@ -84,7 +84,7 @@ digraph { "disease to exposure event association" -> subject [color=blue, label=subject, lp="1782.4,221.5", - pos="e,1659.5,194.33 2867.5,262.55 2535.2,259.43 1862,250.52 1756.4,229 1726,222.8 1693.4,209.83 1668.9,198.66", + pos="e,1659.5,194.27 2605,261.17 2331,256.42 1836.8,245.67 1756.4,229 1726,222.69 1693.4,209.73 1668.9,198.59", style=solid]; predicate [color=blue, height=0.5, @@ -94,7 +94,7 @@ digraph { "disease to exposure event association" -> predicate [color=blue, label=predicate, lp="1861.4,221.5", - pos="e,1801.4,196.12 2866.7,263.23 2535.2,261.23 1871.7,254.09 1827.4,229 1818,223.67 1810.9,214.3 1805.8,205.1", + pos="e,1801.4,196.09 2603.9,261.67 2334.6,257.63 1860.4,247.88 1827.4,229 1818,223.63 1810.9,214.26 1805.9,205.06", style=solid]; object [color=blue, height=0.5, @@ -104,8 +104,8 @@ digraph { "disease to exposure event association" -> object [color=blue, label=object, lp="1940.4,178", - pos="e,1769,105.47 2870.3,260.97 2571.2,254.83 2000.9,237.76 1918.4,196 1898.2,185.78 1901.1,172.77 1882.4,160 1850.3,138.07 1810,120.64 \ -1778.5,108.92", + pos="e,1769,105.47 2601.6,263.23 2456.6,260.63 2250.5,252.53 2071.4,229 2002.4,219.94 1979.5,229.28 1918.4,196 1898.5,185.17 1901.1,172.77 \ +1882.4,160 1850.3,138.07 1810,120.64 1778.5,108.92", style=solid]; negated [color=blue, height=0.5, @@ -114,8 +114,8 @@ digraph { width=1.2999]; "disease to exposure event association" -> negated [color=blue, label=negated, - lp="2242.4,221.5", - pos="e,2052.8,190.38 2871.7,260.47 2663.9,255.71 2335.8,245.82 2213.4,229 2160.7,221.75 2101.7,205.44 2062.5,193.41", + lp="2138.4,221.5", + pos="e,2039.6,194.29 2601.2,263.69 2432.9,261.72 2198.3,254.28 2109.4,229 2087.5,222.79 2065.2,210.57 2048,199.77", style=solid]; qualifiers [color=blue, height=0.5, @@ -124,8 +124,8 @@ digraph { width=2.1304]; "disease to exposure event association" -> qualifiers [color=blue, label=qualifiers, - lp="2373.9,221.5", - pos="e,2200.9,193.28 2873.7,259.71 2697,254.65 2439.1,244.87 2340.4,229 2295.8,221.84 2246.5,207.79 2210.6,196.41", + lp="2217.9,221.5", + pos="e,2163.3,196.38 2602.4,262.51 2438.1,259.69 2218.8,251.66 2184.4,229 2176.2,223.59 2170.6,214.63 2166.8,205.77", style=solid]; publications [color=blue, height=0.5, @@ -134,8 +134,8 @@ digraph { width=1.7332]; "disease to exposure event association" -> publications [color=blue, label=publications, - lp="2508.4,221.5", - pos="e,2350.1,193.26 2877.5,258.72 2733.4,253.41 2540.6,243.87 2464.4,229 2428.2,221.93 2388.6,208.25 2359.5,196.98", + lp="2303.4,221.5", + pos="e,2282.1,193.26 2601.1,263.88 2458.7,261.78 2282.8,254.05 2259.4,229 2249.2,218.15 2259.1,207.15 2273.3,198.24", style=solid]; "has evidence" [color=blue, height=0.5, @@ -144,220 +144,222 @@ digraph { width=2.0943]; "disease to exposure event association" -> "has evidence" [color=blue, label="has evidence", - lp="2649.9,221.5", - pos="e,2504.7,194.32 2869,261.57 2787,257.46 2689.5,248.36 2603.4,229 2572.5,222.06 2539.3,209.29 2514,198.39", + lp="2400.9,221.5", + pos="e,2414,189.51 2606.3,260.69 2495.6,256.74 2372,248.06 2354.4,229 2349.9,224.1 2350.4,219.34 2354.4,214 2361,205.09 2381.8,197.64 \ +2404.1,191.93", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2674.4,178", - width=3.015]; + label=string, + pos="2604.4,178", + width=1.0652]; "disease to exposure event association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2782.9,221.5", - pos="e,2684.8,196.41 2882.7,257.52 2815.6,252.63 2747.5,244.05 2718.4,229 2707.5,223.39 2698.2,213.9 2690.9,204.68", + lp="2522.9,221.5", + pos="e,2575.7,190 2624.2,256.21 2547.6,250.83 2470.3,242.21 2458.4,229 2434.5,202.39 2466,220.13 2556.4,196 2559.6,195.16 2562.8,194.2 \ +2566.1,193.18", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2909.4,178", - width=3.015]; + label=string, + pos="2699.4,178", + width=1.0652]; "disease to exposure event association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2949.4,221.5", - pos="e,2872.8,195.17 2915.3,252.72 2887.4,247.54 2863.6,240 2854.4,229 2846,218.96 2852.9,209.01 2864.3,200.67", + lp="2689.4,221.5", + pos="e,2670,189.59 2653.5,252.33 2626.4,247.16 2603.3,239.72 2594.4,229 2590.1,223.88 2590.5,219.38 2594.4,214 2610.1,192.57 2626.2,204.44 \ +2651.4,196 2654.3,195.02 2657.3,193.99 2660.4,192.95", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="3144.4,178", - width=3.015]; + label=string, + pos="2794.4,178", + width=1.0652]; "disease to exposure event association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="3159.9,221.5", - pos="e,3079.9,192.66 3048.2,246.77 3046.8,236.38 3046.8,223.38 3053.4,214 3058,207.37 3064.1,202 3071,197.65", + lp="2894.9,221.5", + pos="e,2791,196.02 2787.1,246.84 2787.1,237.17 2787.4,224.89 2788.4,214 2788.6,211.42 2789,208.75 2789.3,206.08", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="3326.4,178", + pos="3014.4,178", width=1.5346]; "disease to exposure event association" -> timepoint [color=blue, label=timepoint, - lp="3321.4,221.5", - pos="e,3309.1,195.19 3189.2,252.76 3215.6,247.53 3242.4,239.95 3266.4,229 3274.1,225.48 3288.6,213.47 3301.4,202.1", + lp="3046.4,221.5", + pos="e,3014.4,196.24 2926.8,253.03 2959.9,247.83 2989.1,240.19 3001.4,229 3007.8,223.16 3011.2,214.6 3013,206.2", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="3438.4,178", + pos="3126.4,178", width=1.0652]; "disease to exposure event association" -> "original subject" [color=blue, label="original subject", - lp="3438.4,221.5", - pos="e,3416.3,192.7 3182.3,252 3258.2,244.5 3342.4,235.12 3359.4,229 3370.9,224.86 3372.1,220.57 3382.4,214 3390.6,208.79 3399.4,203.21 \ -3407.7,198.07", + lp="3159.4,221.5", + pos="e,3117.3,195.85 2923.8,252.66 2995.1,245.89 3070.7,237.06 3085.4,229 3096,223.23 3104.9,213.52 3111.6,204.19", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3552.4,178", + pos="3251.4,178", width=1.5887]; "disease to exposure event association" -> "original predicate" [color=blue, label="original predicate", - lp="3578.9,221.5", - pos="e,3535.8,195.4 3184.7,252.28 3206,250.46 3227.8,248.65 3248.4,247 3303,242.63 3443.7,249.95 3494.4,229 3502.1,225.82 3516.1,213.82 \ -3528.4,202.37", + lp="3298.9,221.5", + pos="e,3245.3,195.93 2920,252.31 2941.2,250.5 2962.9,248.67 2983.4,247 3035.8,242.73 3174.2,255.99 3219.4,229 3228.6,223.51 3235.6,214.23 \ +3240.7,205.16", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3666.4,178", + pos="3380.4,178", width=1.0652]; "disease to exposure event association" -> "original object" [color=blue, label="original object", - lp="3708.9,221.5", - pos="e,3663.6,196.36 3181.8,252.02 3204,250.18 3226.8,248.42 3248.4,247 3292.3,244.1 3608.1,253.9 3644.4,229 3652.2,223.62 3657.3,214.79 \ -3660.6,206.03", + lp="3428.9,221.5", + pos="e,3380.4,196.14 2917,252.03 2939.2,250.19 2961.9,248.44 2983.4,247 3004.6,245.58 3349.7,242.27 3366.4,229 3373.4,223.43 3377.1,214.67 \ +3378.9,206.03", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3799.4,178", + pos="3513.4,178", width=2.1304]; "disease to exposure event association" -> "subject category" [color=blue, label="subject category", - lp="3840.9,221.5", - pos="e,3792.4,196.13 3180.7,251.92 3203.2,250.06 3226.5,248.33 3248.4,247 3277,245.26 3739.2,242.69 3764.4,229 3774.2,223.69 3781.8,214.33 \ -3787.4,205.12", + lp="3558.9,221.5", + pos="e,3508.3,196.04 2916,251.91 2938.4,250.07 2961.6,248.34 2983.4,247 3011.2,245.3 3460.5,243.33 3484.4,229 3493.3,223.63 3499.8,214.39 \ +3504.3,205.29", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3970.4,178", + pos="3684.4,178", width=2.1304]; "disease to exposure event association" -> "object category" [color=blue, label="object category", - lp="3987.9,221.5", - pos="e,3954.5,195.64 3179.9,251.84 3202.7,249.98 3226.2,248.26 3248.4,247 3321.2,242.85 3835.6,253.17 3904.4,229 3920.2,223.46 3935.2,\ -212.65 3946.9,202.5", + lp="3704.9,221.5", + pos="e,3669.4,195.87 2914.9,251.86 2937.7,249.99 2961.2,248.27 2983.4,247 3054.3,242.93 3555.8,253.58 3622.4,229 3637.2,223.53 3651.2,\ +212.98 3662.1,202.98", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="4103.4,178", + pos="3817.4,178", width=1.0652]; "disease to exposure event association" -> "subject closure" [color=blue, label="subject closure", - lp="4121.9,221.5", - pos="e,4088,194.74 3179.4,251.79 3202.3,249.93 3226.1,248.22 3248.4,247 3292.7,244.58 4005.1,245.09 4046.4,229 4054.2,225.95 4068.4,213.53 \ -4080.6,201.84", + lp="3842.9,221.5", + pos="e,3805.5,195.36 2914.4,251.8 2937.3,249.94 2961.1,248.22 2983.4,247 3026.7,244.62 3724.2,245.49 3764.4,229 3777.7,223.54 3789.6,\ +213.08 3798.8,203.13", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="4199.4,178", + pos="3930.4,178", width=1.0652]; "disease to exposure event association" -> "object closure" [color=blue, label="object closure", - lp="4241.4,221.5", - pos="e,4197,196.43 3179.1,251.76 3202.1,249.89 3226,248.19 3248.4,247 3274.2,245.63 4157,243.51 4178.4,229 4186.2,223.7 4191.1,214.88 \ -4194.2,206.11", + lp="3966.4,221.5", + pos="e,3925.4,196.1 2914.1,251.76 2937.1,249.89 2961,248.19 2983.4,247 3034.3,244.29 3857.4,254.89 3901.4,229 3910.4,223.71 3916.8,214.47 \ +3921.4,205.37", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="4332.4,178", + pos="4063.4,178", width=2.1304]; "disease to exposure event association" -> "subject category closure" [color=blue, label="subject category closure", - lp="4399.9,221.5", - pos="e,4324.8,196.23 3178.8,251.74 3202,249.86 3225.9,248.17 3248.4,247 3277.4,245.49 4269.5,242.31 4295.4,229 4305.6,223.76 4313.7,214.27 \ -4319.7,204.96", + lp="4127.9,221.5", + pos="e,4053.8,196.3 2913.8,251.74 2937,249.87 2960.9,248.17 2983.4,247 3040.9,244.01 3968.2,253.49 4020.4,229 4031.5,223.78 4040.8,214.17 \ +4048,204.76", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="4521.4,178", + pos="4256.4,178", width=2.1304]; "disease to exposure event association" -> "object category closure" [color=blue, label="object category closure", - lp="4589.9,221.5", - pos="e,4516.1,196.14 3178.6,251.71 3201.8,249.83 3225.8,248.14 3248.4,247 3282.9,245.26 4461.5,246.23 4491.4,229 4500.5,223.75 4507.2,\ -214.53 4511.9,205.42", + lp="4319.9,221.5", + pos="e,4248.8,196.24 2913.6,251.71 2936.8,249.83 2960.8,248.14 2983.4,247 3017.7,245.27 4188.8,244.68 4219.4,229 4229.6,223.77 4237.7,\ +214.29 4243.7,204.97", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4711.4,178", + pos="4446.4,178", width=1.0652]; "disease to exposure event association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4761.4,221.5", - pos="e,4704.8,196.21 3178.3,251.69 3201.6,249.81 3225.7,248.13 3248.4,247 3288,245.03 4642.4,247.79 4677.4,229 4687.1,223.78 4694.6,214.43 \ -4700,205.22", + lp="4493.4,221.5", + pos="e,4438.4,195.78 2913.3,251.7 2936.6,249.81 2960.7,248.13 2983.4,247 3022.9,245.04 4372,246.58 4407.4,229 4418.1,223.68 4426.8,213.86 \ +4433.2,204.32", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4870.4,178", + pos="4605.4,178", width=1.0652]; "disease to exposure event association" -> "object namespace" [color=blue, label="object namespace", - lp="4914.4,221.5", - pos="e,4863,195.76 3178,251.69 3201.4,249.8 3225.6,248.12 3248.4,247 3292.4,244.85 4794.2,249.04 4833.4,229 4843.7,223.71 4851.9,214.03 \ -4857.9,204.59", + lp="4648.4,221.5", + pos="e,4597.1,195.8 2913,251.69 2936.4,249.81 2960.6,248.12 2983.4,247 3027.3,244.85 4525.9,248.26 4565.4,229 4576.3,223.7 4585.1,213.89 \ +4591.7,204.35", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="5021.4,178", + pos="4756.4,178", width=1.0652]; "disease to exposure event association" -> "subject label closure" [color=blue, label="subject label closure", - lp="5074.4,221.5", - pos="e,5013.4,195.79 3178,251.67 3201.4,249.79 3225.6,248.1 3248.4,247 3296.5,244.67 4939.2,250.36 4982.4,229 4993.1,223.69 5001.8,213.88 \ -5008.2,204.34", + lp="4809.4,221.5", + pos="e,4748.1,195.8 2913,251.67 2936.4,249.79 2960.6,248.1 2983.4,247 3031.5,244.67 4673.1,250.08 4716.4,229 4727.3,223.71 4736.1,213.89 \ +4742.7,204.35", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="5192.4,178", + pos="4927.4,178", width=1.0652]; "disease to exposure event association" -> "object label closure" [color=blue, label="object label closure", - lp="5240.9,221.5", - pos="e,5184.1,195.81 3178,251.66 3201.4,249.77 3225.6,248.09 3248.4,247 3301.2,244.46 5104.8,252.14 5152.4,229 5163.3,223.71 5172.1,213.9 \ -5178.7,204.36", + lp="4975.9,221.5", + pos="e,4919.1,195.81 2913,251.66 2936.4,249.77 2960.6,248.09 2983.4,247 3036.2,244.46 4839.8,252.14 4887.4,229 4898.3,223.71 4907.1,213.9 \ +4913.7,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="5354.4,178", + pos="5089.4,178", width=2.347]; "disease to exposure event association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="5402.9,221.5", - pos="e,5345.8,196.3 3177.8,251.66 3201.2,249.77 3225.5,248.09 3248.4,247 3305.7,244.27 5262.8,254.09 5314.4,229 5325.1,223.79 5333.9,\ -214.18 5340.4,204.76", + lp="5137.9,221.5", + pos="e,5080.8,196.3 2912.8,251.66 2936.2,249.77 2960.5,248.09 2983.4,247 3040.7,244.27 4997.8,254.09 5049.4,229 5060.1,223.79 5068.9,\ +214.18 5075.4,204.76", style=solid]; type [height=0.5, - pos="5516.4,178", + pos="5251.4,178", width=0.86659]; "disease to exposure event association" -> type [color=blue, label=type, - lp="5511.4,221.5", - pos="e,5508.1,195.81 3177.8,251.65 3201.2,249.76 3225.5,248.08 3248.4,247 3279.3,245.54 5448.6,242.52 5476.4,229 5487.3,223.72 5496.1,\ -213.91 5502.7,204.36", + lp="5246.4,221.5", + pos="e,5243.1,195.81 2912.8,251.65 2936.2,249.76 2960.5,248.08 2983.4,247 3014.3,245.54 5183.6,242.52 5211.4,229 5222.3,223.72 5231.1,\ +213.91 5237.7,204.36", style=solid]; category [height=0.5, - pos="5617.4,178", + pos="5352.4,178", width=1.4263]; "disease to exposure event association" -> category [color=blue, label=category, - lp="5597.9,221.5", - pos="e,5597.2,194.83 3177.8,251.65 3201.2,249.76 3225.5,248.08 3248.4,247 3311.7,244.01 5470.2,245.75 5531.4,229 5552.1,223.34 5572.9,\ -211.43 5588.9,200.65", + lp="5332.9,221.5", + pos="e,5332.2,194.83 2912.8,251.65 2936.2,249.76 2960.5,248.08 2983.4,247 3046.7,244.01 5205.2,245.75 5266.4,229 5287.1,223.34 5307.9,\ +211.43 5323.9,200.65", style=solid]; subject -> object [label=relation, lp="1712.4,134.5", @@ -372,11 +374,11 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="3295.4,265", + pos="3030.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3426.4,265", + pos="3161.4,265", width=2.0762]; } diff --git a/graphviz/disease_to_exposure_event_association.svg b/graphviz/disease_to_exposure_event_association.svg index d88135a6d8..1093290dc3 100644 --- a/graphviz/disease_to_exposure_event_association.svg +++ b/graphviz/disease_to_exposure_event_association.svg @@ -4,16 +4,16 @@ - + %3 - + disease to exposure event association - -disease to exposure event association + +disease to exposure event association @@ -24,7 +24,7 @@ disease to exposure event association->association - + is_a @@ -37,8 +37,8 @@ disease to exposure event association->disease to entity association mixin - - + + uses @@ -50,8 +50,8 @@ disease to exposure event association->entity to exposure event association mixin - - + + uses @@ -63,7 +63,7 @@ disease to exposure event association->id - + id @@ -76,7 +76,7 @@ disease to exposure event association->iri - + iri @@ -89,8 +89,8 @@ disease to exposure event association->name - - + + name @@ -102,8 +102,8 @@ disease to exposure event association->description - - + + description @@ -115,8 +115,8 @@ disease to exposure event association->has attribute - - + + has attribute @@ -128,8 +128,8 @@ disease to exposure event association->subject - - + + subject @@ -141,8 +141,8 @@ disease to exposure event association->predicate - - + + predicate @@ -154,7 +154,7 @@ disease to exposure event association->object - + object @@ -167,9 +167,9 @@ disease to exposure event association->negated - - -negated + + +negated @@ -180,9 +180,9 @@ disease to exposure event association->qualifiers - - -qualifiers + + +qualifiers @@ -193,9 +193,9 @@ disease to exposure event association->publications - - -publications + + +publications @@ -206,269 +206,269 @@ disease to exposure event association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string disease to exposure event association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string disease to exposure event association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string disease to exposure event association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type disease to exposure event association->timepoint - - -timepoint + + +timepoint original subject - -string + +string disease to exposure event association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie disease to exposure event association->original predicate - - -original predicate + + +original predicate original object - -string + +string disease to exposure event association->original object - - -original object + + +original object subject category - -ontology class + +ontology class disease to exposure event association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class disease to exposure event association->object category - - -object category + + +object category subject closure - -string + +string disease to exposure event association->subject closure - - -subject closure + + +subject closure object closure - -string + +string disease to exposure event association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class disease to exposure event association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class disease to exposure event association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string disease to exposure event association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string disease to exposure event association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string disease to exposure event association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string disease to exposure event association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source disease to exposure event association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type disease to exposure event association->type - - -type + + +type category - -category + +category disease to exposure event association->category - - -category + + +category @@ -498,14 +498,14 @@ association_type - -string + +string association_category - -category type + +category type diff --git a/graphviz/disease_to_phenotypic_feature_association.gv b/graphviz/disease_to_phenotypic_feature_association.gv index 47759da97f..3766d573f8 100644 --- a/graphviz/disease_to_phenotypic_feature_association.gv +++ b/graphviz/disease_to_phenotypic_feature_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,6639.4,283"]; + graph [bb="0,0,6401.4,283"]; node [label="\N"]; "disease to phenotypic feature association" [height=0.5, label="disease to phenotypic feature association", - pos="3732.4,265", + pos="3494.4,265", width=5.6328]; association [height=0.5, pos="62.394,178", width=1.7332]; "disease to phenotypic feature association" -> association [label=is_a, lp="712.39,221.5", - pos="e,106.72,190.74 3530.9,262.91 2945.7,259.55 1252.3,248.39 698.39,229 447.45,220.22 382.85,232.32 134.39,196 128.61,195.16 122.61,\ -194.07 116.66,192.87"]; + pos="e,106.72,190.74 3291.3,264.65 2830.2,265.43 1669,263.45 698.39,229 447.46,220.09 382.85,232.32 134.39,196 128.61,195.16 122.61,194.07 \ +116.66,192.87"]; "entity to phenotypic feature association mixin" [height=0.5, pos="367.39,178", width=6.2286]; "disease to phenotypic feature association" -> "entity to phenotypic feature association mixin" [label=uses, lp="948.89,221.5", - pos="e,493.43,192.91 3530.3,263.47 2975.7,261.68 1438.3,254.51 932.39,229 785.61,221.6 617.95,205.83 503.63,193.97"]; + pos="e,493.71,192.9 3292.2,263.19 2770.9,260.79 1390.1,252.35 932.39,229 785.74,221.52 618.22,205.79 503.91,193.96"]; "disease to entity association mixin" [height=0.5, pos="780.39,178", width=4.7482]; "disease to phenotypic feature association" -> "disease to entity association mixin" [label=uses, - lp="1104.9,221.5", - pos="e,854.69,194.22 3530.7,263.05 2954.8,260.09 1328.6,249.97 1088.4,229 1012.2,222.35 926.42,207.83 864.76,196.15"]; + lp="1103.9,221.5", + pos="e,854.76,194.26 3293.2,262.77 2754.1,259.24 1303.6,248.08 1087.4,229 1011.6,222.31 926.23,207.84 864.8,196.18"]; id [color=blue, height=0.5, label=string, @@ -31,9 +31,9 @@ digraph { width=1.0652]; "disease to phenotypic feature association" -> id [color=blue, label=id, - lp="1224.4,221.5", - pos="e,1036.4,190 3530.1,263.36 2973.3,261.29 1444,253.44 1217.4,229 1144.3,221.12 1126.2,215.65 1055.4,196 1052.3,195.14 1049.1,194.17 \ -1045.9,193.16", + lp="1222.4,221.5", + pos="e,1036.4,189.98 3292.6,263.07 2773.5,260.37 1418.2,251.27 1215.4,229 1143.2,221.07 1125.3,215.5 1055.4,196 1052.3,195.13 1049.1,\ +194.17 1045.9,193.15", style=solid]; iri [color=blue, height=0.5, @@ -42,9 +42,9 @@ digraph { width=1.2277]; "disease to phenotypic feature association" -> iri [color=blue, label=iri, - lp="1341.4,221.5", - pos="e,1141.3,190.23 3530.3,263.08 2991.8,260.34 1548.4,251.02 1333.4,229 1256,221.07 1236.8,215.26 1161.4,196 1158,195.14 1154.5,194.18 \ -1151,193.17", + lp="1335.4,221.5", + pos="e,1141.3,190.2 3293,262.82 2792.6,259.58 1519.1,249.43 1327.4,229 1252.6,221.03 1234.2,214.85 1161.4,196 1158,195.13 1154.5,194.16 \ +1151.1,193.15", style=solid]; name [color=blue, height=0.5, @@ -53,8 +53,8 @@ digraph { width=1.5707]; "disease to phenotypic feature association" -> name [color=blue, label=name, - lp="1452.4,221.5", - pos="e,1266.2,191.3 3530.1,263.44 3007.2,261.64 1636.9,254.52 1432.4,229 1378,222.21 1317.1,206.27 1276,194.2", + lp="1442.4,221.5", + pos="e,1265,191.45 3292.5,263.27 2807.6,261.13 1603.9,253.41 1422.4,229 1371.1,222.1 1313.9,206.45 1274.8,194.48", style=solid]; description [color=blue, height=0.5, @@ -63,8 +63,8 @@ digraph { width=2.0943]; "disease to phenotypic feature association" -> description [color=blue, label=description, - lp="1579.9,221.5", - pos="e,1414.6,193.81 3529.8,264.04 3024,263.66 1732.2,259.66 1539.4,229 1499.6,222.68 1456.1,208.83 1424.2,197.3", + lp="1562.9,221.5", + pos="e,1411.4,194.16 3291.8,264 2823.4,263.49 1692.8,259.11 1522.4,229 1487.3,222.8 1449.3,209.44 1421,198.08", style=solid]; "has attribute" [color=blue, height=0.5, @@ -73,8 +73,8 @@ digraph { width=1.4443]; "disease to phenotypic feature association" -> "has attribute" [color=blue, label="has attribute", - lp="1735.4,221.5", - pos="e,1555.5,191.92 3530.1,263.7 3049.5,262.52 1866.5,256.8 1688.4,229 1645.5,222.31 1598.3,207.31 1565.3,195.48", + lp="1709.4,221.5", + pos="e,1552.2,192.84 3291.8,263.82 2848.4,262.89 1818.8,257.63 1662.4,229 1627.2,222.56 1589.1,208.43 1561.5,196.82", style=solid]; predicate [color=blue, height=0.5, @@ -83,8 +83,8 @@ digraph { width=2.1665]; "disease to phenotypic feature association" -> predicate [color=blue, label=predicate, - lp="1894.4,221.5", - pos="e,1712.4,193.16 3530.6,262.95 3080.6,260.2 2021.9,251.44 1860.4,229 1812.8,222.39 1760,207.91 1722.2,196.22", + lp="1851.4,221.5", + pos="e,1705.2,194.25 3292.3,263.25 2877.9,261.21 1958.8,253.91 1817.4,229 1781.9,222.74 1743.3,209.35 1714.6,198.01", style=solid]; negated [color=blue, height=0.5, @@ -93,8 +93,8 @@ digraph { width=1.2999]; "disease to phenotypic feature association" -> negated [color=blue, label=negated, - lp="2036.4,221.5", - pos="e,1847.2,190.49 3531.5,262.33 3109,258.46 2154.7,247.76 2007.4,229 1954.8,222.3 1896.1,205.86 1857.2,193.65", + lp="1967.4,221.5", + pos="e,1840.3,193.06 3292.3,263.47 2901.1,261.86 2067.3,255.34 1938.4,229 1907.3,222.64 1873.9,208.93 1849.5,197.48", style=solid]; qualifiers [color=blue, height=0.5, @@ -103,8 +103,8 @@ digraph { width=2.1304]; "disease to phenotypic feature association" -> qualifiers [color=blue, label=qualifiers, - lp="2175.9,221.5", - pos="e,1996,193.12 3531.9,262.25 3135,258.4 2276.2,247.99 2142.4,229 2095.3,222.31 2043.1,207.84 2005.7,196.18", + lp="2064.9,221.5", + pos="e,1973.4,195.69 3294.1,262.09 2907.4,258.01 2090.5,247.28 2031.4,229 2013.4,223.42 1995.5,212.31 1981.6,201.97", style=solid]; publications [color=blue, height=0.5, @@ -113,8 +113,8 @@ digraph { width=1.7332]; "disease to phenotypic feature association" -> publications [color=blue, label=publications, - lp="2322.4,221.5", - pos="e,2147.2,192.77 3532,262.14 3162.1,258.27 2398.6,248.08 2278.4,229 2236.2,222.3 2189.8,207.8 2156.7,196.13", + lp="2151.4,221.5", + pos="e,2104.1,196.07 3293.3,262.52 2913.8,259.23 2127.8,249.91 2107.4,229 2101.5,222.97 2100.6,214.36 2101.8,205.99", style=solid]; "has evidence" [color=blue, height=0.5, @@ -123,347 +123,348 @@ digraph { width=2.0943]; "disease to phenotypic feature association" -> "has evidence" [color=blue, label="has evidence", - lp="2482.9,221.5", - pos="e,2306,193.56 3529.5,264.95 3219,265.32 2640.6,261.39 2436.4,229 2394.7,222.39 2348.9,208.39 2315.5,196.89", + lp="2249.9,221.5", + pos="e,2227.8,193.44 3294.1,262.12 2936.2,258.29 2222.1,248.24 2203.4,229 2192.4,217.75 2203.1,206.82 2218.7,198.07", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2469.4,178", - width=3.015]; + label=string, + pos="2399.4,178", + width=1.0652]; "disease to phenotypic feature association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2639.9,221.5", - pos="e,2496.6,195.66 3531.6,262.38 3224.8,259.23 2665.4,250.59 2575.4,229 2551,223.14 2525.5,211.3 2505.6,200.62", + lp="2367.9,221.5", + pos="e,2369.8,189.58 3294.9,261.65 2960.2,257.23 2320.4,246.51 2303.4,229 2298.8,224.22 2299.6,219.46 2303.4,214 2303.9,213.35 2333.9,\ +202.45 2360.3,192.98", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2704.4,178", - width=3.015]; + label=string, + pos="2494.4,178", + width=1.0652]; "disease to phenotypic feature association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2813.4,221.5", - pos="e,2704.3,196.18 3530.7,263.09 3244,260.93 2749.7,253.64 2718.4,229 2711.4,223.47 2707.7,214.73 2705.8,206.08", + lp="2535.4,221.5", + pos="e,2467,190.73 3291.4,264.43 2993.4,264.03 2469.5,259.04 2440.4,229 2429.2,217.46 2442.1,205.19 2458,195.7", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2939.4,178", - width=3.015]; + label=string, + pos="2612.4,178", + width=1.0652]; "disease to phenotypic feature association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="3022.9,221.5", - pos="e,2922.7,195.94 3531.8,262.26 3297,259.21 2937.4,250.97 2916.4,229 2909.8,222.07 2911.9,212.87 2916.9,204.26", + lp="2757.9,221.5", + pos="e,2620.4,195.66 3291.7,264.44 3060.3,263.56 2706.8,257.47 2651.4,229 2640.8,223.53 2632.1,213.68 2625.7,204.17", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="3121.4,178", + pos="2839.4,178", width=1.5346]; "disease to phenotypic feature association" -> timepoint [color=blue, label=timepoint, - lp="3181.4,221.5", - pos="e,3125.3,196.37 3532.6,261.84 3375.6,258.52 3178.4,250.14 3146.4,229 3138.2,223.58 3132.6,214.62 3128.8,205.76", + lp="2922.4,221.5", + pos="e,2850.2,195.66 3299.7,259.86 3136.5,255.22 2924.3,246 2887.4,229 2875.3,223.41 2864.6,213.28 2856.5,203.59", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="3233.4,178", + pos="2951.4,178", width=1.0652]; "disease to phenotypic feature association" -> "original subject" [color=blue, label="original subject", - lp="3281.4,221.5", - pos="e,3224.4,195.9 3530.9,262.94 3398.8,260.07 3246.7,251.78 3225.4,229 3219.5,222.72 3219.3,213.94 3221.3,205.5", + lp="3029.4,221.5", + pos="e,2954.3,196.29 3297.8,260.53 3161.6,256.47 3000.1,247.74 2973.4,229 2965.6,223.54 2960.5,214.69 2957.3,205.94", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3347.4,178", + pos="3076.4,178", width=1.5887]; "disease to phenotypic feature association" -> "original predicate" [color=blue, label="original predicate", - lp="3410.9,221.5", - pos="e,3342.1,196.39 3545.1,258.09 3454.2,253.25 3361.6,244.53 3347.4,229 3341.9,222.96 3340.4,214.59 3340.8,206.43", + lp="3164.9,221.5", + pos="e,3080.4,196.27 3317.8,256.13 3222.2,250.48 3119.9,241.62 3101.4,229 3093.4,223.52 3087.8,214.66 3084,205.92", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3461.4,178", + pos="3205.4,178", width=1.0652]; "disease to phenotypic feature association" -> "original object" [color=blue, label="original object", - lp="3543.9,221.5", - pos="e,3467.6,196.15 3584.6,252.6 3545.1,247.33 3508.8,239.76 3492.4,229 3483.6,223.26 3476.9,214.11 3472,205.2", + lp="3302.9,221.5", + pos="e,3216.2,195.75 3354.7,251.92 3311.5,246.45 3270.2,238.94 3251.4,229 3240.1,223.05 3230.1,213.18 3222.4,203.78", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3594.4,178", + pos="3338.4,178", width=2.1304]; "disease to phenotypic feature association" -> "subject category" [color=blue, label="subject category", - lp="3666.9,221.5", - pos="e,3594.7,196.4 3637.3,249.1 3626.2,244.14 3615.8,237.6 3607.4,229 3601.5,222.97 3598.2,214.6 3596.3,206.44", + lp="3430.9,221.5", + pos="e,3345.8,196.15 3409.6,248.53 3396.1,243.68 3382.8,237.33 3371.4,229 3362.9,222.8 3356,213.71 3350.7,204.98", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3765.4,178", + pos="3509.4,178", width=2.1304]; "disease to phenotypic feature association" -> "object category" [color=blue, label="object category", - lp="3788.9,221.5", - pos="e,3745.6,195.74 3729.8,246.74 3729,236.82 3729.3,224.32 3733.4,214 3734.9,210.32 3736.9,206.79 3739.3,203.48", + lp="3550.9,221.5", + pos="e,3501.1,196.07 3493.2,246.71 3492.9,237 3493.2,224.72 3495.4,214 3495.9,211.27 3496.7,208.48 3497.6,205.72", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3898.4,178", + pos="3642.4,178", width=1.0652]; "disease to phenotypic feature association" -> "subject closure" [color=blue, label="subject closure", - lp="3918.9,221.5", - pos="e,3884.7,194.97 3800.5,248.03 3815.5,243.08 3830.9,236.81 3844.4,229 3856.6,221.93 3868.3,211.65 3877.7,202.25", + lp="3675.9,221.5", + pos="e,3633.9,196.05 3568.7,248.21 3582,243.37 3595.2,237.1 3606.4,229 3615.2,222.62 3622.8,213.38 3628.6,204.58", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3994.4,178", + pos="3755.4,178", width=1.0652]; "disease to phenotypic feature association" -> "object closure" [color=blue, label="object closure", - lp="4037.4,221.5", - pos="e,3992.6,196.43 3891.8,253.8 3929,248.62 3961.9,240.79 3976.4,229 3983.4,223.3 3987.7,214.67 3990.3,206.17", + lp="3796.4,221.5", + pos="e,3752.7,196.01 3649.3,253.31 3686.4,248.11 3719.7,240.41 3734.4,229 3741.8,223.28 3746.6,214.49 3749.7,205.86", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="4127.4,178", + pos="3888.4,178", width=2.1304]; "disease to phenotypic feature association" -> "subject category closure" [color=blue, label="subject category closure", - lp="4195.9,221.5", - pos="e,4119.7,196.39 3878.6,252.51 3973.7,244.58 4081.8,234.51 4091.4,229 4101,223.48 4108.7,214.25 4114.5,205.21", + lp="3954.9,221.5", + pos="e,3880.3,195.91 3639.3,252.41 3733.6,244.43 3840.8,234.34 3850.4,229 3860.5,223.36 3868.7,213.81 3875,204.55", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="4319.4,178", + pos="4081.4,178", width=2.1304]; "disease to phenotypic feature association" -> "object category closure" [color=blue, label="object category closure", - lp="4386.9,221.5", - pos="e,4313.3,196.03 3874,252.1 3897.5,250.28 3921.6,248.51 3944.4,247 3982.5,244.47 4254.4,248.19 4287.4,229 4296.7,223.61 4303.7,214.36 \ -4308.7,205.27", + lp="4145.9,221.5", + pos="e,4074.3,196.06 3636,252.11 3659.5,250.29 3683.6,248.51 3706.4,247 3744.1,244.49 4013.3,247.35 4046.4,229 4056.1,223.6 4063.8,214.22 \ +4069.4,205.03", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4509.4,178", + pos="4271.4,178", width=1.0652]; "disease to phenotypic feature association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4559.4,221.5", - pos="e,4502.4,196.14 3871.7,251.91 3896,250.07 3920.9,248.34 3944.4,247 3973.8,245.32 4448.5,243.05 4474.4,229 4484.2,223.7 4491.8,214.33 \ -4497.4,205.13", + lp="4318.4,221.5", + pos="e,4263.7,195.68 3633.7,251.91 3658,250.07 3682.9,248.34 3706.4,247 3764.9,243.66 4181.4,255.93 4233.4,229 4243.8,223.61 4252.2,213.91 \ +4258.4,204.49", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4668.4,178", + pos="4430.4,178", width=1.0652]; "disease to phenotypic feature association" -> "object namespace" [color=blue, label="object namespace", - lp="4712.4,221.5", - pos="e,4661,195.7 3870.9,251.82 3895.4,249.97 3920.6,248.26 3944.4,247 3982.5,244.97 4597.5,246.63 4631.4,229 4641.7,223.63 4649.9,213.94 \ -4655.9,204.51", + lp="4472.4,221.5", + pos="e,4422.1,195.74 3632.9,251.82 3657.4,249.97 3682.6,248.27 3706.4,247 3744.4,244.98 4356.4,245.92 4390.4,229 4401.2,223.62 4410.1,\ +213.79 4416.7,204.27", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4819.4,178", + pos="4581.4,178", width=1.0652]; "disease to phenotypic feature association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4872.4,221.5", - pos="e,4811.4,195.74 3870.3,251.77 3895,249.91 3920.4,248.22 3944.4,247 3990.8,244.64 4738.9,249.83 4780.4,229 4791.1,223.63 4799.7,213.81 \ -4806.1,204.28", + lp="4632.4,221.5", + pos="e,4572.8,195.77 3632.3,251.77 3657,249.91 3682.4,248.22 3706.4,247 3752.7,244.65 4498.7,249.27 4540.4,229 4551.4,223.66 4560.4,213.84 \ +4567.2,204.3", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4958.4,178", + pos="4720.4,178", width=1.0652]; "disease to phenotypic feature association" -> "object label closure" [color=blue, label="object label closure", - lp="5028.9,221.5", - pos="e,4960.7,196.01 3869.7,251.74 3894.6,249.87 3920.2,248.18 3944.4,247 3972.3,245.63 4929.3,247.32 4950.4,229 4956.9,223.35 4959.6,\ -214.68 4960.5,206.14", + lp="4789.9,221.5", + pos="e,4722,196.09 3631.7,251.74 3656.6,249.87 3682.2,248.18 3706.4,247 3734.3,245.63 4689,246.88 4710.4,229 4717.1,223.43 4720.1,214.79 \ +4721.3,206.25", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="5099.4,178", + pos="4861.4,178", width=2.347]; "disease to phenotypic feature association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="5178.9,221.5", - pos="e,5106.2,196.1 3869.4,251.71 3894.4,249.84 3920.1,248.16 3944.4,247 3976.5,245.46 5079.8,251.92 5102.4,229 5108.3,223.01 5109.3,\ -214.41 5108.3,206.03", + lp="4939.9,221.5", + pos="e,4867.8,196.11 3631.4,251.71 3656.4,249.85 3682.1,248.16 3706.4,247 3738.5,245.46 4840.8,251.9 4863.4,229 4869.3,223.01 4870.4,\ +214.42 4869.6,206.04", style=solid]; type [height=0.5, - pos="5233.4,178", + pos="4995.4,178", width=0.86659]; "disease to phenotypic feature association" -> type [color=blue, label=type, - lp="5273.4,221.5", - pos="e,5246.9,194.33 3869.2,251.69 3894.2,249.83 3920.1,248.14 3944.4,247 3962.5,246.15 5239.6,241.94 5252.4,229 5259.3,221.96 5257.2,\ -212.12 5252.4,203.04", + lp="5034.4,221.5", + pos="e,5008.4,194.37 3631.2,251.7 3656.2,249.83 3682.1,248.14 3706.4,247 3724.5,246.15 5000.6,241.93 5013.4,229 5020.3,222 5018.3,212.18 \ +5013.7,203.08", style=solid]; category [height=0.5, - pos="5334.4,178", + pos="5096.4,178", width=1.4263]; "disease to phenotypic feature association" -> category [color=blue, label=category, - lp="5344.9,221.5", - pos="e,5325.8,195.8 3869.2,251.69 3894.2,249.82 3920.1,248.14 3944.4,247 3981.8,245.25 5259.6,245.26 5293.4,229 5304.4,223.71 5313.4,\ -213.89 5320.2,204.35", + lp="5105.9,221.5", + pos="e,5087.5,195.81 3631.2,251.69 3656.2,249.82 3682.1,248.14 3706.4,247 3743.8,245.25 5020.6,245.04 5054.4,229 5065.5,223.72 5074.8,\ +213.91 5081.7,204.36", style=solid]; subject [height=0.5, - pos="5448.4,178", + pos="5210.4,178", width=1.2277]; "disease to phenotypic feature association" -> subject [color=blue, label=subject, - lp="5435.4,221.5", - pos="e,5432.8,195 3869.2,251.67 3894.2,249.8 3920.1,248.13 3944.4,247 4024.1,243.31 5304.7,254.35 5380.4,229 5397,223.42 5413,212.12 \ -5425.3,201.67", + lp="5196.4,221.5", + pos="e,5194.5,195 3631.2,251.67 3656.2,249.8 3682.1,248.13 3706.4,247 3786,243.31 5065.7,254.07 5141.4,229 5158.2,223.43 5174.4,212.13 \ +5186.9,201.68", style=solid]; object [height=0.5, - pos="5491.4,91", + pos="5253.4,91", width=1.0832]; "disease to phenotypic feature association" -> object [color=blue, label=object, - lp="5534.4,178", - pos="e,5504.8,108.09 3868.9,251.68 3894,249.8 3920,248.12 3944.4,247 3986.6,245.06 5426.1,244.55 5465.4,229 5506.7,212.67 5509.2,186.07 \ -5514.4,142 5515.2,135.38 5516.3,133.39 5514.4,127 5513.4,123.55 5511.9,120.13 5510.1,116.85", + lp="5296.4,178", + pos="e,5266.8,108.09 3630.9,251.68 3656,249.8 3682,248.12 3706.4,247 3748.6,245.06 5187,244.27 5226.4,229 5268,212.87 5271.1,186.29 5276.4,\ +142 5277.2,135.38 5278.3,133.39 5276.4,127 5275.4,123.55 5273.9,120.13 5272.1,116.85", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="5675.4,178", + pos="5437.4,178", width=2.3651]; "disease to phenotypic feature association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="5663.4,221.5", - pos="e,5643.2,194.72 3868.9,251.67 3894,249.79 3920,248.12 3944.4,247 4033.1,242.95 5455.1,245.37 5542.4,229 5574.1,223.05 5608.1,210.13 \ -5633.8,198.91", + lp="5425.4,221.5", + pos="e,5405.2,194.72 3630.9,251.67 3656,249.79 3682,248.12 3706.4,247 3795.1,242.95 5217.1,245.37 5304.4,229 5336.1,223.05 5370.1,210.13 \ +5395.8,198.91", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="5854.4,178", + pos="5616.4,178", width=2.1123]; "disease to phenotypic feature association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="5844.4,221.5", - pos="e,5825.6,194.85 3868.6,251.66 3893.8,249.78 3919.9,248.11 3944.4,247 4043.8,242.52 5638,249.15 5735.4,229 5763.7,223.14 5793.8,210.46 \ -5816.6,199.33", + lp="5606.4,221.5", + pos="e,5587.6,194.85 3630.6,251.66 3655.8,249.78 3681.9,248.11 3706.4,247 3805.8,242.52 5400,249.15 5497.4,229 5525.7,223.14 5555.8,210.46 \ +5578.6,199.33", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="5984.4,178", + pos="5746.4,178", width=1.011]; "disease to phenotypic feature association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="5992.9,221.5", - pos="e,5967.7,194.31 3868.6,251.64 3893.8,249.77 3919.9,248.09 3944.4,247 3998.9,244.57 5857.2,245.06 5909.4,229 5927.8,223.32 5945.9,\ -211.5 5959.7,200.78", + lp="5754.9,221.5", + pos="e,5729.7,194.31 3630.6,251.64 3655.8,249.77 3681.9,248.09 3706.4,247 3760.9,244.57 5619.2,245.06 5671.4,229 5689.8,223.32 5707.9,\ +211.5 5721.7,200.78", style=solid]; "sex qualifier" [color=blue, height=0.5, label="biological sex", - pos="6112.4,178", + pos="5874.4,178", width=2.0401]; "disease to phenotypic feature association" -> "sex qualifier" [color=blue, label="sex qualifier", - lp="6120.4,221.5", - pos="e,6097.1,195.74 3868.6,251.63 3893.8,249.76 3919.9,248.09 3944.4,247 4002.8,244.41 5993.2,248.26 6048.4,229 6063.9,223.6 6078.5,\ -212.8 6089.8,202.62", + lp="5882.4,221.5", + pos="e,5859.1,195.74 3630.6,251.63 3655.8,249.76 3681.9,248.09 3706.4,247 3764.8,244.41 5755.2,248.26 5810.4,229 5825.9,223.6 5840.5,\ +212.8 5851.8,202.62", style=solid]; "has count" [color=blue, height=0.5, label=integer, - pos="6248.4,178", + pos="6010.4,178", width=1.2277]; "disease to phenotypic feature association" -> "has count" [color=blue, label="has count", - lp="6236.4,221.5", - pos="e,6230.1,194.57 3868.6,251.62 3893.8,249.75 3919.9,248.08 3944.4,247 4006.1,244.28 6109.1,246.27 6168.4,229 6187.8,223.34 6207.2,\ -211.47 6222,200.72", + lp="5998.4,221.5", + pos="e,5992.1,194.57 3630.6,251.62 3655.8,249.75 3681.9,248.08 3706.4,247 3768.1,244.28 5871.1,246.27 5930.4,229 5949.8,223.34 5969.2,\ +211.47 5984,200.72", style=solid]; "has total" [color=blue, height=0.5, label=integer, - pos="6354.4,178", + pos="6116.4,178", width=1.2277]; "disease to phenotypic feature association" -> "has total" [color=blue, label="has total", - lp="6339.9,221.5", - pos="e,6336.4,194.57 3868.3,251.64 3893.6,249.75 3919.8,248.08 3944.4,247 4009.1,244.16 6213.3,247.27 6275.4,229 6294.7,223.33 6313.8,\ -211.47 6328.3,200.72", + lp="6101.9,221.5", + pos="e,6098.4,194.57 3630.3,251.64 3655.6,249.75 3681.8,248.08 3706.4,247 3771.1,244.16 5975.3,247.27 6037.4,229 6056.7,223.33 6075.8,\ +211.47 6090.3,200.72", style=solid]; "has quotient" [color=blue, height=0.5, label=double, - pos="6458.4,178", + pos="6220.4,178", width=1.1735]; "disease to phenotypic feature association" -> "has quotient" [color=blue, label="has quotient", - lp="6454.4,221.5", - pos="e,6439.7,194.34 3868.3,251.63 3893.6,249.75 3919.8,248.08 3944.4,247 4011.9,244.05 6310.4,247.32 6375.4,229 6395.6,223.31 6415.8,\ -211.33 6431.2,200.51", + lp="6216.4,221.5", + pos="e,6201.7,194.34 3630.3,251.63 3655.6,249.75 3681.8,248.08 3706.4,247 3773.9,244.05 6072.4,247.32 6137.4,229 6157.6,223.31 6177.8,\ +211.33 6193.2,200.51", style=solid]; "has percentage" [color=blue, height=0.5, label=double, - pos="6565.4,178", + pos="6327.4,178", width=1.1735]; "disease to phenotypic feature association" -> "has percentage" [color=blue, label="has percentage", - lp="6584.4,221.5", - pos="e,6551.4,195 3868.3,251.62 3893.6,249.74 3919.8,248.07 3944.4,247 4015.4,243.91 6436.4,252.9 6503.4,229 6518.7,223.54 6533,212.56 \ -6544,202.28", + lp="6346.4,221.5", + pos="e,6313.4,195 3630.3,251.62 3655.6,249.74 3681.8,248.07 3706.4,247 3777.4,243.91 6198.4,252.9 6265.4,229 6280.7,223.54 6295,212.56 \ +6306,202.28", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3991.4,265", + pos="3753.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="4122.4,265", + pos="3884.4,265", width=2.0762]; subject -> object [label=relation, - lp="5486.4,134.5", - pos="e,5473.5,107.23 5449.5,159.55 5450.7,149.57 5453.2,137.07 5458.4,127 5460.6,122.68 5463.5,118.52 5466.7,114.66"]; + lp="5248.4,134.5", + pos="e,5235.5,107.23 5211.5,159.55 5212.7,149.57 5215.2,137.07 5220.4,127 5222.6,122.68 5225.5,118.52 5228.7,114.66"]; relation [height=0.5, - pos="5436.4,18", + pos="5198.4,18", width=1.2999]; - subject -> relation [pos="e,5437.7,36.188 5447.1,159.79 5445,132.48 5441,78.994 5438.5,46.38", + subject -> relation [pos="e,5199.7,36.188 5209.1,159.79 5207,132.48 5203,78.994 5200.5,46.38", style=dotted]; "disease to phenotypic feature association_subject" [color=blue, height=0.5, label=disease, - pos="4260.4,265", + pos="4022.4,265", width=1.2638]; - object -> relation [pos="e,5449.2,35.54 5478.9,73.889 5472,64.939 5463.2,53.617 5455.4,43.584", + object -> relation [pos="e,5211.2,35.54 5240.9,73.889 5234,64.939 5225.2,53.617 5217.4,43.584", style=dotted]; "disease to phenotypic feature association_object" [color=blue, height=0.5, label="phenotypic feature", - pos="4422.4,265", + pos="4184.4,265", width=2.7442]; } diff --git a/graphviz/disease_to_phenotypic_feature_association.svg b/graphviz/disease_to_phenotypic_feature_association.svg index 988ed9d807..464f4a64b9 100644 --- a/graphviz/disease_to_phenotypic_feature_association.svg +++ b/graphviz/disease_to_phenotypic_feature_association.svg @@ -4,16 +4,16 @@ - + %3 - + disease to phenotypic feature association - -disease to phenotypic feature association + +disease to phenotypic feature association @@ -24,7 +24,7 @@ disease to phenotypic feature association->association - + is_a @@ -37,8 +37,8 @@ disease to phenotypic feature association->entity to phenotypic feature association mixin - - + + uses @@ -50,9 +50,9 @@ disease to phenotypic feature association->disease to entity association mixin - - -uses + + +uses @@ -63,9 +63,9 @@ disease to phenotypic feature association->id - - -id + + +id @@ -76,9 +76,9 @@ disease to phenotypic feature association->iri - - -iri + + +iri @@ -89,9 +89,9 @@ disease to phenotypic feature association->name - - -name + + +name @@ -102,9 +102,9 @@ disease to phenotypic feature association->description - - -description + + +description @@ -115,9 +115,9 @@ disease to phenotypic feature association->has attribute - - -has attribute + + +has attribute @@ -128,9 +128,9 @@ disease to phenotypic feature association->predicate - - -predicate + + +predicate @@ -141,9 +141,9 @@ disease to phenotypic feature association->negated - - -negated + + +negated @@ -154,9 +154,9 @@ disease to phenotypic feature association->qualifiers - - -qualifiers + + +qualifiers @@ -167,9 +167,9 @@ disease to phenotypic feature association->publications - - -publications + + +publications @@ -180,448 +180,448 @@ disease to phenotypic feature association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string disease to phenotypic feature association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string disease to phenotypic feature association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string disease to phenotypic feature association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type disease to phenotypic feature association->timepoint - - -timepoint + + +timepoint original subject - -string + +string disease to phenotypic feature association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie disease to phenotypic feature association->original predicate - - -original predicate + + +original predicate original object - -string + +string disease to phenotypic feature association->original object - - -original object + + +original object subject category - -ontology class + +ontology class disease to phenotypic feature association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class disease to phenotypic feature association->object category - - -object category + + +object category subject closure - -string + +string disease to phenotypic feature association->subject closure - - -subject closure + + +subject closure object closure - -string + +string disease to phenotypic feature association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class disease to phenotypic feature association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class disease to phenotypic feature association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string disease to phenotypic feature association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string disease to phenotypic feature association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string disease to phenotypic feature association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string disease to phenotypic feature association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source disease to phenotypic feature association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type disease to phenotypic feature association->type - - -type + + +type category - -category + +category disease to phenotypic feature association->category - - -category + + +category subject - -subject + +subject disease to phenotypic feature association->subject - - -subject + + +subject object - -object + +object disease to phenotypic feature association->object - - -object + + +object frequency qualifier - -frequency value + +frequency value disease to phenotypic feature association->frequency qualifier - - -frequency qualifier + + +frequency qualifier severity qualifier - -severity value + +severity value disease to phenotypic feature association->severity qualifier - - -severity qualifier + + +severity qualifier onset qualifier - -onset + +onset disease to phenotypic feature association->onset qualifier - - -onset qualifier + + +onset qualifier sex qualifier - -biological sex + +biological sex disease to phenotypic feature association->sex qualifier - - -sex qualifier + + +sex qualifier has count - -integer + +integer disease to phenotypic feature association->has count - - -has count + + +has count has total - -integer + +integer disease to phenotypic feature association->has total - - -has total + + +has total has quotient - -double + +double disease to phenotypic feature association->has quotient - - -has quotient + + +has quotient has percentage - -double + +double disease to phenotypic feature association->has percentage - - -has percentage + + +has percentage association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + disease to phenotypic feature association_subject - -disease + +disease object->relation - - + + disease to phenotypic feature association_object - -phenotypic feature + +phenotypic feature diff --git a/graphviz/drug_to_gene_association.gv b/graphviz/drug_to_gene_association.gv index d9a14e4143..08dbd5ff56 100644 --- a/graphviz/drug_to_gene_association.gv +++ b/graphviz/drug_to_gene_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,5164.4,283"]; + graph [bb="0,0,4906.4,283"]; node [label="\N"]; "drug to gene association" [height=0.5, label="drug to gene association", - pos="2796.4,265", + pos="2538.4,265", width=3.4664]; association [height=0.5, pos="62.394,178", width=1.7332]; "drug to gene association" -> association [label=is_a, - lp="466.39,221.5", - pos="e,107.28,190.69 2671.8,263.59 2251.9,261.98 890.16,254.86 452.39,229 310.11,220.59 273.9,219.98 133.39,196 128.08,195.09 122.58,\ -194.02 117.09,192.86"]; + lp="464.39,221.5", + pos="e,107.28,190.69 2414.1,263.34 2025.3,261.04 835.81,252.25 450.39,229 309,220.47 273.02,219.88 133.39,196 128.08,195.09 122.58,194.02 \ +117.09,192.86"]; "drug to entity association mixin" [height=0.5, pos="301.39,178", width=4.4052]; "drug to gene association" -> "drug to entity association mixin" [label=uses, - lp="614.89,221.5", - pos="e,372.71,194.12 2671.5,264.49 2268.5,265.68 1005.2,266.26 598.39,229 524.93,222.27 442.23,207.77 382.79,196.11"]; + lp="612.89,221.5", + pos="e,372.53,194.14 2413.6,264.2 2042.8,264.39 951.03,262.06 596.39,229 523.54,222.21 441.56,207.75 382.54,196.13"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "drug to gene association" -> id [color=blue, label=id, - lp="735.39,221.5", - pos="e,545.37,190.01 2671.9,263.21 2254.7,260.38 920.73,249.8 728.39,229 654.48,221 636.06,215.79 564.39,196 561.28,195.14 558.08,194.18 \ -554.89,193.17", + lp="732.39,221.5", + pos="e,545.38,189.99 2413.4,264.56 2059.2,265.68 1053.2,265.45 725.39,229 652.8,220.93 634.77,215.57 564.39,196 561.29,195.14 558.09,\ +194.17 554.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,9 @@ digraph { width=1.2277]; "drug to gene association" -> iri [color=blue, label=iri, - lp="853.39,221.5", - pos="e,650.01,190.16 2671.3,264.51 2299,265.59 1201.5,265.5 845.39,229 766.66,220.93 747.11,215.46 670.39,196 666.97,195.13 663.43,194.16 \ -659.9,193.14", + lp="847.39,221.5", + pos="e,650.3,190.21 2413.5,264.22 2074.8,264.36 1144.4,261.67 839.39,229 763.3,220.85 744.51,215.05 670.39,196 667.02,195.13 663.54,194.17 \ +660.05,193.16", style=solid]; name [color=blue, height=0.5, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "drug to gene association" -> name [color=blue, label=name, - lp="967.39,221.5", - pos="e,775.59,191.06 2672.1,263.12 2285.1,260.19 1117.2,249.7 947.39,229 891,222.12 827.78,205.98 785.37,193.88", + lp="957.39,221.5", + pos="e,774.8,191.31 2414.3,262.84 2063.8,259.36 1081.9,248.01 937.39,229 884.2,222 824.74,206.18 784.38,194.19", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "drug to gene association" -> description [color=blue, label=description, - lp="1098.9,221.5", - pos="e,925.36,193.52 2672.1,263.38 2300.8,261.27 1216.2,253.1 1058.4,229 1015.9,222.51 969.07,208.43 935.04,196.86", + lp="1082.9,221.5", + pos="e,922.53,193.86 2414.1,263.13 2079.4,260.51 1175.6,251.42 1042.4,229 1004.3,222.59 962.73,208.91 932.08,197.48", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "drug to gene association" -> "has attribute" [color=blue, label="has attribute", - lp="1260.4,221.5", - pos="e,1066.4,191.41 2672.2,263 2324.2,259.94 1355.8,249.67 1213.4,229 1165.7,222.07 1112.7,206.59 1076.2,194.67", + lp="1235.4,221.5", + pos="e,1063.5,192.18 2414.5,262.78 2103.7,259.44 1307.1,249.02 1188.4,229 1148.3,222.24 1104.3,207.57 1073.2,195.87", style=solid]; subject [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=1.9318]; "drug to gene association" -> subject [color=blue, label=subject, - lp="1425.4,221.5", - pos="e,1216.8,191.65 2671.6,263.92 2376.8,263.25 1643.5,258.55 1399.4,229 1339.6,221.76 1272.4,206.08 1226.5,194.2", + lp="1384.4,221.5", + pos="e,1211.7,192.68 2413.6,263.95 2153,263.25 1558.8,258.35 1358.4,229 1311.1,222.07 1258.6,207.4 1221.3,195.73", style=solid]; predicate [color=blue, height=0.5, @@ -87,8 +87,8 @@ digraph { width=2.1665]; "drug to gene association" -> predicate [color=blue, label=predicate, - lp="1563.4,221.5", - pos="e,1380.3,193.17 2671.5,264.15 2396.8,263.9 1747,259.94 1529.4,229 1481.5,222.19 1428.4,207.8 1390.2,196.2", + lp="1498.4,221.5", + pos="e,1368.3,194.64 2414.9,262.35 2152.3,258.49 1555.2,247.76 1464.4,229 1434.3,222.78 1402.1,210.01 1377.6,198.94", style=solid]; negated [color=blue, height=0.5, @@ -97,8 +97,8 @@ digraph { width=1.2999]; "drug to gene association" -> negated [color=blue, label=negated, - lp="1707.4,221.5", - pos="e,1515,190.39 2672,263.17 2422.2,261 1867.1,253.49 1678.4,229 1624.6,222.02 1564.4,205.52 1524.6,193.37", + lp="1602.4,221.5", + pos="e,1501.7,194.16 2414.5,262.64 2172.2,259.52 1652.4,250.41 1573.4,229 1550.9,222.91 1527.9,210.58 1510.4,199.68", style=solid]; qualifiers [color=blue, height=0.5, @@ -107,8 +107,8 @@ digraph { width=2.1304]; "drug to gene association" -> qualifiers [color=blue, label=qualifiers, - lp="1840.9,221.5", - pos="e,1663.3,193.2 2672,263.12 2444.6,260.92 1970.4,253.47 1807.4,229 1761.1,222.05 1709.8,207.75 1672.8,196.22", + lp="1681.9,221.5", + pos="e,1625.8,195.99 2414.5,262.35 2177.5,258.76 1680.3,248.89 1648.4,229 1639.8,223.63 1633.7,214.51 1629.6,205.52", style=solid]; publications [color=blue, height=0.5, @@ -117,8 +117,8 @@ digraph { width=1.7332]; "drug to gene association" -> publications [color=blue, label=publications, - lp="1978.4,221.5", - pos="e,1813,193.08 2671.9,263.06 2468.1,260.84 2072.2,253.42 1934.4,229 1895.7,222.15 1853.4,208.15 1822.6,196.7", + lp="1767.4,221.5", + pos="e,1745.5,193.31 2414.2,263.12 2191.8,260.93 1746.9,253.5 1723.4,229 1713.3,218.5 1722.8,207.57 1736.5,198.61", style=solid]; "has evidence" [color=blue, height=0.5, @@ -127,227 +127,230 @@ digraph { width=2.0943]; "drug to gene association" -> "has evidence" [color=blue, label="has evidence", - lp="2124.9,221.5", - pos="e,1968.8,194.09 2672.9,262.22 2498.4,258.98 2188.6,250.36 2078.4,229 2043.9,222.31 2006.4,209.1 1978.3,197.94", + lp="1864.9,221.5", + pos="e,1876.7,189.71 2414.9,262.37 2214.5,259.12 1838.6,250.21 1818.4,229 1813.8,224.17 1814.4,219.35 1818.4,214 1824.9,205.25 1845.2,\ +197.84 1867,192.13", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2136.4,178", - width=3.015]; + label=string, + pos="2066.4,178", + width=1.0652]; "drug to gene association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2263.9,221.5", - pos="e,2152,195.95 2674.9,260.79 2513.2,255.92 2242.5,245.44 2199.4,229 2184.6,223.35 2170.5,212.89 2159.5,202.99", + lp="1995.9,221.5", + pos="e,2037.4,189.98 2416.1,261.2 2243.6,256.64 1947.8,246.34 1931.4,229 1885.8,180.74 1871.1,237.12 2018.4,196 2021.5,195.13 2024.7,\ +194.17 2027.9,193.15", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2371.4,178", - width=3.015]; + label=string, + pos="2161.4,178", + width=1.0652]; "drug to gene association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2430.4,221.5", - pos="e,2347.2,195.77 2672.2,263.09 2543.5,260.83 2357.9,253.32 2335.4,229 2328,220.97 2332.2,211.37 2340,202.74", + lp="2162.4,221.5", + pos="e,2131.8,189.56 2413.9,263.32 2282.3,261.27 2090.6,253.97 2067.4,229 2062.9,224.11 2063.6,219.48 2067.4,214 2068.3,212.74 2096.9,\ +202.19 2122.3,193", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2606.4,178", - width=3.015]; + label=string, + pos="2256.4,178", + width=1.0652]; "drug to gene association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2639.9,221.5", - pos="e,2557.2,194.17 2672.3,262.73 2613.5,259.22 2552.1,250.31 2533.4,229 2523,217.1 2532.7,206.69 2548.1,198.49", + lp="2376.9,221.5", + pos="e,2256.6,196.37 2416.7,260.94 2356.7,256.96 2292.5,248.16 2270.4,229 2263.8,223.29 2260.2,214.77 2258.3,206.36", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2788.4,178", + pos="2482.4,178", width=1.5346]; "drug to gene association" -> timepoint [color=blue, label=timepoint, - lp="2786.4,221.5", - pos="e,2765.6,194.47 2766.8,247.2 2760.6,242.2 2754.9,236.11 2751.4,229 2746.7,219.42 2751.1,209.79 2758.4,201.57", + lp="2528.4,221.5", + pos="e,2483.3,196.31 2510.8,247.35 2504.2,242.21 2497.8,236.03 2493.4,229 2489.2,222.28 2486.5,214.16 2484.9,206.44", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2900.4,178", + pos="2594.4,178", width=1.0652]; "drug to gene association" -> "original subject" [color=blue, label="original subject", - lp="2900.4,221.5", - pos="e,2876.4,192.24 2811,246.75 2820.1,236.6 2832.3,223.86 2844.4,214 2851.6,208.17 2859.8,202.54 2867.7,197.56", + lp="2629.4,221.5", + pos="e,2584.3,195.84 2550.8,247.07 2554.9,241.38 2559.4,234.97 2563.4,229 2568.7,221.09 2574.2,212.33 2579.1,204.38", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3014.4,178", + pos="2720.4,178", width=1.5887]; "drug to gene association" -> "original predicate" [color=blue, label="original predicate", - lp="3042.9,221.5", - pos="e,2999.2,195.85 2886.3,252.47 2909.9,247.29 2934.8,239.8 2956.4,229 2969.5,222.46 2982,212.32 2992.1,202.87", + lp="2767.9,221.5", + pos="e,2713.8,196.33 2635.1,253.46 2654.3,248.21 2673.4,240.44 2689.4,229 2697.7,223.06 2704.2,214.14 2709.1,205.48", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3128.4,178", + pos="2854.4,178", width=1.0652]; "drug to gene association" -> "original object" [color=blue, label="original object", - lp="3170.9,221.5", - pos="e,3125.4,196.17 2885.7,252.36 2900.6,250.51 2915.9,248.65 2930.4,247 2969.5,242.53 3074.6,252.13 3106.4,229 3114.1,223.4 3119.1,\ -214.52 3122.4,205.79", + lp="2898.9,221.5", + pos="e,2852.5,196.08 2628.1,252.41 2642.9,250.56 2658.1,248.7 2672.4,247 2708.6,242.71 2806.6,251.31 2835.4,229 2842.7,223.36 2847.2,\ +214.59 2849.9,205.95", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3261.4,178", + pos="2987.4,178", width=2.1304]; "drug to gene association" -> "subject category" [color=blue, label="subject category", - lp="3301.9,221.5", - pos="e,3254.3,196.03 2883.5,252.11 2899.1,250.22 2915.2,248.42 2930.4,247 2963.2,243.92 3197.6,245.1 3226.4,229 3236.1,223.56 3243.7,\ -214.18 3249.4,204.99", + lp="3029.9,221.5", + pos="e,2981,195.99 2625.9,252.1 2641.4,250.22 2657.3,248.43 2672.4,247 2703.7,244.02 2927.2,244.75 2954.4,229 2963.8,223.52 2971.1,214.12 \ +2976.4,204.95", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3432.4,178", + pos="3158.4,178", width=2.1304]; "drug to gene association" -> "object category" [color=blue, label="object category", - lp="3449.9,221.5", - pos="e,3415.9,195.81 2882.8,251.95 2898.6,250.05 2915,248.3 2930.4,247 2978.6,242.95 3319.8,245.19 3365.4,229 3381.2,223.4 3396.3,212.69 \ -3408.2,202.61", + lp="3176.9,221.5", + pos="e,3142.5,195.8 2624.8,251.96 2640.6,250.07 2657,248.31 2672.4,247 2719,243.05 3049.4,245.02 3093.4,229 3108.8,223.38 3123.6,212.67 \ +3135.1,202.6", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3565.4,178", + pos="3291.4,178", width=1.0652]; "drug to gene association" -> "subject closure" [color=blue, label="subject closure", - lp="3583.9,221.5", - pos="e,3549.9,194.72 2882.1,251.9 2898.1,249.99 2914.7,248.23 2930.4,247 2994.4,241.95 3448.6,252.57 3508.4,229 3516.2,225.92 3530.4,\ -213.5 3542.6,201.81", + lp="3314.9,221.5", + pos="e,3278.9,195.33 2624.4,251.87 2640.3,249.97 2656.8,248.23 2672.4,247 2734.9,242.05 3178.3,252.54 3236.4,229 3250.1,223.44 3262.6,\ +212.82 3272.2,202.79", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3661.4,178", + pos="3399.4,178", width=1.0652]; "drug to gene association" -> "object closure" [color=blue, label="object closure", - lp="3703.4,221.5", - pos="e,3659,196.41 2882,251.83 2898.1,249.92 2914.7,248.19 2930.4,247 2969.7,244.01 3607.8,251.25 3640.4,229 3648.2,223.68 3653.1,214.85 \ -3656.2,206.09", + lp="3437.4,221.5", + pos="e,3395.4,196.02 2624,251.83 2640.1,249.92 2656.7,248.19 2672.4,247 2711.2,244.04 3340.4,249.64 3373.4,229 3381.9,223.67 3387.8,214.56 \ +3391.8,205.56", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3794.4,178", + pos="3532.4,178", width=2.1304]; "drug to gene association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3861.9,221.5", - pos="e,3786.8,196.21 2881.7,251.83 2897.8,249.9 2914.6,248.17 2930.4,247 2976.2,243.6 3716.6,250.13 3757.4,229 3767.6,223.73 3775.7,214.24 \ -3781.7,204.94", + lp="3596.9,221.5", + pos="e,3523.5,196.26 2623.7,251.83 2639.8,249.91 2656.6,248.17 2672.4,247 2717.8,243.63 3450.5,248.92 3491.4,229 3502.2,223.73 3511.2,\ +214.11 3517.9,204.71", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3983.4,178", + pos="3725.4,178", width=2.1304]; "drug to gene association" -> "object category closure" [color=blue, label="object category closure", - lp="4051.9,221.5", - pos="e,3978.1,196.13 2881.7,251.77 2897.8,249.86 2914.6,248.14 2930.4,247 2958.7,244.96 3928.8,243.22 3953.4,229 3962.5,223.74 3969.2,\ -214.51 3973.9,205.4", + lp="3788.9,221.5", + pos="e,3717.8,196.23 2623.7,251.77 2639.8,249.86 2656.6,248.14 2672.4,247 2728.7,242.94 3638.2,254.85 3688.4,229 3698.6,223.75 3706.7,\ +214.27 3712.7,204.96", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4173.4,178", + pos="3915.4,178", width=1.0652]; "drug to gene association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4223.4,221.5", - pos="e,4166.7,196.2 2881.3,251.78 2897.6,249.85 2914.5,248.12 2930.4,247 2963.9,244.63 4109.8,244.93 4139.4,229 4149.1,223.77 4156.6,\ -214.42 4162,205.21", + lp="3962.4,221.5", + pos="e,3907.4,195.77 2623.3,251.78 2639.6,249.85 2656.5,248.12 2672.4,247 2705.8,244.64 3846.4,243.9 3876.4,229 3887.1,223.67 3895.8,\ +213.85 3902.2,204.31", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4332.4,178", + pos="4074.4,178", width=1.0652]; "drug to gene association" -> "object namespace" [color=blue, label="object namespace", - lp="4376.4,221.5", - pos="e,4325,195.76 2881.3,251.76 2897.6,249.83 2914.5,248.11 2930.4,247 2968.2,244.36 4261.6,246.29 4295.4,229 4305.7,223.7 4313.9,214.02 \ -4319.9,204.58", + lp="4116.4,221.5", + pos="e,4066.1,195.79 2623.3,251.76 2639.6,249.83 2656.5,248.11 2672.4,247 2710.1,244.36 4000.4,245.62 4034.4,229 4045.3,223.69 4054.1,\ +213.88 4060.7,204.34", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4483.4,178", + pos="4225.4,178", width=1.0652]; "drug to gene association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4536.4,221.5", - pos="e,4475.4,195.78 2881.3,251.74 2897.6,249.82 2914.5,248.1 2930.4,247 2972.4,244.1 4406.7,247.68 4444.4,229 4455.1,223.69 4463.8,213.87 \ -4470.2,204.33", + lp="4278.4,221.5", + pos="e,4216.8,195.81 2623.3,251.74 2639.6,249.82 2656.5,248.1 2672.4,247 2714.3,244.1 4146.5,247.19 4184.4,229 4195.4,223.71 4204.4,213.9 \ +4211.2,204.36", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4654.4,178", + pos="4396.4,178", width=1.0652]; "drug to gene association" -> "object label closure" [color=blue, label="object label closure", - lp="4702.9,221.5", - pos="e,4646.1,195.8 2881.3,251.73 2897.6,249.8 2914.5,248.09 2930.4,247 2977.1,243.8 4572.3,249.49 4614.4,229 4625.3,223.71 4634.1,213.89 \ -4640.7,204.35", + lp="4444.9,221.5", + pos="e,4388.1,195.8 2623.3,251.73 2639.6,249.8 2656.5,248.09 2672.4,247 2719.1,243.8 4314.3,249.49 4356.4,229 4367.3,223.71 4376.1,213.89 \ +4382.7,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4816.4,178", + pos="4558.4,178", width=2.347]; "drug to gene association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4864.9,221.5", - pos="e,4807.8,196.3 2881,251.76 2897.3,249.82 2914.4,248.09 2930.4,247 2981.6,243.52 4730.3,251.44 4776.4,229 4787.1,223.79 4795.9,214.17 \ -4802.4,204.76", + lp="4606.9,221.5", + pos="e,4549.8,196.3 2623,251.76 2639.3,249.82 2656.4,248.09 2672.4,247 2723.6,243.52 4472.3,251.44 4518.4,229 4529.1,223.79 4537.9,214.17 \ +4544.4,204.76", style=solid]; type [height=0.5, - pos="4950.4,178", + pos="4692.4,178", width=0.86659]; "drug to gene association" -> type [color=blue, label=type, - lp="4964.4,221.5", - pos="e,4951.2,196.19 2881,251.75 2897.3,249.81 2914.4,248.08 2930.4,247 2958.2,245.12 4916.6,246.37 4938.4,229 4945.2,223.55 4948.6,214.93 \ -4950.2,206.37", + lp="4706.4,221.5", + pos="e,4693.2,196.19 2623,251.75 2639.3,249.81 2656.4,248.08 2672.4,247 2700.2,245.12 4658.6,246.37 4680.4,229 4687.2,223.55 4690.6,214.93 \ +4692.2,206.37", style=solid]; category [height=0.5, - pos="5051.4,178", + pos="4793.4,178", width=1.4263]; "drug to gene association" -> category [color=blue, label=category, - lp="5043.9,221.5", - pos="e,5035.8,195.26 2881,251.74 2897.3,249.8 2914.4,248.08 2930.4,247 2987.3,243.15 4930.3,247.22 4984.4,229 5000.6,223.54 5016.1,212.52 \ -5028.1,202.21", + lp="4785.9,221.5", + pos="e,4777.8,195.26 2623,251.74 2639.3,249.8 2656.4,248.08 2672.4,247 2729.3,243.15 4672.3,247.22 4726.4,229 4742.6,223.54 4758.1,212.52 \ +4770.1,202.21", style=solid]; object [height=0.5, pos="1238.4,91", width=1.0832]; "drug to gene association" -> object [color=blue, label=object, - lp="5142.4,178", - pos="e,1277.5,91.926 2881,251.74 2897.3,249.8 2914.4,248.08 2930.4,247 2990,242.99 5024.5,252.5 5079.4,229 5110.5,215.69 5135.1,184.11 \ -5111.4,160 5041.1,88.423 1733.3,91.209 1287.8,91.91", + lp="4884.4,178", + pos="e,1277.6,91.976 2623,251.74 2639.3,249.8 2656.4,248.08 2672.4,247 2732,242.99 4766.5,252.5 4821.4,229 4852.5,215.69 4877.1,184.13 \ +4853.4,160 4788,93.321 1716.3,91.853 1287.8,91.973", style=solid]; subject -> object [label=relation, lp="1237.4,134.5", @@ -360,18 +363,18 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="2977.4,265", + pos="2719.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3108.4,265", + pos="2850.4,265", width=2.0762]; object -> relation [pos="e,1196.2,35.54 1225.9,73.889 1219,64.939 1210.2,53.617 1202.4,43.584", style=dotted]; "drug to gene association_object" [color=blue, height=0.5, label="gene or gene product", - pos="3311.4,265", + pos="3053.4,265", width=3.0692]; } diff --git a/graphviz/drug_to_gene_association.svg b/graphviz/drug_to_gene_association.svg index 3839ec8c48..13bc2996bf 100644 --- a/graphviz/drug_to_gene_association.svg +++ b/graphviz/drug_to_gene_association.svg @@ -4,16 +4,16 @@ - + %3 - + drug to gene association - -drug to gene association + +drug to gene association @@ -24,9 +24,9 @@ drug to gene association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ drug to gene association->drug to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ drug to gene association->id - - -id + + +id @@ -63,9 +63,9 @@ drug to gene association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ drug to gene association->name - - -name + + +name @@ -89,9 +89,9 @@ drug to gene association->description - - -description + + +description @@ -102,9 +102,9 @@ drug to gene association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ drug to gene association->subject - - -subject + + +subject @@ -128,9 +128,9 @@ drug to gene association->predicate - - -predicate + + +predicate @@ -141,9 +141,9 @@ drug to gene association->negated - - -negated + + +negated @@ -154,9 +154,9 @@ drug to gene association->qualifiers - - -qualifiers + + +qualifiers @@ -167,9 +167,9 @@ drug to gene association->publications - - -publications + + +publications @@ -180,269 +180,269 @@ drug to gene association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string drug to gene association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string drug to gene association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string drug to gene association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type drug to gene association->timepoint - - -timepoint + + +timepoint original subject - -string + +string drug to gene association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie drug to gene association->original predicate - - -original predicate + + +original predicate original object - -string + +string drug to gene association->original object - - -original object + + +original object subject category - -ontology class + +ontology class drug to gene association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class drug to gene association->object category - - -object category + + +object category subject closure - -string + +string drug to gene association->subject closure - - -subject closure + + +subject closure object closure - -string + +string drug to gene association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class drug to gene association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class drug to gene association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string drug to gene association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string drug to gene association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string drug to gene association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string drug to gene association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source drug to gene association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type drug to gene association->type - - -type + + +type category - -category + +category drug to gene association->category - - -category + + +category @@ -453,9 +453,9 @@ drug to gene association->object - - -object + + +object @@ -479,14 +479,14 @@ association_type - -string + +string association_category - -category type + +category type @@ -497,8 +497,8 @@ drug to gene association_object - -gene or gene product + +gene or gene product diff --git a/graphviz/druggable_gene_to_disease_association.gv b/graphviz/druggable_gene_to_disease_association.gv index 3c6ebc3ca7..0d45981deb 100644 --- a/graphviz/druggable_gene_to_disease_association.gv +++ b/graphviz/druggable_gene_to_disease_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,6036.8,283"]; + graph [bb="0,0,6783.6,283"]; node [label="\N"]; "druggable gene to disease association" [height=0.5, label="druggable gene to disease association", - pos="3285.8,265", + pos="3578.8,265", width=5.2176]; "gene to disease association" [height=0.5, pos="137.79,178", width=3.8274]; "druggable gene to disease association" -> "gene to disease association" [label=is_a, lp="762.79,221.5", - pos="e,234.98,190.85 3099,262.81 2593.6,259.37 1206.2,248.41 748.79,229 542.23,220.24 490.64,215.21 284.79,196 271.95,194.8 258.49,193.42 \ -245.15,191.97"]; + pos="e,234.98,190.85 3391.8,263.12 2846.8,260.33 1265.6,250.56 748.79,229 542.22,220.38 490.64,215.21 284.79,196 271.95,194.8 258.49,\ +193.42 245.15,191.97"]; "entity to disease association mixin" [height=0.5, pos="464.79,178", width=4.7482]; "druggable gene to disease association" -> "entity to disease association mixin" [label=uses, - lp="972.29,221.5", - pos="e,569.46,192.31 3098.4,263.28 2621.7,261.11 1370.9,253.21 955.79,229 826.57,221.46 678.89,205.41 579.52,193.52"]; + lp="973.29,221.5", + pos="e,569.19,192.3 3391.3,263.64 2873.6,262.31 1430.9,256.2 956.79,229 827.1,221.56 678.84,205.45 579.27,193.51"]; "gene to entity association mixin" [height=0.5, pos="812.79,178", width=4.4232]; "druggable gene to disease association" -> "gene to entity association mixin" [label=uses, - lp="1121.3,221.5", - pos="e,883.19,194.18 3097.9,264.69 2642.4,265.77 1488.8,264.75 1104.8,229 1032.7,222.29 951.5,207.82 893.09,196.17"]; + lp="1123.3,221.5", + pos="e,883.38,194.16 3391.7,263.02 2854.5,259.96 1331.5,249.57 1106.8,229 1034,222.34 952.18,207.83 893.35,196.15"]; id [color=blue, height=0.5, label=string, @@ -31,9 +31,9 @@ digraph { width=1.0652]; "druggable gene to disease association" -> id [color=blue, label=id, - lp="1228.8,221.5", - pos="e,1057.8,189.89 3098.7,263.04 2625.4,260.29 1404.7,251.12 1221.8,229 1156.2,221.06 1140.3,214.4 1076.8,196 1073.7,195.1 1070.5,194.11 \ -1067.3,193.08", + lp="1238.8,221.5", + pos="e,1057.8,189.95 3391.4,263.31 2872.9,261.09 1443.3,252.86 1231.8,229 1161.8,221.1 1144.6,215.13 1076.8,196 1073.7,195.12 1070.5,\ +194.15 1067.3,193.13", style=solid]; iri [color=blue, height=0.5, @@ -42,8 +42,9 @@ digraph { width=1.2277]; "druggable gene to disease association" -> iri [color=blue, label=iri, - lp="1316.8,221.5", - pos="e,1161.6,190.71 3098.6,263.23 2639.6,260.97 1482.6,252.95 1308.8,229 1260.6,222.36 1207,206.19 1171.2,194.02", + lp="1340.8,221.5", + pos="e,1162.7,190.09 3391.4,263.24 2888.6,260.9 1534,252.46 1332.8,229 1265,221.09 1248.7,213.78 1182.8,196 1179.4,195.09 1175.9,194.1 \ +1172.5,193.07", style=solid]; name [color=blue, height=0.5, @@ -52,8 +53,8 @@ digraph { width=1.5707]; "druggable gene to disease association" -> name [color=blue, label=name, - lp="1399.8,221.5", - pos="e,1277.8,193.45 3097.8,264.23 2649.9,264.25 1544.9,261.02 1379.8,229 1347.5,222.74 1312.7,209.14 1287.2,197.7", + lp="1438.8,221.5", + pos="e,1283.6,192.27 3391,263.85 2901.4,263.06 1610.4,258.19 1418.8,229 1375.2,222.36 1327.1,207.48 1293.2,195.67", style=solid]; description [color=blue, height=0.5, @@ -62,8 +63,8 @@ digraph { width=2.0943]; "druggable gene to disease association" -> description [color=blue, label=description, - lp="1484.3,221.5", - pos="e,1409,196.31 3097.8,264.45 2643.6,264.99 1518,262.89 1443.8,229 1432.3,223.75 1422.5,213.99 1415,204.48", + lp="1544.3,221.5", + pos="e,1424.4,195.03 3392,263 2899.1,260.07 1594.7,250.34 1503.8,229 1479,223.18 1453.2,210.97 1433.3,200.08", style=solid]; "has attribute" [color=blue, height=0.5, @@ -72,349 +73,432 @@ digraph { width=1.4443]; "druggable gene to disease association" -> "has attribute" [color=blue, label="has attribute", - lp="1580.8,221.5", - pos="e,1533.7,195.99 3098.4,263.67 2652,262.45 1560.9,256.63 1533.8,229 1527.7,222.82 1527.8,214.07 1530.1,205.61", - style=solid]; - object [color=blue, - height=0.5, - label="named thing", - pos="5140.8,91", - width=1.9318]; - "druggable gene to disease association" -> object [color=blue, - label=object, - lp="1662.8,178", - pos="e,5071,92.013 3099.8,262.45 2768.8,259.18 2090,250.09 1853.8,229 1754.7,220.15 1571.1,231.04 1640.8,160 1702.7,96.892 4544.2,92.327 \ -5060.7,92.019", + lp="1666.8,221.5", + pos="e,1561.6,194.99 3391.2,263.47 2917.3,261.75 1703.3,254.84 1619.8,229 1601.5,223.36 1583.6,211.89 1569.7,201.36", style=solid]; negated [color=blue, height=0.5, label=boolean, - pos="1740.8,178", + pos="1660.8,178", width=1.2999]; "druggable gene to disease association" -> negated [color=blue, label=negated, - lp="1960.8,221.5", - pos="e,1774.4,190.53 3097.9,264.06 2780.5,263.34 2151.3,258.13 1931.8,229 1880.2,222.15 1822.5,205.82 1784.2,193.68", + lp="1783.8,221.5", + pos="e,1682.4,194.28 3392,262.76 2942.8,259.45 1832.9,249.28 1754.8,229 1732.1,223.11 1708.8,210.77 1691.1,199.83", style=solid]; qualifiers [color=blue, height=0.5, label="ontology class", - pos="1881.8,178", + pos="1801.8,178", width=2.1304]; "druggable gene to disease association" -> qualifiers [color=blue, label=qualifiers, - lp="2097.3,221.5", - pos="e,1922.7,193.29 3098.1,264.11 2806.3,263.34 2257.4,257.93 2063.8,229 2018.6,222.25 1968.7,208.02 1932.6,196.47", + lp="1864.3,221.5", + pos="e,1806.8,196.1 3392.2,262.66 2948.3,259.15 1864,248.6 1830.8,229 1821.8,223.71 1815.3,214.47 1810.8,205.37", style=solid]; publications [color=blue, height=0.5, label=publication, - pos="2038.8,178", + pos="1958.8,178", width=1.7332]; "druggable gene to disease association" -> publications [color=blue, label=publications, - lp="2239.8,221.5", - pos="e,2073.3,193.05 3097.9,264.21 2833.1,263.43 2363.5,257.82 2195.8,229 2156.7,222.29 2114,208.2 2083,196.69", + lp="1949.8,221.5", + pos="e,1926.8,193.56 3391.5,263.49 2960.2,261.86 1931.5,255.23 1905.8,229 1895.8,218.82 1904.9,207.92 1918.2,198.9", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2227.8,178", - width=3.015]; + label=string, + pos="2077.8,178", + width=1.0652]; "druggable gene to disease association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2392.3,221.5", - pos="e,2253.3,195.61 3101.5,261.47 2844.2,257.3 2400.3,247.53 2327.8,229 2304.7,223.1 2280.7,211.34 2262,200.71", + lp="2065.3,221.5", + pos="e,2049.4,190.16 3391.8,263.24 2979.2,261.11 2024.8,253.55 2000.8,229 1996.1,224.23 1997.2,219.61 2000.8,214 2003.3,210.14 2021.7,\ +201.68 2040,194.05", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2462.8,178", - width=3.015]; + label=string, + pos="2172.8,178", + width=1.0652]; "druggable gene to disease association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2563.8,221.5", - pos="e,2459.8,196.33 3100.3,262.06 2866.3,258.74 2491.6,250.14 2468.8,229 2462.7,223.32 2460.3,214.91 2459.7,206.59", + lp="2232.8,221.5", + pos="e,2152.2,193.29 3392.3,262.83 3007.5,259.96 2159.4,251.13 2137.8,229 2129.4,220.36 2135.4,209.5 2144.6,200.12", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2697.8,178", - width=3.015]; + label=string, + pos="2307.8,178", + width=1.0652]; "druggable gene to disease association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2772.3,221.5", - pos="e,2676,195.87 3105.7,259.82 2928.1,254.79 2680.9,244.96 2665.8,229 2658.6,221.43 2662.1,212.04 2668.9,203.46", + lp="2456.3,221.5", + pos="e,2316.7,195.75 3392.5,262.69 3060.3,259.79 2395.8,251.23 2349.8,229 2338.7,223.64 2329.4,213.81 2322.5,204.28", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2879.8,178", + pos="2534.8,178", width=1.5346]; "druggable gene to disease association" -> timepoint [color=blue, label=timepoint, - lp="2926.8,221.5", - pos="e,2879.2,196.43 3113.1,257.9 3015.3,252.83 2909.1,243.96 2891.8,229 2885.3,223.36 2881.9,214.85 2880.4,206.44", + lp="2622.8,221.5", + pos="e,2547.1,195.79 3390.9,264.48 3124,264.08 2659.6,258.99 2587.8,229 2574.7,223.54 2562.9,213.28 2553.8,203.47", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2991.8,178", + pos="2646.8,178", width=1.0652]; "druggable gene to disease association" -> "original subject" [color=blue, label="original subject", - lp="3024.8,221.5", - pos="e,2976,194.82 3125.4,255.61 3052.6,250.12 2980.1,241.58 2968.8,229 2962.1,221.56 2964.7,211.85 2970.2,202.97", + lp="2731.8,221.5", + pos="e,2651.8,196.03 3394.7,261.38 3139.6,257.1 2706,247.2 2675.8,229 2666.9,223.62 2660.4,214.37 2655.9,205.28", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3105.8,178", + pos="2771.8,178", width=1.5887]; "druggable gene to disease association" -> "original predicate" [color=blue, label="original predicate", - lp="3151.3,221.5", - pos="e,3092,195.79 3148.5,252.67 3120.6,247.5 3097,239.97 3087.8,229 3082,222.04 3083.3,213.05 3087.1,204.61", + lp="2871.3,221.5", + pos="e,2779.2,196.1 3390.8,263.97 3179.1,262.6 2857.7,256.01 2807.8,229 2797.8,223.6 2789.9,214.09 2784.1,204.8", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3219.8,178", + pos="2900.8,178", width=1.0652]; "druggable gene to disease association" -> "original object" [color=blue, label="original object", - lp="3275.3,221.5", - pos="e,3217.3,196.01 3243.2,247.37 3235.6,242.55 3228.6,236.5 3223.8,229 3219.5,222.26 3217.8,213.93 3217.3,206.01", + lp="3014.3,221.5", + pos="e,2915.3,195.23 3400,259.4 3232.7,254.19 3002.7,244.38 2962.8,229 2947.8,223.24 2933.7,212.45 2922.7,202.36", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3352.8,178", + pos="3033.8,178", width=2.1304]; "druggable gene to disease association" -> "subject category" [color=blue, label="subject category", - lp="3396.3,221.5", - pos="e,3345.8,196.18 3309,246.89 3315.2,241.6 3321.7,235.45 3326.8,229 3332.5,221.84 3337.5,213.25 3341.5,205.22", + lp="3152.3,221.5", + pos="e,3048.4,196.12 3392.7,262.44 3279.1,259.21 3145.9,250.67 3092.8,229 3078.9,223.34 3065.9,213.12 3055.7,203.38", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3523.8,178", + pos="3204.8,178", width=2.1304]; "druggable gene to disease association" -> "object category" [color=blue, label="object category", - lp="3540.3,221.5", - pos="e,3507.1,195.66 3394.5,250.21 3416.7,245.18 3439.5,238.33 3459.8,229 3474.1,222.41 3488.1,212.04 3499.4,202.44", + lp="3283.3,221.5", + pos="e,3208.1,196.2 3419.7,255.34 3334.6,249.44 3244,240.58 3227.8,229 3220,223.44 3214.8,214.56 3211.3,205.82", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3656.8,178", + pos="3337.8,178", width=1.0652]; "druggable gene to disease association" -> "subject closure" [color=blue, label="subject closure", - lp="3677.3,221.5", - pos="e,3643.6,194.94 3422.5,252.58 3499.3,245.49 3583.1,236.35 3599.8,229 3613.6,222.9 3626.5,212.23 3636.5,202.3", + lp="3406.3,221.5", + pos="e,3338.1,196.3 3431.7,253.73 3396.4,248.55 3365,240.74 3351.8,229 3345.3,223.22 3341.7,214.67 3339.7,206.27", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3754.8,178", + pos="3450.8,178", width=1.0652]; "druggable gene to disease association" -> "object closure" [color=blue, label="object closure", - lp="3796.8,221.5", - pos="e,3752.6,196.23 3418.8,252.26 3440.2,250.44 3462.1,248.63 3482.8,247 3510.8,244.79 3712.1,245.56 3734.8,229 3742.3,223.53 3747,214.79 \ -3749.9,206.14", + lp="3525.8,221.5", + pos="e,3455.6,195.94 3508.1,248.21 3496.4,243.39 3485.1,237.13 3475.8,229 3468.6,222.7 3463.2,213.81 3459.3,205.27", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3887.8,178", + pos="3583.8,178", width=2.1304]; "druggable gene to disease association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3955.3,221.5", - pos="e,3880.1,196.1 3416.3,252.05 3438.5,250.21 3461.3,248.45 3482.8,247 3523.6,244.24 3814.7,248.31 3850.8,229 3860.9,223.59 3869,214.08 \ -3875,204.8", + lp="3667.3,221.5", + pos="e,3581.5,196.06 3578.7,246.86 3578.8,237.2 3579.1,224.92 3579.8,214 3580,211.44 3580.2,208.77 3580.4,206.11", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="4077.8,178", + pos="3776.8,178", width=2.1304]; "druggable gene to disease association" -> "object category closure" [color=blue, label="object category closure", - lp="4145.3,221.5", - pos="e,4072.1,196.09 3414.5,251.89 3437.2,250.03 3460.7,248.31 3482.8,247 3514.1,245.15 4019.6,244.68 4046.8,229 4056,223.69 4062.8,214.46 \ -4067.7,205.35", + lp="3850.3,221.5", + pos="e,3773.4,196.34 3689.2,250.36 3717.7,245.01 3743.6,237.97 3754.8,229 3762,223.2 3766.9,214.54 3770.2,206.05", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4267.8,178", + pos="3966.8,178", width=1.0652]; "druggable gene to disease association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4317.8,221.5", - pos="e,4260.8,196.18 3413.7,251.8 3436.7,249.94 3460.4,248.23 3482.8,247 3524.4,244.71 4196.1,248.69 4232.8,229 4242.6,223.74 4250.2,\ -214.39 4255.9,205.18", + lp="4020.8,221.5", + pos="e,3961.4,196.3 3712.7,252.35 3812.7,243.44 3932.9,232.14 3937.8,229 3946.3,223.5 3952.7,214.52 3957.2,205.68", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4426.8,178", + pos="4125.8,178", width=1.0652]; "druggable gene to disease association" -> "object namespace" [color=blue, label="object namespace", - lp="4470.8,221.5", - pos="e,4419.4,195.73 3413.1,251.77 3436.3,249.9 3460.2,248.19 3482.8,247 3533.1,244.33 4345,252.13 4389.8,229 4400.1,223.67 4408.3,213.98 \ -4414.3,204.55", + lp="4172.8,221.5", + pos="e,4119.4,196.02 3710.1,252.12 3732.1,250.3 3754.6,248.52 3775.8,247 3811,244.48 4062.2,246.59 4092.8,229 4102.3,223.55 4109.5,214.16 \ +4114.8,204.98", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4577.8,178", + pos="4220.8,178", width=1.0652]; "druggable gene to disease association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4630.8,221.5", - pos="e,4569.8,195.76 3412.9,251.74 3436.1,249.86 3460.2,248.17 3482.8,247 3541.4,243.98 4486.3,255.19 4538.8,229 4549.5,223.66 4558.1,\ -213.83 4564.5,204.3", + lp="4319.8,221.5", + pos="e,4235.3,195.15 3708.3,251.95 3730.8,250.1 3753.9,248.36 3775.8,247 3801.6,245.39 4222.9,247.63 4240.8,229 4247.5,222.03 4245.5,\ +212.52 4240.8,203.67", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4748.8,178", + pos="4315.8,178", width=1.0652]; "druggable gene to disease association" -> "object label closure" [color=blue, label="object label closure", - lp="4796.3,221.5", - pos="e,4740.5,195.78 3412.6,251.71 3435.9,249.84 3460.1,248.15 3482.8,247 3516.8,245.28 4678.2,243.98 4708.8,229 4719.6,223.68 4728.5,\ -213.87 4735.1,204.33", + lp="4471.3,221.5", + pos="e,4345.1,189.71 3707.2,251.85 3730,250 3753.6,248.28 3775.8,247 3810.3,245.01 4373.7,253.8 4397.8,229 4402.4,224.22 4401.5,219.56 \ +4397.8,214 4395.1,209.87 4374.5,201.11 4354.7,193.39", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4889.8,178", + pos="4456.8,178", width=2.347]; "druggable gene to disease association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4951.3,221.5", - pos="e,4887.7,196.42 3412.6,251.68 3435.9,249.81 3460.1,248.13 3482.8,247 3521.3,245.09 4838,250.81 4869.8,229 4877.5,223.69 4882.3,214.87 \ -4885.2,206.11", + lp="4620.3,221.5", + pos="e,4512,191.74 3706.7,251.79 3729.7,249.93 3753.4,248.23 3775.8,247 3797.1,245.83 4529.9,244.28 4544.8,229 4558.6,214.81 4543.2,203.42 \ +4521.5,195.11", style=solid]; type [height=0.5, - pos="5023.8,178", + pos="4590.8,178", width=0.86659]; "druggable gene to disease association" -> type [color=blue, label=type, - lp="5047.8,221.5", - pos="e,5029.7,196.12 3412.3,251.68 3435.7,249.8 3460,248.12 3482.8,247 3504.2,245.95 5009.7,244.23 5024.8,229 5030.7,223.03 5032,214.44 \ -5031.3,206.05", + lp="4713.8,221.5", + pos="e,4614.9,189.52 3706.1,251.76 3729.3,249.89 3753.2,248.19 3775.8,247 3801.3,245.65 4675.9,247.21 4693.8,229 4698.5,224.24 4697.8,\ +219.33 4693.8,214 4676.6,191.06 4658.9,205.51 4631.8,196 4629.4,195.15 4626.9,194.24 4624.4,193.29", style=solid]; category [height=0.5, - pos="5124.8,178", + pos="4691.8,178", width=1.4263]; "druggable gene to disease association" -> category [color=blue, label=category, - lp="5124.3,221.5", - pos="e,5111.8,195.44 3412.3,251.67 3435.7,249.79 3460,248.11 3482.8,247 3526.8,244.86 5026.7,244.75 5067.8,229 5081.9,223.6 5094.8,212.99 \ -5104.8,202.93", - style=solid]; - subject [height=0.5, - pos="5238.8,178", - width=1.2277]; - "druggable gene to disease association" -> subject [color=blue, - label=subject, - lp="5218.8,221.5", - pos="e,5220.8,194.55 3412.3,251.66 3435.7,249.78 3460,248.1 3482.8,247 3575.9,242.49 5070.4,255.42 5159.8,229 5179,223.31 5198.1,211.44 \ -5212.7,200.69", - style=solid]; - predicate [height=0.5, - pos="5355.8,178", - width=1.5165]; - "druggable gene to disease association" -> predicate [color=blue, - label=predicate, - lp="5325.8,221.5", - pos="e,5331.4,194.11 3412.1,251.67 3435.6,249.79 3459.9,248.1 3482.8,247 3580.8,242.28 5153.1,250.76 5248.8,229 5274.8,223.08 5302,210.27 \ -5322.5,199.1", - style=solid]; - "has evidence" [height=0.5, - pos="5498.8,178", - width=1.9679]; - "druggable gene to disease association" -> "has evidence" [color=blue, - label="has evidence", - lp="5464.3,221.5", - pos="e,5467.2,194.25 3412.1,251.66 3435.6,249.78 3459.9,248.1 3482.8,247 3587.2,242 5261,247.93 5363.8,229 5396.5,222.97 5431.7,209.69 \ -5458,198.33", + lp="4770.3,221.5", + pos="e,4717,193.74 3706.1,251.75 3729.3,249.88 3753.2,248.18 3775.8,247 3802.4,245.61 4715.1,248 4733.8,229 4742.7,219.95 4735.8,209.26 \ +4725.2,200.1", + style=solid]; + "subject aspect qualifier" [height=0.5, + pos="4879.8,178", + width=3.3039]; + "druggable gene to disease association" -> "subject aspect qualifier" [color=blue, + label="subject aspect qualifier", + lp="4920.3,221.5", + pos="e,4861.3,195.97 3706.1,251.72 3729.3,249.86 3753.2,248.17 3775.8,247 3832.9,244.04 4751.2,246.23 4805.8,229 4823,223.56 4839.9,212.72 \ +4853.2,202.52", + style=solid]; + "object direction qualifier" [height=0.5, + pos="5141.8,178", + width=3.4664]; + "druggable gene to disease association" -> "object direction qualifier" [color=blue, + label="object direction qualifier", + lp="5148.8,221.5", + pos="e,5107.7,195.42 3705.6,251.71 3728.9,249.84 3753.1,248.14 3775.8,247 3912.5,240.11 4873.2,254.3 5007.8,229 5039.1,223.12 5072.6,\ +210.6 5098.3,199.56", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="5672.8,178", + pos="5369.8,178", width=2.3651]; "druggable gene to disease association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="5644.8,221.5", - pos="e,5635.6,194.25 3412.1,251.65 3435.6,249.76 3459.9,248.09 3482.8,247 3595.6,241.64 5403.3,246.73 5514.8,229 5553.1,222.91 5594.9,\ -209.35 5625.9,197.89", + lp="5359.8,221.5", + pos="e,5338.4,194.83 3705.3,251.69 3728.7,249.81 3753,248.12 3775.8,247 3938.4,239 5081,259.91 5240.8,229 5271.5,223.06 5304.4,210.2 \ +5329.3,199.02", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="5851.8,178", + pos="5548.8,178", width=2.1123]; "druggable gene to disease association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="5831.8,221.5", - pos="e,5819.9,194.38 3412.1,251.63 3435.6,249.75 3459.9,248.08 3482.8,247 3606.8,241.16 5594.7,251.39 5716.8,229 5749.4,223.02 5784.5,\ -209.8 5810.7,198.46", + lp="5539.8,221.5", + pos="e,5520.5,194.84 3705.3,251.66 3728.7,249.78 3753,248.11 3775.8,247 3867.7,242.54 5341.8,247.94 5431.8,229 5459.6,223.15 5489,210.56 \ +5511.4,199.47", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="5988.8,178", + pos="5678.8,178", width=1.011]; "druggable gene to disease association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="5985.3,221.5", - pos="e,5969.2,193.39 3411.8,251.64 3435.4,249.75 3459.8,248.08 3482.8,247 3549.8,243.86 5831.9,245.76 5896.8,229 5919.7,223.08 5943.1,\ -210.23 5960.6,199.05", + lp="5687.3,221.5", + pos="e,5662.4,194.3 3705.1,251.67 3728.6,249.78 3752.9,248.1 3775.8,247 3826.5,244.56 5556.3,244.11 5604.8,229 5623.1,223.31 5640.9,211.49 \ +5654.5,200.77", + style=solid]; + "sex qualifier" [color=blue, + height=0.5, + label="biological sex", + pos="5806.8,178", + width=2.0401]; + "druggable gene to disease association" -> "sex qualifier" [color=blue, + label="sex qualifier", + lp="5814.8,221.5", + pos="e,5791.5,195.74 3705.1,251.65 3728.6,249.77 3752.9,248.09 3775.8,247 3830.4,244.4 5691.2,247.03 5742.8,229 5758.3,223.6 5772.9,212.8 \ +5784.2,202.62", + style=solid]; + "has count" [color=blue, + height=0.5, + label=integer, + pos="5942.8,178", + width=1.2277]; + "druggable gene to disease association" -> "has count" [color=blue, + label="has count", + lp="5930.8,221.5", + pos="e,5924.5,194.57 3705.1,251.64 3728.6,249.76 3752.9,248.08 3775.8,247 3833.7,244.26 5807.1,245.22 5862.8,229 5882.2,223.33 5901.6,\ +211.46 5916.4,200.71", + style=solid]; + "has total" [color=blue, + height=0.5, + label=integer, + pos="6048.8,178", + width=1.2277]; + "druggable gene to disease association" -> "has total" [color=blue, + label="has total", + lp="6034.3,221.5", + pos="e,6030.8,194.57 3705.1,251.63 3728.6,249.75 3752.9,248.08 3775.8,247 3836.7,244.13 5911.3,246.21 5969.8,229 5989.1,223.33 6008.1,\ +211.46 6022.7,200.71", + style=solid]; + "has quotient" [color=blue, + height=0.5, + label=double, + pos="6152.8,178", + width=1.1735]; + "druggable gene to disease association" -> "has quotient" [color=blue, + label="has quotient", + lp="6148.8,221.5", + pos="e,6134.1,194.34 3704.8,251.65 3728.4,249.76 3752.8,248.08 3775.8,247 3839.4,244.01 6008.5,246.31 6069.8,229 6090,223.31 6110.1,211.32 \ +6125.6,200.51", + style=solid]; + "has percentage" [color=blue, + height=0.5, + label=double, + pos="6254.8,178", + width=1.1735]; + "druggable gene to disease association" -> "has percentage" [color=blue, + label="has percentage", + lp="6277.8,221.5", + pos="e,6241.8,195.46 3704.8,251.64 3728.4,249.75 3752.8,248.08 3775.8,247 3843,243.86 6134.9,252.94 6197.8,229 6211.9,223.63 6224.8,213.02 \ +6234.8,202.96", + style=solid]; + object [height=0.5, + pos="6381.8,91", + width=1.0832]; + "druggable gene to disease association" -> object [color=blue, + label=object, + lp="6377.8,178", + pos="e,6375.1,108.97 3704.8,251.63 3728.4,249.75 3752.8,248.07 3775.8,247 3811.3,245.35 6304,249.87 6332.8,229 6358.9,210.01 6344.9,190.44 \ +6355.8,160 6360.7,146.2 6366.5,130.94 6371.4,118.38", + style=solid]; + subject [height=0.5, + pos="6452.8,178", + width=1.2277]; + "druggable gene to disease association" -> subject [color=blue, + label=subject, + lp="6424.8,221.5", + pos="e,6432.1,194.12 3704.8,251.63 3728.4,249.74 3752.8,248.07 3775.8,247 3847.5,243.66 6291.3,246.93 6360.8,229 6383.3,223.2 6406.2,\ +210.74 6423.6,199.71", + style=solid]; + predicate [height=0.5, + pos="6569.8,178", + width=1.5165]; + "druggable gene to disease association" -> predicate [color=blue, + label=predicate, + lp="6534.8,221.5", + pos="e,6543.9,193.9 3704.8,251.63 3728.4,249.74 3752.8,248.07 3775.8,247 3924.5,240.1 6309.2,259.8 6454.8,229 6482.9,223.05 6512.7,209.92 \ +6534.8,198.61", + style=solid]; + "has evidence" [height=0.5, + pos="6712.8,178", + width=1.9679]; + "druggable gene to disease association" -> "has evidence" [color=blue, + label="has evidence", + lp="6674.3,221.5", + pos="e,6680.5,194.04 3704.8,251.62 3728.4,249.73 3752.8,248.06 3775.8,247 3931,239.81 6419.8,256.01 6572.8,229 6607,222.96 6644,209.44 \ +6671.3,197.99", style=solid]; - relation [height=0.5, - pos="5189.8,18", - width=1.2999]; - object -> relation [pos="e,5178.3,35.705 5152.4,73.174 5158.4,64.509 5165.8,53.768 5172.4,44.141", - style=dotted]; association_type [color=blue, height=0.5, label=string, - pos="3529.8,265", + pos="3822.8,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3660.8,265", + pos="3953.8,265", width=2.0762]; + "gene to disease or phenotypic feature association_subject aspect qualifier" [color=blue, + height=0.5, + label=GeneOrGeneProductOrChemicalEntityAspectEnum, + pos="4295.8,265", + width=6.9147]; + "gene to disease or phenotypic feature association_object direction qualifier" [color=blue, + height=0.5, + label=DirectionQualifierEnum, + pos="4683.8,265", + width=3.358]; + relation [height=0.5, + pos="6416.8,18", + width=1.2999]; + object -> relation [pos="e,6408.3,36.198 6390.1,73.174 6394.2,64.896 6399.2,54.723 6403.8,45.438", + style=dotted]; + "gene to disease association_object" [color=blue, + height=0.5, + label=disease, + pos="4867.8,265", + width=1.2638]; subject -> object [label=relation, - lp="5196.8,134.5", - pos="e,5147.2,108.97 5206.3,165.59 5193.5,159.94 5179.4,152.13 5168.8,142 5161.8,135.31 5156.1,126.48 5151.6,118.1"]; - subject -> relation [pos="e,5201,35.828 5237.4,159.99 5235.3,139.02 5230.4,102.55 5219.8,73 5216.3,63.258 5211.2,53.189 5206.2,44.423", + lp="6410.8,134.5", + pos="e,6378,109.01 6416.4,167.42 6403.6,162.12 6390.4,154.06 6382.8,142 6378.5,135.26 6377.2,126.93 6377.2,119.01"]; + subject -> relation [pos="e,6421,36.005 6449.1,160.05 6444.7,139.44 6436.9,103.63 6429.8,73 6427.8,64.183 6425.5,54.574 6423.4,45.938", style=dotted]; "druggable gene to disease association_subject" [color=blue, height=0.5, label="gene or gene product", - pos="3863.8,265", + pos="5041.8,265", width=3.0692]; "druggable gene to disease association_predicate" [color=blue, height=0.5, label="predicate type", - pos="4069.8,265", + pos="5247.8,265", width=2.1665]; "druggable gene to disease association_has evidence" [color=blue, height=0.5, label=DruggableGeneCategoryEnum, - pos="4318.8,265", + pos="5496.8,265", width=4.2607]; } diff --git a/graphviz/druggable_gene_to_disease_association.svg b/graphviz/druggable_gene_to_disease_association.svg index 3b70c2409e..2809a6e379 100644 --- a/graphviz/druggable_gene_to_disease_association.svg +++ b/graphviz/druggable_gene_to_disease_association.svg @@ -4,16 +4,16 @@ - + %3 - + druggable gene to disease association - -druggable gene to disease association + +druggable gene to disease association @@ -24,7 +24,7 @@ druggable gene to disease association->gene to disease association - + is_a @@ -37,9 +37,9 @@ druggable gene to disease association->entity to disease association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ druggable gene to disease association->gene to entity association mixin - - -uses + + +uses @@ -63,9 +63,9 @@ druggable gene to disease association->id - - -id + + +id @@ -76,9 +76,9 @@ druggable gene to disease association->iri - - -iri + + +iri @@ -89,9 +89,9 @@ druggable gene to disease association->name - - -name + + +name @@ -102,9 +102,9 @@ druggable gene to disease association->description - - -description + + +description @@ -115,454 +115,563 @@ druggable gene to disease association->has attribute - - -has attribute - - - -object - -named thing - - - -druggable gene to disease association->object - - -object + + +has attribute - + negated - -boolean + +boolean - + druggable gene to disease association->negated - - -negated + + +negated - + qualifiers - -ontology class + +ontology class - + druggable gene to disease association->qualifiers - - -qualifiers + + +qualifiers - + publications - -publication + +publication - + druggable gene to disease association->publications - - -publications + + +publications - + knowledge source - -information resource + +string - + druggable gene to disease association->knowledge source - - -knowledge source + + +knowledge source - + primary knowledge source - -information resource + +string - + druggable gene to disease association->primary knowledge source - - -primary knowledge source + + +primary knowledge source - + aggregator knowledge source - -information resource + +string - + druggable gene to disease association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source - + timepoint - -time type + +time type - + druggable gene to disease association->timepoint - - -timepoint + + +timepoint - + original subject - -string + +string - + druggable gene to disease association->original subject - - -original subject + + +original subject - + original predicate - -uriorcurie + +uriorcurie - + druggable gene to disease association->original predicate - - -original predicate + + +original predicate - + original object - -string + +string - + druggable gene to disease association->original object - - -original object + + +original object - + subject category - -ontology class + +ontology class - + druggable gene to disease association->subject category - - -subject category + + +subject category - + object category - -ontology class + +ontology class - + druggable gene to disease association->object category - - -object category + + +object category - + subject closure - -string + +string - + druggable gene to disease association->subject closure - - -subject closure + + +subject closure - + object closure - -string + +string - + druggable gene to disease association->object closure - - -object closure + + +object closure - + subject category closure - -ontology class + +ontology class - + druggable gene to disease association->subject category closure - - -subject category closure + + +subject category closure - + object category closure - -ontology class + +ontology class - + druggable gene to disease association->object category closure - - -object category closure + + +object category closure - + subject namespace - -string + +string - + druggable gene to disease association->subject namespace - - -subject namespace + + +subject namespace - + object namespace - -string + +string - + druggable gene to disease association->object namespace - - -object namespace + + +object namespace - + subject label closure - -string + +string - + druggable gene to disease association->subject label closure - - -subject label closure + + +subject label closure - + object label closure - -string + +string - + druggable gene to disease association->object label closure - - -object label closure + + +object label closure - + retrieval source ids - -retrieval source + +retrieval source - + druggable gene to disease association->retrieval source ids - - -retrieval source ids + + +retrieval source ids - + type - -type + +type - + druggable gene to disease association->type - - -type + + +type - + category - -category + +category - + druggable gene to disease association->category - - -category + + +category - - -subject - -subject - - - -druggable gene to disease association->subject - - -subject - - - -predicate - -predicate + + +subject aspect qualifier + +subject aspect qualifier - - -druggable gene to disease association->predicate - - -predicate + + +druggable gene to disease association->subject aspect qualifier + + +subject aspect qualifier - - -has evidence - -has evidence + + +object direction qualifier + +object direction qualifier - - -druggable gene to disease association->has evidence - - -has evidence + + +druggable gene to disease association->object direction qualifier + + +object direction qualifier - + frequency qualifier - -frequency value + +frequency value - + druggable gene to disease association->frequency qualifier - - -frequency qualifier + + +frequency qualifier - + severity qualifier - -severity value + +severity value - + druggable gene to disease association->severity qualifier - - -severity qualifier + + +severity qualifier - + onset qualifier - -onset + +onset - + druggable gene to disease association->onset qualifier - - -onset qualifier + + +onset qualifier - + + +sex qualifier + +biological sex + + + +druggable gene to disease association->sex qualifier + + +sex qualifier + + + +has count + +integer + + + +druggable gene to disease association->has count + + +has count + + + +has total + +integer + + + +druggable gene to disease association->has total + + +has total + + -relation - -relation +has quotient + +double - + + +druggable gene to disease association->has quotient + + +has quotient + + + +has percentage + +double + + -object->relation - - +druggable gene to disease association->has percentage + + +has percentage + + + +object + +object + + + +druggable gene to disease association->object + + +object + + + +subject + +subject + + + +druggable gene to disease association->subject + + +subject + + + +predicate + +predicate + + + +druggable gene to disease association->predicate + + +predicate + + + +has evidence + +has evidence + + + +druggable gene to disease association->has evidence + + +has evidence - + association_type - -string + +string - + association_category - -category type + +category type + + + +gene to disease or phenotypic feature association_subject aspect qualifier + +GeneOrGeneProductOrChemicalEntityAspectEnum + + + +gene to disease or phenotypic feature association_object direction qualifier + +DirectionQualifierEnum + + + +relation + +relation + + + +object->relation + + + + + +gene to disease association_object + +disease - + subject->object - - -relation + + +relation - + subject->relation - - + + - + druggable gene to disease association_subject - -gene or gene product + +gene or gene product - + druggable gene to disease association_predicate - -predicate type + +predicate type - + druggable gene to disease association_has evidence - -DruggableGeneCategoryEnum + +DruggableGeneCategoryEnum diff --git a/graphviz/entity_to_disease_association.gv b/graphviz/entity_to_disease_association.gv index 86ee270b4d..7fcb7d759c 100644 --- a/graphviz/entity_to_disease_association.gv +++ b/graphviz/entity_to_disease_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,5142.4,283"]; + graph [bb="0,0,4904.4,283"]; node [label="\N"]; "entity to disease association" [height=0.5, label="entity to disease association", - pos="2544.4,265", + pos="2306.4,265", width=3.9538]; association [height=0.5, pos="62.394,178", width=1.7332]; "entity to disease association" -> association [label=is_a, lp="280.39,221.5", - pos="e,102.91,191.8 2402.4,263.68 1937.3,262.36 477.01,256.08 266.39,229 213.1,222.15 153.57,206.62 112.64,194.67"]; + pos="e,102.91,191.77 2164.3,263.4 1732.4,261.31 452.8,253.13 266.39,229 213.11,222.1 153.58,206.58 112.65,194.65"]; id [color=blue, height=0.5, label=string, @@ -19,7 +19,7 @@ digraph { "entity to disease association" -> id [color=blue, label=id, lp="396.39,221.5", - pos="e,210.38,189.98 2402.7,263.24 1955,260.62 587.97,250.9 389.39,229 317.22,221.04 299.34,215.5 229.39,196 226.29,195.13 223.09,194.17 \ + pos="e,210.38,189.98 2165,262.93 1751.6,259.59 563.8,248.41 389.39,229 317.23,220.97 299.34,215.5 229.39,196 226.29,195.13 223.09,194.17 \ 219.89,193.15", style=solid]; iri [color=blue, @@ -30,8 +30,8 @@ digraph { "entity to disease association" -> iri [color=blue, label=iri, lp="503.39,221.5", - pos="e,315.31,190.16 2402.5,263.11 1969.5,260.17 683.15,249.78 495.39,229 423.23,221.01 405.62,214.45 335.39,196 332.02,195.11 328.55,\ -194.14 325.06,193.12", + pos="e,315.31,190.16 2164,264.63 1795.6,265.73 817.58,265.03 495.39,229 423.24,220.93 405.62,214.45 335.39,196 332.02,195.11 328.55,194.14 \ +325.06,193.12", style=solid]; name [color=blue, height=0.5, @@ -41,7 +41,7 @@ digraph { "entity to disease association" -> name [color=blue, label=name, lp="607.39,221.5", - pos="e,438.25,191.78 2402.6,263.47 1982.9,261.61 765.15,254.09 587.39,229 538.92,222.16 485.05,206.79 447.81,194.88", + pos="e,438.25,191.75 2164.7,263.08 1781.1,260.32 741.16,250.9 587.39,229 538.92,222.1 485.06,206.73 447.82,194.85", style=solid]; description [color=blue, height=0.5, @@ -51,7 +51,7 @@ digraph { "entity to disease association" -> description [color=blue, label=description, lp="723.89,221.5", - pos="e,582.77,194.4 2401.9,264.13 1995.6,264.09 849.98,261.11 683.39,229 651.71,222.89 617.7,209.84 592.13,198.6", + pos="e,582.78,194.38 2164.2,263.69 1795.3,262.5 826.27,256.75 683.39,229 651.72,222.85 617.7,209.8 592.14,198.57", style=solid]; "has attribute" [color=blue, height=0.5, @@ -61,7 +61,7 @@ digraph { "entity to disease association" -> "has attribute" [color=blue, label="has attribute", lp="862.39,221.5", - pos="e,722.86,193.55 2402,264.19 2016,264.26 968.26,261.42 815.39,229 786.11,222.79 754.98,209.44 731.91,198.1", + pos="e,722.86,193.53 2164.4,263.68 1817.3,262.46 944.73,256.65 815.39,229 786.12,222.74 754.99,209.4 731.92,198.07", style=solid]; subject [color=blue, height=0.5, @@ -71,7 +71,7 @@ digraph { "entity to disease association" -> subject [color=blue, label=subject, lp="989.39,221.5", - pos="e,866.52,194.37 2402.2,263.71 2040.1,262.55 1101.9,256.88 963.39,229 932.94,222.87 900.37,209.91 875.84,198.72", + pos="e,866.53,194.34 2164.8,263.09 1843.5,260.64 1078.5,252.39 963.39,229 932.95,222.81 900.38,209.85 875.85,198.67", style=solid]; predicate [color=blue, height=0.5, @@ -81,7 +81,7 @@ digraph { "entity to disease association" -> predicate [color=blue, label=predicate, lp="1068.4,221.5", - pos="e,1008.4,196.14 2402.2,264.3 2037.4,264.6 1093.3,262.14 1034.4,229 1025,223.7 1017.9,214.33 1012.8,205.13", + pos="e,1008.4,196.12 2164.3,263.64 1842.6,262.34 1082.8,256.37 1034.4,229 1025,223.67 1017.9,214.31 1012.8,205.11", style=solid]; object [color=blue, height=0.5, @@ -91,7 +91,7 @@ digraph { "entity to disease association" -> object [color=blue, label=object, lp="1147.4,178", - pos="e,976.03,105.47 2403.8,262.06 2132.3,257.95 1544.4,247.23 1342.4,229 1245.2,220.23 1212.5,240.02 1125.4,196 1105.2,185.79 1108.1,\ + pos="e,976.03,105.47 2165.9,261.96 1928.1,258.05 1456.4,248.11 1291.4,229 1216.7,220.34 1191.7,231.46 1125.4,196 1105.4,185.33 1108.1,\ 172.77 1089.4,160 1057.3,138.07 1017,120.64 985.5,108.92", style=solid]; negated [color=blue, @@ -101,8 +101,8 @@ digraph { width=1.2999]; "entity to disease association" -> negated [color=blue, label=negated, - lp="1452.4,221.5", - pos="e,1260,190.39 2402.7,263.03 2144.9,260.69 1608.5,253.01 1423.4,229 1369.6,222.02 1309.4,205.52 1269.6,193.37", + lp="1369.4,221.5", + pos="e,1250.9,193.42 2166.3,261.81 1917.8,257.49 1418.5,246.74 1340.4,229 1312.2,222.59 1282.2,209.35 1260,198.1", style=solid]; qualifiers [color=blue, height=0.5, @@ -111,8 +111,8 @@ digraph { width=2.1304]; "entity to disease association" -> qualifiers [color=blue, label=qualifiers, - lp="1585.9,221.5", - pos="e,1408.3,193.2 2402.7,262.96 2168.8,260.58 1712,252.94 1552.4,229 1506.1,222.05 1454.8,207.75 1417.8,196.22", + lp="1461.9,221.5", + pos="e,1381.4,195.81 2164.4,263.21 1933.5,261.2 1495.2,254.09 1428.4,229 1413.6,223.44 1399.7,212.89 1388.8,202.9", style=solid]; publications [color=blue, height=0.5, @@ -121,8 +121,8 @@ digraph { width=1.7332]; "entity to disease association" -> publications [color=blue, label=publications, - lp="1724.4,221.5", - pos="e,1558.3,193.08 2402.8,262.85 2194.3,260.38 1814.8,252.69 1680.4,229 1641.5,222.15 1598.9,208.14 1567.9,196.7", + lp="1547.4,221.5", + pos="e,1508.5,195.61 2165,262.85 1940.7,260.31 1525.9,252.47 1503.4,229 1496.9,222.18 1498.6,212.97 1503.1,204.31", style=solid]; "has evidence" [color=blue, height=0.5, @@ -131,228 +131,230 @@ digraph { width=2.0943]; "entity to disease association" -> "has evidence" [color=blue, label="has evidence", - lp="1871.9,221.5", - pos="e,1714.3,194.09 2404,261.84 2226.8,258.3 1932.3,249.49 1825.4,229 1790.4,222.3 1752.4,209.09 1724,197.93", + lp="1645.9,221.5", + pos="e,1630.8,191.81 2166.1,261.96 1965.5,258.34 1618.6,249.18 1599.4,229 1586.5,215.42 1601.1,203.99 1621.2,195.5", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1881.4,178", - width=3.015]; + label=string, + pos="1811.4,178", + width=1.0652]; "entity to disease association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2011.9,221.5", - pos="e,1897.9,195.96 2407.3,260.16 2244.4,254.94 1989.3,244.45 1947.4,229 1931.9,223.3 1917.1,212.69 1905.4,202.7", + lp="1763.9,221.5", + pos="e,1782.1,189.74 2167.7,260.76 1993.5,256 1715.3,245.8 1699.4,229 1694.8,224.15 1695.4,219.31 1699.4,214 1717.2,190.45 1735.2,204.94 \ +1763.4,196 1766.3,195.07 1769.4,194.07 1772.4,193.05", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2116.4,178", - width=3.015]; + label=string, + pos="1906.4,178", + width=1.0652]; "entity to disease association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2178.4,221.5", - pos="e,2094.1,195.74 2402.9,262.76 2275.5,260.13 2104.9,252.25 2083.4,229 2076.2,221.21 2080,211.68 2087.1,203.04", + lp="1930.4,221.5", + pos="e,1877.1,189.79 2164.6,263.03 2034.2,260.61 1857.6,252.9 1835.4,229 1830.9,224.11 1831.9,219.66 1835.4,214 1839.4,207.54 1853.2,\ +200.12 1867.6,193.78", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2351.4,178", - width=3.015]; + label=string, + pos="2024.4,178", + width=1.0652]; "entity to disease association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2387.9,221.5", - pos="e,2304.5,194.27 2404.5,261.66 2350.9,257.53 2298.4,248.41 2281.4,229 2271.3,217.45 2280.6,207.11 2295.3,198.87", + lp="2144.9,221.5", + pos="e,2024.6,196.37 2169.9,259.86 2114.5,255.44 2058.7,246.59 2038.4,229 2031.8,223.29 2028.2,214.77 2026.3,206.36", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2533.4,178", + pos="2250.4,178", width=1.5346]; "entity to disease association" -> timepoint [color=blue, label=timepoint, - lp="2534.4,221.5", - pos="e,2512,194.95 2514.8,247.2 2508.6,242.2 2502.9,236.11 2499.4,229 2494.9,219.85 2498.7,210.46 2505.2,202.32", + lp="2296.4,221.5", + pos="e,2251.3,196.31 2278.3,246.98 2271.9,241.92 2265.7,235.86 2261.4,229 2257.2,222.28 2254.5,214.16 2252.9,206.44", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2645.4,178", + pos="2362.4,178", width=1.0652]; "entity to disease association" -> "original subject" [color=blue, label="original subject", - lp="2648.4,221.5", - pos="e,2622.4,192.59 2559.1,246.86 2568.2,236.75 2580.4,224.01 2592.4,214 2599.1,208.42 2606.7,202.95 2614,198.05", + lp="2397.4,221.5", + pos="e,2352.3,195.84 2318.8,247.07 2322.9,241.38 2327.4,234.97 2331.4,229 2336.7,221.09 2342.2,212.33 2347.1,204.38", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2759.4,178", + pos="2488.4,178", width=1.5887]; "entity to disease association" -> "original predicate" [color=blue, label="original predicate", - lp="2789.9,221.5", - pos="e,2745.2,195.87 2639.9,251.62 2661.8,246.49 2684.6,239.24 2704.4,229 2716.9,222.55 2728.7,212.55 2738.2,203.17", + lp="2535.9,221.5", + pos="e,2481.8,196.33 2407.4,252.23 2425.2,247.01 2442.6,239.58 2457.4,229 2465.7,223.06 2472.2,214.14 2477.1,205.48", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2873.4,178", + pos="2622.4,178", width=1.0652]; "entity to disease association" -> "original object" [color=blue, label="original object", - lp="2917.9,221.5", - pos="e,2871.5,196.07 2647.1,252.49 2737.2,242.36 2854.1,229.2 2854.4,229 2861.7,223.35 2866.2,214.58 2868.9,205.94", + lp="2666.9,221.5", + pos="e,2620.4,196.05 2409.3,252.49 2494.3,242.89 2601.4,230.54 2603.4,229 2610.7,223.33 2615.1,214.55 2617.9,205.92", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3006.4,178", + pos="2755.4,178", width=2.1304]; "entity to disease association" -> "subject category" [color=blue, label="subject category", - lp="3048.9,221.5", - pos="e,3000,195.99 2644.5,252.14 2661.8,250.28 2679.6,248.48 2696.4,247 2727.1,244.29 2946.7,244.49 2973.4,229 2982.8,223.52 2990.1,214.12 \ -2995.4,204.94", + lp="2797.9,221.5", + pos="e,2749,195.98 2406.5,252.18 2423.8,250.32 2441.6,248.51 2458.4,247 2487.7,244.37 2697,243.81 2722.4,229 2731.8,223.5 2739.1,214.1 \ +2744.3,204.93", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3177.4,178", + pos="2926.4,178", width=2.1304]; "entity to disease association" -> "object category" [color=blue, label="object category", - lp="3195.9,221.5", - pos="e,3161.5,195.8 2643.2,251.96 2660.9,250.09 2679.2,248.33 2696.4,247 2742.5,243.43 3068.9,244.84 3112.4,229 3127.8,223.38 3142.6,\ -212.67 3154.1,202.6", + lp="2942.9,221.5", + pos="e,2910.5,195.79 2405.2,251.98 2422.9,250.1 2441.2,248.35 2458.4,247 2547.8,240.01 2777.2,259.75 2861.4,229 2876.8,223.36 2891.5,\ +212.65 2903.1,202.59", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3310.4,178", + pos="3059.4,178", width=1.0652]; "entity to disease association" -> "subject closure" [color=blue, label="subject closure", - lp="3333.9,221.5", - pos="e,3297.9,195.33 2642.4,251.88 2660.3,250 2678.9,248.26 2696.4,247 2758.4,242.54 3197.8,252.34 3255.4,229 3269.1,223.44 3281.6,212.82 \ -3291.2,202.79", + lp="3081.9,221.5", + pos="e,3046.3,195.33 2404.4,251.9 2422.3,250.01 2440.9,248.26 2458.4,247 2518.7,242.64 2946.2,251.24 3002.4,229 3016.4,223.45 3029.3,\ +212.82 3039.3,202.79", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3408.4,178", + pos="3167.4,178", width=1.0652]; "entity to disease association" -> "object closure" [color=blue, label="object closure", - lp="3450.4,221.5", - pos="e,3406.3,196.38 2642,251.84 2660.1,249.94 2678.8,248.21 2696.4,247 2734.8,244.36 3356.8,250.97 3388.4,229 3396.1,223.64 3400.8,214.81 \ -3403.7,206.05", + lp="3204.4,221.5", + pos="e,3163,196.04 2404,251.84 2422.1,249.95 2440.8,248.22 2458.4,247 2496.2,244.39 3108.1,248.84 3140.4,229 3149,223.69 3155.1,214.58 \ +3159.2,205.58", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3541.4,178", + pos="3300.4,178", width=2.1304]; "entity to disease association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3608.9,221.5", - pos="e,3533.8,196.21 2641.6,251.83 2659.8,249.92 2678.6,248.19 2696.4,247 2741.2,244 3464.5,249.65 3504.4,229 3514.6,223.73 3522.7,214.24 \ -3528.7,204.93", + lp="3364.9,221.5", + pos="e,3291.2,196.27 2403.6,251.83 2421.8,249.92 2440.6,248.19 2458.4,247 2502.8,244.03 3218.3,248.23 3258.4,229 3269.4,223.74 3278.5,\ +214.12 3285.4,204.72", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3731.4,178", + pos="3493.4,178", width=2.1304]; "entity to disease association" -> "object category closure" [color=blue, label="object category closure", - lp="3798.9,221.5", - pos="e,3725.7,196.14 2641.6,251.76 2659.8,249.86 2678.6,248.15 2696.4,247 2724.2,245.2 3676.1,242.78 3700.4,229 3709.6,223.76 3716.5,\ -214.53 3721.3,205.42", + lp="3556.9,221.5", + pos="e,3485.8,196.23 2403.6,251.76 2421.8,249.86 2440.6,248.15 2458.4,247 2513.7,243.41 3407.1,254.4 3456.4,229 3466.6,223.75 3474.7,\ +214.27 3480.7,204.96", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3921.4,178", + pos="3683.4,178", width=1.0652]; "entity to disease association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3971.4,221.5", - pos="e,3914.7,195.72 2641.2,251.77 2659.5,249.85 2678.5,248.13 2696.4,247 2729.4,244.91 3857.2,244.49 3886.4,229 3896.5,223.66 3904.3,\ -213.97 3909.9,204.54", + lp="3730.4,221.5", + pos="e,3675.4,195.77 2403.2,251.77 2421.5,249.85 2440.5,248.13 2458.4,247 2491.3,244.92 3614.9,243.68 3644.4,229 3655.1,223.67 3663.8,\ +213.85 3670.2,204.31", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4080.4,178", + pos="3842.4,178", width=1.0652]; "entity to disease association" -> "object namespace" [color=blue, label="object namespace", - lp="4124.4,221.5", - pos="e,4073,195.75 2641.2,251.74 2659.5,249.83 2678.5,248.12 2696.4,247 2733.7,244.67 4010.1,246.07 4043.4,229 4053.7,223.7 4061.9,214.02 \ -4067.9,204.58", + lp="3884.4,221.5", + pos="e,3834.1,195.79 2403.2,251.74 2421.5,249.83 2440.5,248.12 2458.4,247 2495.7,244.67 3768.9,245.4 3802.4,229 3813.3,223.69 3822.1,\ +213.87 3828.7,204.34", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4231.4,178", + pos="3993.4,178", width=1.0652]; "entity to disease association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4284.4,221.5", - pos="e,4223.4,195.78 2641.2,251.72 2659.5,249.81 2678.5,248.11 2696.4,247 2737.9,244.44 4155.2,247.46 4192.4,229 4203.1,223.68 4211.8,\ -213.87 4218.2,204.33", + lp="4046.4,221.5", + pos="e,3984.8,195.81 2403.2,251.72 2421.5,249.81 2440.5,248.11 2458.4,247 2499.8,244.44 3915,246.98 3952.4,229 3963.4,223.71 3972.4,213.9 \ +3979.2,204.36", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4402.4,178", + pos="4164.4,178", width=1.0652]; "entity to disease association" -> "object label closure" [color=blue, label="object label closure", - lp="4450.9,221.5", - pos="e,4394.1,195.8 2640.8,251.74 2659.2,249.82 2678.4,248.1 2696.4,247 2742.6,244.17 4320.8,249.27 4362.4,229 4373.3,223.71 4382.1,213.89 \ -4388.7,204.35", + lp="4212.9,221.5", + pos="e,4156.1,195.8 2402.8,251.74 2421.2,249.82 2440.4,248.1 2458.4,247 2504.6,244.17 4082.8,249.27 4124.4,229 4135.3,223.71 4144.1,213.89 \ +4150.7,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4564.4,178", + pos="4326.4,178", width=2.347]; "entity to disease association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4612.9,221.5", - pos="e,4555.8,196.3 2640.8,251.73 2659.2,249.81 2678.4,248.09 2696.4,247 2747.1,243.92 4478.7,251.22 4524.4,229 4535.1,223.79 4543.9,\ -214.17 4550.4,204.76", + lp="4374.9,221.5", + pos="e,4317.8,196.3 2402.8,251.73 2421.2,249.81 2440.4,248.09 2458.4,247 2509.1,243.92 4240.7,251.22 4286.4,229 4297.1,223.79 4305.9,\ +214.17 4312.4,204.76", style=solid]; type [height=0.5, - pos="4712.4,178", + pos="4474.4,178", width=0.86659]; "entity to disease association" -> type [color=blue, label=type, - lp="4716.4,221.5", - pos="e,4708.4,196.08 2640.8,251.72 2659.2,249.8 2678.4,248.09 2696.4,247 2724,245.34 4662.8,243.45 4686.4,229 4695,223.74 4700.9,214.64 \ -4704.8,205.63", + lp="4478.4,221.5", + pos="e,4470.4,196.08 2402.8,251.72 2421.2,249.8 2440.4,248.09 2458.4,247 2486,245.34 4424.8,243.45 4448.4,229 4457,223.74 4462.9,214.64 \ +4466.8,205.63", style=solid]; category [height=0.5, - pos="4813.4,178", + pos="4575.4,178", width=1.4263]; "entity to disease association" -> category [color=blue, label=category, - lp="4799.9,221.5", - pos="e,4795.3,195.05 2640.8,251.72 2659.2,249.79 2678.4,248.08 2696.4,247 2753,243.6 4682.1,245.33 4736.4,229 4754.8,223.45 4773,211.98 \ -4787.1,201.44", + lp="4561.9,221.5", + pos="e,4557.3,195.05 2402.8,251.72 2421.2,249.79 2440.4,248.08 2458.4,247 2515,243.6 4444.1,245.33 4498.4,229 4516.8,223.45 4535,211.98 \ +4549.1,201.44", style=solid]; "FDA approval status" [color=blue, height=0.5, label=FDAApprovalStatusEnum, - pos="5012.4,178", + pos="4774.4,178", width=3.6108]; "entity to disease association" -> "FDA approval status" [color=blue, label="FDA approval status", - lp="4978.9,221.5", - pos="e,4968.4,194.99 2640.8,251.71 2659.2,249.79 2678.4,248.08 2696.4,247 2933.6,232.77 4600.1,262.6 4835.4,229 4877.5,222.98 4923.8,\ -209.67 4958.5,198.29", + lp="4740.9,221.5", + pos="e,4730.4,194.99 2402.8,251.71 2421.2,249.79 2440.4,248.08 2458.4,247 2695.6,232.77 4362.1,262.6 4597.4,229 4639.5,222.98 4685.8,\ +209.67 4720.5,198.29", style=solid]; subject -> object [label=relation, lp="919.39,134.5", @@ -367,11 +369,11 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="2743.4,265", + pos="2505.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2874.4,265", + pos="2636.4,265", width=2.0762]; } diff --git a/graphviz/entity_to_disease_association.svg b/graphviz/entity_to_disease_association.svg index b26cf7b329..3395640ef5 100644 --- a/graphviz/entity_to_disease_association.svg +++ b/graphviz/entity_to_disease_association.svg @@ -4,16 +4,16 @@ - + %3 - + entity to disease association - -entity to disease association + +entity to disease association @@ -24,8 +24,8 @@ entity to disease association->association - - + + is_a @@ -37,7 +37,7 @@ entity to disease association->id - + id @@ -50,7 +50,7 @@ entity to disease association->iri - + iri @@ -63,8 +63,8 @@ entity to disease association->name - - + + name @@ -76,8 +76,8 @@ entity to disease association->description - - + + description @@ -89,8 +89,8 @@ entity to disease association->has attribute - - + + has attribute @@ -102,8 +102,8 @@ entity to disease association->subject - - + + subject @@ -115,8 +115,8 @@ entity to disease association->predicate - - + + predicate @@ -128,7 +128,7 @@ entity to disease association->object - + object @@ -141,9 +141,9 @@ entity to disease association->negated - - -negated + + +negated @@ -154,9 +154,9 @@ entity to disease association->qualifiers - - -qualifiers + + +qualifiers @@ -167,9 +167,9 @@ entity to disease association->publications - - -publications + + +publications @@ -180,282 +180,282 @@ entity to disease association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string entity to disease association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string entity to disease association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string entity to disease association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type entity to disease association->timepoint - - -timepoint + + +timepoint original subject - -string + +string entity to disease association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie entity to disease association->original predicate - - -original predicate + + +original predicate original object - -string + +string entity to disease association->original object - - -original object + + +original object subject category - -ontology class + +ontology class entity to disease association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class entity to disease association->object category - - -object category + + +object category subject closure - -string + +string entity to disease association->subject closure - - -subject closure + + +subject closure object closure - -string + +string entity to disease association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class entity to disease association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class entity to disease association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string entity to disease association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string entity to disease association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string entity to disease association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string entity to disease association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source entity to disease association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type entity to disease association->type - - -type + + +type category - -category + +category entity to disease association->category - - -category + + +category FDA approval status - -FDAApprovalStatusEnum + +FDAApprovalStatusEnum entity to disease association->FDA approval status - - -FDA approval status + + +FDA approval status @@ -485,14 +485,14 @@ association_type - -string + +string association_category - -category type + +category type diff --git a/graphviz/entity_to_phenotypic_feature_association.gv b/graphviz/entity_to_phenotypic_feature_association.gv index 491adfc347..c200104fe5 100644 --- a/graphviz/entity_to_phenotypic_feature_association.gv +++ b/graphviz/entity_to_phenotypic_feature_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,5142.4,283"]; + graph [bb="0,0,4904.4,283"]; node [label="\N"]; "entity to phenotypic feature association" [height=0.5, label="entity to phenotypic feature association", - pos="2544.4,265", + pos="2306.4,265", width=5.4342]; association [height=0.5, pos="62.394,178", width=1.7332]; "entity to phenotypic feature association" -> association [label=is_a, lp="280.39,221.5", - pos="e,102.91,191.8 2349.2,263.52 1835.2,261.88 469.53,255.12 266.39,229 213.1,222.15 153.57,206.62 112.64,194.67"]; + pos="e,102.91,191.77 2111.6,263.13 1636.8,260.66 445.72,252.22 266.39,229 213.11,222.1 153.58,206.58 112.65,194.65"]; id [color=blue, height=0.5, label=string, @@ -19,7 +19,7 @@ digraph { "entity to phenotypic feature association" -> id [color=blue, label=id, lp="396.39,221.5", - pos="e,210.38,189.98 2350,262.92 1856.5,259.89 580.7,250.09 389.39,229 317.22,221.04 299.34,215.5 229.39,196 226.29,195.13 223.09,194.17 \ + pos="e,210.38,189.98 2112.6,262.5 1659.6,258.7 556.93,247.64 389.39,229 317.23,220.97 299.34,215.5 229.39,196 226.29,195.13 223.09,194.17 \ 219.89,193.15", style=solid]; iri [color=blue, @@ -30,8 +30,8 @@ digraph { "entity to phenotypic feature association" -> iri [color=blue, label=iri, lp="503.39,221.5", - pos="e,315.31,190.16 2350.1,262.74 1874.2,259.37 676.07,249 495.39,229 423.23,221.01 405.62,214.45 335.39,196 332.02,195.11 328.55,194.14 \ -325.06,193.12", + pos="e,315.31,190.16 2110.4,264.77 1708.6,265.59 803.03,263.4 495.39,229 423.24,220.93 405.62,214.45 335.39,196 332.02,195.11 328.55,\ +194.14 325.06,193.12", style=solid]; name [color=blue, height=0.5, @@ -41,7 +41,7 @@ digraph { "entity to phenotypic feature association" -> name [color=blue, label=name, lp="607.39,221.5", - pos="e,438.25,191.78 2349.4,263.22 1888.7,260.99 758.16,253.11 587.39,229 538.92,222.16 485.05,206.79 447.81,194.88", + pos="e,438.25,191.75 2112.1,262.69 1694,259.5 734.6,249.97 587.39,229 538.92,222.1 485.06,206.73 447.82,194.85", style=solid]; description [color=blue, height=0.5, @@ -51,7 +51,7 @@ digraph { "entity to phenotypic feature association" -> description [color=blue, label=description, lp="723.89,221.5", - pos="e,582.77,194.4 2348.6,264.11 1903.8,263.8 843.19,259.81 683.39,229 651.71,222.89 617.7,209.84 592.13,198.6", + pos="e,582.78,194.38 2111.1,263.5 1710.1,261.94 819.87,255.51 683.39,229 651.72,222.85 617.7,209.8 592.14,198.57", style=solid]; "has attribute" [color=blue, height=0.5, @@ -61,7 +61,7 @@ digraph { "entity to phenotypic feature association" -> "has attribute" [color=blue, label="has attribute", lp="862.39,221.5", - pos="e,722.86,193.55 2348.7,264.18 1927.7,263.96 961.69,260.03 815.39,229 786.11,222.79 754.98,209.44 731.91,198.1", + pos="e,722.86,193.53 2111.3,263.47 1735.7,261.85 938.55,255.33 815.39,229 786.12,222.74 754.99,209.4 731.92,198.07", style=solid]; subject [color=blue, height=0.5, @@ -71,7 +71,7 @@ digraph { "entity to phenotypic feature association" -> subject [color=blue, label=subject, lp="989.39,221.5", - pos="e,866.52,194.37 2349.3,263.52 1956.3,261.99 1095.6,255.61 963.39,229 932.94,222.87 900.37,209.91 875.84,198.72", + pos="e,866.53,194.34 2112.1,262.67 1766.9,259.76 1072.6,251.19 963.39,229 932.95,222.81 900.38,209.85 875.85,198.67", style=solid]; predicate [color=blue, height=0.5, @@ -81,7 +81,7 @@ digraph { "entity to phenotypic feature association" -> predicate [color=blue, label=predicate, lp="1068.4,221.5", - pos="e,1008.4,196.14 2348.6,264.32 1952.9,264.31 1090.6,260.62 1034.4,229 1025,223.7 1017.9,214.33 1012.8,205.13", + pos="e,1008.4,196.12 2111.2,263.4 1766.2,261.67 1080.3,254.96 1034.4,229 1025,223.67 1017.9,214.31 1012.8,205.11", style=solid]; object [color=blue, height=0.5, @@ -91,7 +91,7 @@ digraph { "entity to phenotypic feature association" -> object [color=blue, label=object, lp="1147.4,178", - pos="e,976.03,105.47 2352.7,261.26 2064.4,256.66 1532.5,246.16 1342.4,229 1245.2,220.23 1212.5,240.02 1125.4,196 1105.2,185.79 1108.1,\ + pos="e,976.03,105.47 2115.3,261.1 1866.6,256.68 1445.4,246.84 1291.4,229 1216.7,220.34 1191.7,231.46 1125.4,196 1105.4,185.33 1108.1,\ 172.77 1089.4,160 1057.3,138.07 1017,120.64 985.5,108.92", style=solid]; negated [color=blue, @@ -101,8 +101,8 @@ digraph { width=1.2999]; "entity to phenotypic feature association" -> negated [color=blue, label=negated, - lp="1452.4,221.5", - pos="e,1260,190.39 2350.6,262.52 2078.4,259.65 1596.8,251.49 1423.4,229 1369.6,222.02 1309.4,205.52 1269.6,193.37", + lp="1369.4,221.5", + pos="e,1250.9,193.42 2115.8,260.9 1855.8,256.09 1413.6,245.6 1340.4,229 1312.2,222.59 1282.2,209.35 1260,198.1", style=solid]; qualifiers [color=blue, height=0.5, @@ -111,8 +111,8 @@ digraph { width=2.1304]; "entity to phenotypic feature association" -> qualifiers [color=blue, label=qualifiers, - lp="1585.9,221.5", - pos="e,1408.3,193.2 2350.7,262.38 2106.5,259.44 1700.8,251.27 1552.4,229 1506.1,222.05 1454.8,207.75 1417.8,196.22", + lp="1461.9,221.5", + pos="e,1381.4,195.81 2112.2,262.7 1873,260.1 1490.5,252.31 1428.4,229 1413.6,223.44 1399.7,212.89 1388.8,202.9", style=solid]; publications [color=blue, height=0.5, @@ -121,8 +121,8 @@ digraph { width=1.7332]; "entity to phenotypic feature association" -> publications [color=blue, label=publications, - lp="1724.4,221.5", - pos="e,1558.3,193.08 2350.9,262.17 2136.4,259.08 1804.3,250.83 1680.4,229 1641.5,222.15 1598.9,208.14 1567.9,196.7", + lp="1547.4,221.5", + pos="e,1508.5,195.61 2113,262.2 1882.1,259.08 1524.2,250.75 1503.4,229 1496.9,222.18 1498.6,212.97 1503.1,204.31", style=solid]; "has evidence" [color=blue, height=0.5, @@ -131,228 +131,229 @@ digraph { width=2.0943]; "entity to phenotypic feature association" -> "has evidence" [color=blue, label="has evidence", - lp="1871.9,221.5", - pos="e,1714.3,194.09 2354.1,260.77 2175.9,256.64 1922.8,247.67 1825.4,229 1790.4,222.3 1752.4,209.09 1724,197.93", + lp="1645.9,221.5", + pos="e,1630.8,191.81 2115.4,260.98 1912.1,256.8 1617.1,247.57 1599.4,229 1586.5,215.42 1601.1,203.99 1621.2,195.5", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1881.4,178", - width=3.015]; + label=string, + pos="1811.4,178", + width=1.0652]; "entity to phenotypic feature association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2011.9,221.5", - pos="e,1897.9,195.96 2361.2,258.62 2200.1,253.01 1985.5,243.06 1947.4,229 1931.9,223.3 1917.1,212.69 1905.4,202.7", + lp="1763.9,221.5", + pos="e,1782.1,189.74 2120.4,259.4 1947.4,254.19 1713.9,244.35 1699.4,229 1694.8,224.15 1695.4,219.31 1699.4,214 1717.2,190.45 1735.2,\ +204.94 1763.4,196 1766.3,195.07 1769.4,194.07 1772.4,193.05", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2116.4,178", - width=3.015]; + label=string, + pos="1906.4,178", + width=1.0652]; "entity to phenotypic feature association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2178.4,221.5", - pos="e,2094.1,195.74 2352.5,261.48 2234.5,257.88 2102.2,249.29 2083.4,229 2076.2,221.21 2080,211.68 2087.1,203.04", + lp="1930.4,221.5", + pos="e,1877.1,189.79 2113.7,261.84 1992.2,258.42 1854.8,249.9 1835.4,229 1830.9,224.11 1831.9,219.66 1835.4,214 1839.4,207.54 1853.2,\ +200.12 1867.6,193.78", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2351.4,178", - width=3.015]; + label=string, + pos="2024.4,178", + width=1.0652]; "entity to phenotypic feature association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2387.9,221.5", - pos="e,2304.5,194.27 2365.7,257.63 2327.2,252.43 2294.2,243.64 2281.4,229 2271.3,217.45 2280.6,207.11 2295.3,198.87", + lp="2144.9,221.5", + pos="e,2024.6,196.37 2134.6,256.37 2092.2,251.25 2054.4,242.82 2038.4,229 2031.8,223.29 2028.2,214.77 2026.3,206.36", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2533.4,178", + pos="2250.4,178", width=1.5346]; "entity to phenotypic feature association" -> timepoint [color=blue, label=timepoint, - lp="2534.4,221.5", - pos="e,2512,194.95 2514.8,247.2 2508.6,242.2 2502.9,236.11 2499.4,229 2494.9,219.85 2498.7,210.46 2505.2,202.32", + lp="2296.4,221.5", + pos="e,2251.3,196.31 2278.3,246.98 2271.9,241.92 2265.7,235.86 2261.4,229 2257.2,222.28 2254.5,214.16 2252.9,206.44", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2645.4,178", + pos="2362.4,178", width=1.0652]; "entity to phenotypic feature association" -> "original subject" [color=blue, label="original subject", - lp="2648.4,221.5", - pos="e,2622.4,192.59 2559.1,246.86 2568.2,236.75 2580.4,224.01 2592.4,214 2599.1,208.42 2606.7,202.95 2614,198.05", + lp="2397.4,221.5", + pos="e,2352.3,195.84 2319.1,246.71 2323.1,241.11 2327.5,234.84 2331.4,229 2336.7,221.09 2342.2,212.33 2347.1,204.38", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2759.4,178", + pos="2488.4,178", width=1.5887]; "entity to phenotypic feature association" -> "original predicate" [color=blue, label="original predicate", - lp="2789.9,221.5", - pos="e,2745.2,195.87 2647.9,249.67 2667.3,244.69 2687,238 2704.4,229 2716.9,222.55 2728.7,212.55 2738.2,203.17", + lp="2535.9,221.5", + pos="e,2481.8,196.33 2414.9,249.89 2430,244.86 2444.7,238.09 2457.4,229 2465.7,223.06 2472.2,214.14 2477.1,205.48", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2873.4,178", + pos="2622.4,178", width=1.0652]; "entity to phenotypic feature association" -> "original object" [color=blue, label="original object", - lp="2917.9,221.5", - pos="e,2871.5,196.07 2679.2,251.94 2759.4,244.24 2847.1,234.67 2854.4,229 2861.7,223.35 2866.2,214.58 2868.9,205.94", + lp="2666.9,221.5", + pos="e,2620.4,196.05 2437.7,251.59 2514,243.86 2596.5,234.4 2603.4,229 2610.7,223.33 2615.1,214.55 2617.9,205.92", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3006.4,178", + pos="2755.4,178", width=2.1304]; "entity to phenotypic feature association" -> "subject category" [color=blue, label="subject category", - lp="3048.9,221.5", - pos="e,2999.7,196.42 2684.2,252.36 2706,250.56 2728.3,248.72 2749.4,247 2799.2,242.94 2930.4,254.41 2973.4,229 2982.6,223.58 2989.7,214.49 \ -2994.9,205.54", + lp="2797.9,221.5", + pos="e,2748.7,196.41 2446.3,252.41 2566.8,242.39 2721.6,229.45 2722.4,229 2731.6,223.56 2738.7,214.47 2743.9,205.52", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3177.4,178", + pos="2926.4,178", width=2.1304]; "entity to phenotypic feature association" -> "object category" [color=blue, label="object category", - lp="3193.9,221.5", - pos="e,3161.5,195.76 2680.8,252.05 2703.7,250.23 2727.2,248.47 2749.4,247 2830,241.66 3036.6,256.89 3112.4,229 3127.8,223.33 3142.5,212.61 \ -3154.1,202.55", + lp="2942.9,221.5", + pos="e,2910.5,195.75 2442.8,252.09 2465.7,250.26 2489.2,248.49 2511.4,247 2589.1,241.78 2788.3,255.96 2861.4,229 2876.8,223.31 2891.5,\ +212.6 2903.1,202.54", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3310.4,178", + pos="3059.4,178", width=1.0652]; "entity to phenotypic feature association" -> "subject closure" [color=blue, label="subject closure", - lp="3332.9,221.5", - pos="e,3297.3,195.32 2679.1,251.92 2702.5,250.08 2726.7,248.35 2749.4,247 2805.3,243.68 3201.3,249.67 3253.4,229 3267.4,223.43 3280.3,\ -212.8 3290.3,202.78", + lp="3081.9,221.5", + pos="e,3046.3,195.32 2441.1,251.94 2464.5,250.09 2488.7,248.36 2511.4,247 2565.9,243.74 2951.7,249.17 3002.4,229 3016.4,223.42 3029.3,\ +212.8 3039.3,202.77", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3408.4,178", + pos="3167.4,178", width=1.0652]; "entity to phenotypic feature association" -> "object closure" [color=blue, label="object closure", - lp="3450.4,221.5", - pos="e,3406.3,196.37 2678.3,251.84 2702,249.99 2726.4,248.28 2749.4,247 2784.9,245.03 3359.3,249.32 3388.4,229 3396.1,223.64 3400.8,214.8 \ -3403.7,206.04", + lp="3204.4,221.5", + pos="e,3163,196.03 2440.3,251.85 2464,250 2488.4,248.28 2511.4,247 2546.3,245.05 3110.6,247.34 3140.4,229 3149,223.68 3155.1,214.57 3159.2,\ +205.57", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3541.4,178", + pos="3300.4,178", width=2.1304]; "entity to phenotypic feature association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3608.9,221.5", - pos="e,3533.8,196.2 2677.7,251.8 2701.6,249.94 2726.2,248.24 2749.4,247 2791.3,244.77 3467.2,248.33 3504.4,229 3514.6,223.72 3522.7,214.23 \ -3528.7,204.93", + lp="3364.9,221.5", + pos="e,3291.1,196.26 2439.7,251.8 2463.6,249.95 2488.2,248.24 2511.4,247 2552.8,244.78 3221,246.99 3258.4,229 3269.3,223.74 3278.5,214.11 \ +3285.4,204.71", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3731.4,178", + pos="3493.4,178", width=2.1304]; "entity to phenotypic feature association" -> "object category closure" [color=blue, label="object category closure", - lp="3798.9,221.5", - pos="e,3725.7,196.14 2677.2,251.74 2701.2,249.88 2726,248.19 2749.4,247 2775.8,245.66 3677.4,242.07 3700.4,229 3709.6,223.75 3716.5,214.53 \ -3721.3,205.42", + lp="3556.9,221.5", + pos="e,3485.8,196.22 2439.2,251.75 2463.2,249.88 2488,248.19 2511.4,247 2563.8,244.33 3409.7,253.08 3456.4,229 3466.6,223.75 3474.7,214.26 \ +3480.7,204.95", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3921.4,178", + pos="3683.4,178", width=1.0652]; "entity to phenotypic feature association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3971.4,221.5", - pos="e,3914.4,196.21 2676.6,251.73 2700.8,249.85 2725.9,248.16 2749.4,247 2780.9,245.44 3858.5,243.81 3886.4,229 3896.2,223.78 3903.9,\ -214.44 3909.5,205.22", + lp="3730.4,221.5", + pos="e,3675.4,195.77 2438.6,251.73 2462.8,249.85 2487.9,248.16 2511.4,247 2542.8,245.45 3616.2,243.03 3644.4,229 3655.1,223.66 3663.8,\ +213.84 3670.2,204.31", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4080.4,178", + pos="3842.4,178", width=1.0652]; "entity to phenotypic feature association" -> "object namespace" [color=blue, label="object namespace", - lp="4124.4,221.5", - pos="e,4073,195.75 2676.4,251.71 2700.6,249.83 2725.8,248.14 2749.4,247 2785.3,245.26 4011.4,245.4 4043.4,229 4053.7,223.7 4061.9,214.02 \ -4067.9,204.58", + lp="3884.4,221.5", + pos="e,3834.1,195.79 2438.4,251.71 2462.6,249.83 2487.8,248.14 2511.4,247 2547.2,245.27 3770.2,244.76 3802.4,229 3813.3,223.69 3822.1,\ +213.87 3828.7,204.33", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4231.4,178", + pos="3993.4,178", width=1.0652]; "entity to phenotypic feature association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4284.4,221.5", - pos="e,4223.4,195.78 2676.4,251.68 2700.6,249.81 2725.8,248.13 2749.4,247 2789.4,245.09 4156.5,246.81 4192.4,229 4203.1,223.68 4211.8,\ -213.86 4218.2,204.33", + lp="4046.4,221.5", + pos="e,3984.8,195.8 2438.4,251.68 2462.6,249.81 2487.8,248.13 2511.4,247 2551.4,245.09 3916.3,246.35 3952.4,229 3963.4,223.71 3972.4,\ +213.9 3979.2,204.35", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4402.4,178", + pos="4164.4,178", width=1.0652]; "entity to phenotypic feature association" -> "object label closure" [color=blue, label="object label closure", - lp="4450.9,221.5", - pos="e,4394.1,195.8 2676.1,251.68 2700.4,249.8 2725.7,248.11 2749.4,247 2794.2,244.9 4322.1,248.64 4362.4,229 4373.3,223.7 4382.1,213.89 \ -4388.7,204.35", + lp="4212.9,221.5", + pos="e,4156.1,195.8 2438.1,251.68 2462.4,249.8 2487.7,248.11 2511.4,247 2556.2,244.9 4084.1,248.64 4124.4,229 4135.3,223.7 4144.1,213.89 \ +4150.7,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4564.4,178", + pos="4326.4,178", width=2.347]; "entity to phenotypic feature association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4612.9,221.5", - pos="e,4555.8,196.3 2676.1,251.66 2700.4,249.78 2725.7,248.1 2749.4,247 2798.6,244.71 4480.1,250.58 4524.4,229 4535.1,223.78 4543.9,214.17 \ -4550.4,204.76", + lp="4374.9,221.5", + pos="e,4317.8,196.3 2438.1,251.66 2462.4,249.78 2487.7,248.1 2511.4,247 2560.6,244.71 4242.1,250.58 4286.4,229 4297.1,223.78 4305.9,214.17 \ +4312.4,204.76", style=solid]; type [height=0.5, - pos="4712.4,178", + pos="4474.4,178", width=0.86659]; "entity to phenotypic feature association" -> type [color=blue, label=type, - lp="4716.4,221.5", - pos="e,4708.4,196.08 2675.8,251.66 2700.2,249.78 2725.6,248.1 2749.4,247 2776.3,245.76 4663.5,243.07 4686.4,229 4695,223.74 4700.8,214.64 \ -4704.8,205.63", + lp="4478.4,221.5", + pos="e,4470.4,196.08 2437.8,251.66 2462.2,249.78 2487.6,248.1 2511.4,247 2538.3,245.76 4425.5,243.07 4448.4,229 4457,223.74 4462.8,214.64 \ +4466.8,205.63", style=solid]; category [height=0.5, - pos="4813.4,178", + pos="4575.4,178", width=1.4263]; "entity to phenotypic feature association" -> category [color=blue, label=category, - lp="4799.9,221.5", - pos="e,4795.3,195.04 2675.8,251.66 2700.2,249.77 2725.6,248.09 2749.4,247 2804.5,244.47 4683.5,244.92 4736.4,229 4754.8,223.44 4773,211.98 \ -4787.1,201.43", + lp="4561.9,221.5", + pos="e,4557.3,195.04 2437.8,251.66 2462.2,249.77 2487.6,248.09 2511.4,247 2566.5,244.47 4445.5,244.92 4498.4,229 4516.8,223.44 4535,211.98 \ +4549.1,201.43", style=solid]; "FDA approval status" [color=blue, height=0.5, label=FDAApprovalStatusEnum, - pos="5012.4,178", + pos="4774.4,178", width=3.6108]; "entity to phenotypic feature association" -> "FDA approval status" [color=blue, label="FDA approval status", - lp="4978.9,221.5", - pos="e,4968.4,194.98 2675.8,251.65 2700.2,249.77 2725.6,248.09 2749.4,247 2980.9,236.41 4605.9,261.8 4835.4,229 4877.5,222.98 4923.8,\ -209.66 4958.5,198.29", + lp="4740.9,221.5", + pos="e,4730.4,194.98 2437.8,251.65 2462.2,249.77 2487.6,248.09 2511.4,247 2742.9,236.41 4367.9,261.8 4597.4,229 4639.5,222.98 4685.8,\ +209.66 4720.5,198.29", style=solid]; subject -> object [label=relation, lp="919.39,134.5", @@ -367,11 +368,11 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="2796.4,265", + pos="2558.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2927.4,265", + pos="2689.4,265", width=2.0762]; } diff --git a/graphviz/entity_to_phenotypic_feature_association.svg b/graphviz/entity_to_phenotypic_feature_association.svg index b85d8246a8..8f993f742b 100644 --- a/graphviz/entity_to_phenotypic_feature_association.svg +++ b/graphviz/entity_to_phenotypic_feature_association.svg @@ -4,16 +4,16 @@ - + %3 - + entity to phenotypic feature association - -entity to phenotypic feature association + +entity to phenotypic feature association @@ -24,8 +24,8 @@ entity to phenotypic feature association->association - - + + is_a @@ -37,7 +37,7 @@ entity to phenotypic feature association->id - + id @@ -50,7 +50,7 @@ entity to phenotypic feature association->iri - + iri @@ -63,8 +63,8 @@ entity to phenotypic feature association->name - - + + name @@ -76,8 +76,8 @@ entity to phenotypic feature association->description - - + + description @@ -89,8 +89,8 @@ entity to phenotypic feature association->has attribute - - + + has attribute @@ -102,8 +102,8 @@ entity to phenotypic feature association->subject - - + + subject @@ -115,8 +115,8 @@ entity to phenotypic feature association->predicate - - + + predicate @@ -128,7 +128,7 @@ entity to phenotypic feature association->object - + object @@ -141,9 +141,9 @@ entity to phenotypic feature association->negated - - -negated + + +negated @@ -154,9 +154,9 @@ entity to phenotypic feature association->qualifiers - - -qualifiers + + +qualifiers @@ -167,9 +167,9 @@ entity to phenotypic feature association->publications - - -publications + + +publications @@ -180,282 +180,282 @@ entity to phenotypic feature association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string entity to phenotypic feature association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string entity to phenotypic feature association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string entity to phenotypic feature association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type entity to phenotypic feature association->timepoint - - -timepoint + + +timepoint original subject - -string + +string entity to phenotypic feature association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie entity to phenotypic feature association->original predicate - - -original predicate + + +original predicate original object - -string + +string entity to phenotypic feature association->original object - - -original object + + +original object subject category - -ontology class + +ontology class entity to phenotypic feature association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class entity to phenotypic feature association->object category - - -object category + + +object category subject closure - -string + +string entity to phenotypic feature association->subject closure - - -subject closure + + +subject closure object closure - -string + +string entity to phenotypic feature association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class entity to phenotypic feature association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class entity to phenotypic feature association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string entity to phenotypic feature association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string entity to phenotypic feature association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string entity to phenotypic feature association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string entity to phenotypic feature association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source entity to phenotypic feature association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type entity to phenotypic feature association->type - - -type + + +type category - -category + +category entity to phenotypic feature association->category - - -category + + +category FDA approval status - -FDAApprovalStatusEnum + +FDAApprovalStatusEnum entity to phenotypic feature association->FDA approval status - - -FDA approval status + + +FDA approval status @@ -485,14 +485,14 @@ association_type - -string + +string association_category - -category type + +category type diff --git a/graphviz/exon_to_transcript_relationship.gv b/graphviz/exon_to_transcript_relationship.gv index ae2e88c490..31d04013bc 100644 --- a/graphviz/exon_to_transcript_relationship.gv +++ b/graphviz/exon_to_transcript_relationship.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4962.5,283"]; + graph [bb="0,0,4744.5,283"]; node [label="\N"]; "exon to transcript relationship" [height=0.5, label="exon to transcript relationship", - pos="2666.5,265", + pos="2448.5,265", width=4.2427]; "sequence feature relationship" [height=0.5, pos="149.49,178", width=4.1524]; "exon to transcript relationship" -> "sequence feature relationship" [label=is_a, - lp="455.49,221.5", - pos="e,219,194.01 2514.5,262.97 2046.5,259.59 646.03,248.01 441.49,229 368.99,222.26 287.38,207.69 228.91,196"]; + lp="454.49,221.5", + pos="e,218.76,193.97 2295.8,264.36 1891.6,264.82 799.88,262.81 440.49,229 368.24,222.2 286.91,207.63 228.64,195.97"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "exon to transcript relationship" -> id [color=blue, label=id, - lp="572.49,221.5", - pos="e,384.47,190 2514.3,263.09 2063.9,260.15 757.07,249.93 565.49,229 492.44,221.02 474.29,215.65 403.49,196 400.38,195.14 397.18,194.17 \ -393.98,193.16", + lp="570.49,221.5", + pos="e,384.47,189.98 2296.9,262.8 1879.5,259.26 733.25,247.92 563.49,229 491.33,220.96 473.43,215.5 403.49,196 400.38,195.13 397.18,194.17 \ +393.98,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "exon to transcript relationship" -> iri [color=blue, label=iri, - lp="689.49,221.5", - pos="e,489.39,190.23 2514.7,262.83 2081.9,259.28 861.47,247.71 681.49,229 604.07,220.95 584.91,215.26 509.49,196 506.11,195.14 502.63,\ -194.18 499.14,193.17", + lp="683.49,221.5", + pos="e,489.4,190.2 2295.7,264.45 1925.3,264.97 987.21,262.79 675.49,229 600.7,220.89 582.31,214.85 509.49,196 506.11,195.13 502.63,194.16 \ +499.15,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "exon to transcript relationship" -> name [color=blue, label=name, - lp="801.49,221.5", - pos="e,614.11,191.15 2514.5,263.04 2096.7,260.13 950.92,250.29 781.49,229 726.67,222.11 665.3,206.11 623.92,194.05", + lp="791.49,221.5", + pos="e,613.28,191.41 2296.8,262.81 1912.4,259.5 919.87,249.11 771.49,229 719.84,222 662.19,206.31 622.87,194.36", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "exon to transcript relationship" -> description [color=blue, label=description, - lp="929.99,221.5", - pos="e,762.9,193.65 2514.2,263.41 2113,261.5 1047.3,254.11 889.49,229 849.13,222.58 804.89,208.66 772.54,197.14", + lp="913.99,221.5", + pos="e,760.28,194.12 2296.3,263.24 1928.3,261.03 1010.8,253.13 873.49,229 837.61,222.69 798.64,209.24 769.7,197.88", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "exon to transcript relationship" -> "has attribute" [color=blue, label="has attribute", - lp="1087.5,221.5", - pos="e,904.07,191.75 2514.6,263.02 2138.4,260.26 1183.4,251.15 1040.5,229 996.35,222.16 947.61,207 913.67,195.15", + lp="1061.5,221.5", + pos="e,900.92,192.67 2296.7,262.95 1953.4,260.19 1137.8,251.35 1014.5,229 978.27,222.43 938.89,208.24 910.49,196.65", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "exon to transcript relationship" -> predicate [color=blue, label=predicate, - lp="1248.5,221.5", - pos="e,1061.9,193.09 2513.5,264.67 2193.3,265.37 1461.5,263.03 1214.5,229 1165.3,222.22 1110.6,207.65 1071.5,195.99", + lp="1205.5,221.5", + pos="e,1054.5,194.06 2297.3,262.3 1983.1,258.41 1279.6,247.73 1171.5,229 1134.3,222.56 1093.9,209.02 1063.9,197.66", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "exon to transcript relationship" -> negated [color=blue, label=negated, - lp="1394.5,221.5", - pos="e,1196.4,190.23 2514.2,263.55 2220,262.08 1583.4,255.81 1365.5,229 1309.6,222.13 1247,205.38 1206.1,193.16", + lp="1325.5,221.5", + pos="e,1189.7,192.51 2297.5,262.13 2007.4,258.15 1392,247.62 1296.5,229 1262.4,222.36 1225.6,208.2 1199,196.64", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "exon to transcript relationship" -> qualifiers [color=blue, label=qualifiers, - lp="1531,221.5", - pos="e,1345.7,193.02 2513.9,263.62 2243.2,262.24 1689,256.09 1497.5,229 1448.7,222.11 1394.6,207.65 1355.7,196.05", + lp="1429,221.5", + pos="e,1325.7,195.39 2296.7,262.78 2025.9,260.05 1479.9,251.76 1395.5,229 1373.8,223.15 1351.5,211.43 1334.2,200.81", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "exon to transcript relationship" -> publications [color=blue, label=publications, - lp="1673.5,221.5", - pos="e,1496,192.66 2513.9,263.57 2268,262.07 1795,255.69 1629.5,229 1586.6,222.09 1539.4,207.61 1505.6,196.01", + lp="1520.5,221.5", + pos="e,1460.5,196.26 2296.5,263.01 2031.2,260.66 1508.8,253 1476.5,229 1469.2,223.57 1465,214.84 1462.6,206.19", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,263 +110,264 @@ digraph { width=2.0943]; "exon to transcript relationship" -> "has evidence" [color=blue, label="has evidence", - lp="1827,221.5", - pos="e,1653.5,193.55 2514.7,262.66 2299.6,259.97 1917.1,252.01 1780.5,229 1740.1,222.2 1695.7,208.38 1663.2,196.99", + lp="1619,221.5", + pos="e,1587.9,194.93 2296.3,263.33 2052,261.49 1597.1,254.62 1572.5,229 1564.1,220.25 1570,210.18 1579.8,201.37", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1817.5,178", - width=3.015]; + label=string, + pos="1747.5,178", + width=1.0652]; "exon to transcript relationship" -> "knowledge source" [color=blue, label="knowledge source", - lp="1977,221.5", - pos="e,1842,195.78 2513.4,264.72 2326.4,264.24 2021.6,258.67 1912.5,229 1890.7,223.09 1868.3,211.61 1850.8,201.13", + lp="1737,221.5", + pos="e,1717.4,189.28 2297.2,262.48 2077.5,259.52 1693.7,251.19 1672.5,229 1667.9,224.18 1668.9,219.62 1672.5,214 1676.9,207.12 1692.1,\ +199.47 1707.7,193.08", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2052.5,178", - width=3.015]; + label=string, + pos="1842.5,178", + width=1.0652]; "exon to transcript relationship" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2146.5,221.5", - pos="e,2046.7,196 2518.3,260.62 2341.5,255.84 2067.3,245.77 2051.5,229 2045.7,222.9 2044.5,214.27 2045.1,205.9", + lp="1903.5,221.5", + pos="e,1822.2,193.48 2299.5,260.96 2115.6,256.46 1825.2,246.6 1808.5,229 1800.4,220.46 1805.9,209.82 1814.7,200.55", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2287.5,178", - width=3.015]; + label=string, + pos="1984.5,178", + width=1.0652]; "exon to transcript relationship" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2355,221.5", - pos="e,2261.7,195.53 2516.9,261.19 2404.5,257.49 2266.8,248.9 2248.5,229 2240.8,220.62 2245.7,210.86 2254.2,202.2", + lp="2124,221.5", + pos="e,1991,195.93 2305.6,258.58 2189.9,253.17 2042.1,243.55 2017.5,229 2008.1,223.44 2000.8,214.03 1995.6,204.86", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2469.5,178", + pos="2210.5,178", width=1.5346]; "exon to transcript relationship" -> timepoint [color=blue, label=timepoint, - lp="2506.5,221.5", - pos="e,2465.2,196.26 2543.5,254.29 2511.1,249.1 2482.1,241.16 2471.5,229 2466.1,222.83 2464.4,214.43 2464.4,206.27", + lp="2286.5,221.5", + pos="e,2220.1,196.09 2321.4,255 2297.1,249.59 2272.6,241.38 2251.5,229 2241.4,223.07 2232.7,213.64 2225.9,204.56", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2581.5,178", + pos="2322.5,178", width=1.0652]; "exon to transcript relationship" -> "original subject" [color=blue, label="original subject", - lp="2604.5,221.5", - pos="e,2561.4,193.75 2575.2,250.43 2564.8,245.28 2555.5,238.33 2548.5,229 2541.8,220.01 2546.6,209.73 2554.4,200.83", + lp="2388.5,221.5", + pos="e,2321.7,196.26 2363,250.04 2351.5,245 2340.8,238.19 2332.5,229 2326.9,222.83 2324,214.43 2322.7,206.27", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2695.5,178", + pos="2448.5,178", width=1.5887]; "exon to transcript relationship" -> "original predicate" [color=blue, label="original predicate", - lp="2731,221.5", - pos="e,2678.7,195.4 2664.1,246.84 2663.5,236.95 2663.7,224.45 2667.5,214 2668.8,210.42 2670.6,206.94 2672.7,203.64", + lp="2512,221.5", + pos="e,2448.5,196.18 2448.5,246.8 2448.5,235.16 2448.5,219.55 2448.5,206.24", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2809.5,178", + pos="2577.5,178", width=1.0652]; "exon to transcript relationship" -> "original object" [color=blue, label="original object", - lp="2856,221.5", - pos="e,2808.4,196.46 2759.6,250.71 2772.5,245.59 2784.7,238.57 2794.5,229 2800.6,223.04 2804.2,214.69 2806.4,206.52", + lp="2634,221.5", + pos="e,2581.9,195.99 2530.1,249.78 2551.2,244.38 2569.9,237.45 2576.5,229 2581.5,222.62 2582.9,214.26 2582.8,206.21", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2942.5,178", + pos="2710.5,178", width=2.1304]; "exon to transcript relationship" -> "subject category" [color=blue, label="subject category", - lp="2986,221.5", - pos="e,2936.3,196.16 2776.9,252.54 2836.3,245.61 2899.8,236.67 2911.5,229 2920.2,223.28 2927,214.13 2931.9,205.22", + lp="2761,221.5", + pos="e,2707.8,196.01 2560.6,252.75 2618.3,246.07 2678.8,237.3 2689.5,229 2696.9,223.28 2701.7,214.49 2704.8,205.86", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3113.5,178", + pos="2881.5,178", width=2.1304]; "exon to transcript relationship" -> "object category" [color=blue, label="object category", - lp="3131,221.5", - pos="e,3097.6,195.83 2774.9,252.27 2792.8,250.43 2811.2,248.61 2828.5,247 2877.5,242.43 3003.6,246.92 3049.5,229 3064.4,223.18 3078.7,\ -212.7 3089.9,202.83", + lp="2903,221.5", + pos="e,2867.4,196.05 2556.9,252.31 2574.8,250.47 2593.2,248.64 2610.5,247 2658,242.51 2780.6,247.67 2824.5,229 2838,223.25 2850.6,213.02 \ +2860.4,203.3", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3246.5,178", + pos="3014.5,178", width=1.0652]; "exon to transcript relationship" -> "subject closure" [color=blue, label="subject closure", - lp="3268,221.5", - pos="e,3233.7,195.25 2772.7,252.01 2791.3,250.15 2810.4,248.39 2828.5,247 2868.6,243.9 3153.2,244.28 3190.5,229 3204.3,223.32 3217,212.69 \ -3226.8,202.68", + lp="3039,221.5", + pos="e,3002.8,195.22 2554.7,252.03 2573.3,250.17 2592.4,248.41 2610.5,247 2649.5,243.96 2926.5,244.55 2962.5,229 2975.5,223.35 2987.3,\ +212.86 2996.2,202.95", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3346.5,178", + pos="3127.5,178", width=1.0652]; "exon to transcript relationship" -> "object closure" [color=blue, label="object closure", - lp="3388.5,221.5", - pos="e,3344.4,196.34 2771.8,251.89 2790.7,250.02 2810.2,248.29 2828.5,247 2856.1,245.05 3303.8,244.93 3326.5,229 3334.2,223.61 3338.9,\ -214.77 3341.8,206.01", + lp="3162.5,221.5", + pos="e,3122.1,196.05 2553.8,251.9 2572.7,250.03 2592.2,248.3 2610.5,247 2664.5,243.17 3050.9,256.54 3097.5,229 3106.5,223.65 3113.2,214.41 \ +3117.9,205.31", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3479.5,178", + pos="3260.5,178", width=2.1304]; "exon to transcript relationship" -> "subject category closure" [color=blue, label="subject category closure", - lp="3547,221.5", - pos="e,3471.8,196.18 2771.4,251.83 2790.4,249.96 2810,248.24 2828.5,247 2862.5,244.72 3412.2,244.8 3442.5,229 3452.6,223.69 3460.7,214.2 \ -3466.7,204.9", + lp="3323,221.5", + pos="e,3250.6,196.25 2553.4,251.83 2572.4,249.96 2592,248.24 2610.5,247 2644.1,244.74 3186,243.33 3216.5,229 3227.8,223.67 3237.4,213.91 \ +3244.8,204.41", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3671.5,178", + pos="3453.5,178", width=2.1304]; "exon to transcript relationship" -> "object category closure" [color=blue, label="object category closure", - lp="3738,221.5", - pos="e,3665.2,196.16 2770.5,251.8 2789.8,249.91 2809.7,248.19 2828.5,247 2873.4,244.15 3599.1,250.77 3638.5,229 3648,223.72 3655.3,214.36 \ -3660.6,205.15", + lp="3516,221.5", + pos="e,3445.2,196.23 2552.5,251.81 2571.8,249.91 2591.7,248.19 2610.5,247 2655.1,244.17 3374.6,249.05 3414.5,229 3424.9,223.76 3433.4,\ +214.27 3439.8,204.96", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3861.5,178", + pos="3643.5,178", width=1.0652]; "exon to transcript relationship" -> "subject namespace" [color=blue, label="subject namespace", - lp="3910.5,221.5", - pos="e,3854.4,195.72 2770.5,251.74 2789.8,249.85 2809.7,248.15 2828.5,247 2883.8,243.61 3776.4,254.7 3825.5,229 3835.7,223.66 3843.7,\ -213.97 3849.5,204.54", + lp="3689.5,221.5", + pos="e,3635.2,195.77 2552.5,251.74 2571.8,249.85 2591.7,248.15 2610.5,247 2665.6,243.62 3554,253.35 3603.5,229 3614.3,223.67 3623.2,213.84 \ +3629.8,204.31", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4020.5,178", + pos="3802.5,178", width=1.0652]; "exon to transcript relationship" -> "object namespace" [color=blue, label="object namespace", - lp="4064.5,221.5", - pos="e,4012.8,195.76 2770.1,251.74 2789.5,249.84 2809.6,248.14 2828.5,247 2860.5,245.08 3953.9,243.47 3982.5,229 3993,223.7 4001.3,214.03 \ -4007.5,204.59", + lp="3843.5,221.5", + pos="e,3793.9,195.79 2552.1,251.74 2571.5,249.84 2591.6,248.14 2610.5,247 2642.4,245.08 3732.7,242.9 3761.5,229 3772.5,223.69 3781.5,\ +213.88 3788.3,204.34", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4171.5,178", + pos="3953.5,178", width=1.0652]; "exon to transcript relationship" -> "subject label closure" [color=blue, label="subject label closure", - lp="4224.5,221.5", - pos="e,4163.5,195.78 2770.1,251.72 2789.5,249.82 2809.6,248.12 2828.5,247 2864.6,244.86 4100,245.12 4132.5,229 4143.2,223.67 4151.9,213.85 \ -4158.3,204.32", + lp="4005.5,221.5", + pos="e,3944.6,195.81 2552.1,251.72 2571.5,249.82 2591.6,248.12 2610.5,247 2646.6,244.86 3878.8,244.49 3911.5,229 3922.6,223.72 3931.9,\ +213.9 3938.8,204.36", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4342.5,178", + pos="4124.5,178", width=1.0652]; "exon to transcript relationship" -> "object label closure" [color=blue, label="object label closure", - lp="4390,221.5", - pos="e,4334.2,195.8 2770.1,251.69 2789.5,249.8 2809.6,248.11 2828.5,247 2869.4,244.61 4265.7,246.96 4302.5,229 4313.3,223.7 4322.2,213.88 \ -4328.8,204.34", + lp="4173,221.5", + pos="e,4115.9,195.81 2552.1,251.69 2571.5,249.8 2591.6,248.11 2610.5,247 2651.3,244.61 4046.6,246.73 4083.5,229 4094.5,223.71 4103.5,\ +213.9 4110.3,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4504.5,178", + pos="4286.5,178", width=2.347]; "exon to transcript relationship" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4553,221.5", - pos="e,4495.6,196.31 2769.6,251.72 2789.2,249.81 2809.4,248.1 2828.5,247 2873.8,244.38 4422.5,248.65 4463.5,229 4474.3,223.79 4483.3,\ -214.18 4490,204.77", + lp="4335,221.5", + pos="e,4277.9,196.29 2551.6,251.72 2571.2,249.81 2591.4,248.1 2610.5,247 2655.9,244.38 4205.6,248.91 4246.5,229 4257.2,223.78 4266,214.16 \ +4272.5,204.75", style=solid]; type [height=0.5, - pos="4638.5,178", + pos="4420.5,178", width=0.86659]; "exon to transcript relationship" -> type [color=blue, label=type, - lp="4652.5,221.5", - pos="e,4639.3,196.18 2769.6,251.7 2789.2,249.79 2809.4,248.09 2828.5,247 2853.4,245.57 4607,244.56 4626.5,229 4633.3,223.54 4636.7,214.93 \ -4638.2,206.37", + lp="4434.5,221.5", + pos="e,4421.3,196.18 2551.6,251.7 2571.2,249.79 2591.4,248.09 2610.5,247 2635.4,245.57 4389,244.56 4408.5,229 4415.3,223.54 4418.7,214.93 \ +4420.2,206.37", style=solid]; category [height=0.5, - pos="4739.5,178", + pos="4521.5,178", width=1.4263]; "exon to transcript relationship" -> category [color=blue, label=category, - lp="4733,221.5", - pos="e,4723.9,195.25 2769.6,251.7 2789.2,249.79 2809.4,248.09 2828.5,247 2879.6,244.07 4624,245.38 4672.5,229 4688.7,223.53 4704.2,212.51 \ -4716.2,202.2", + lp="4515,221.5", + pos="e,4505.9,195.25 2551.6,251.7 2571.2,249.79 2591.4,248.09 2610.5,247 2661.6,244.07 4406,245.38 4454.5,229 4470.7,223.53 4486.2,212.51 \ +4498.2,202.2", style=solid]; subject [height=0.5, - pos="4853.5,178", + pos="4635.5,178", width=1.2277]; "exon to transcript relationship" -> subject [color=blue, label=subject, - lp="4829.5,221.5", - pos="e,4834.2,194.33 2769.6,251.69 2789.2,249.78 2809.4,248.09 2828.5,247 2936.1,240.87 4664.6,257.8 4768.5,229 4789.2,223.25 4810.1,\ -211.09 4826,200.2", + lp="4611.5,221.5", + pos="e,4616.2,194.33 2551.6,251.69 2571.2,249.78 2591.4,248.09 2610.5,247 2718.1,240.87 4446.6,257.8 4550.5,229 4571.2,223.25 4592.1,\ +211.09 4608,200.2", style=solid]; object [height=0.5, - pos="4896.5,91", + pos="4678.5,91", width=1.0832]; "exon to transcript relationship" -> object [color=blue, label=object, - lp="4940.5,178", - pos="e,4909.9,108.09 2769.6,251.68 2789.2,249.78 2809.4,248.08 2828.5,247 2884.8,243.8 4805.8,246.24 4859.5,229 4883.8,221.2 4892.1,217.1 \ -4906.5,196 4920.4,175.59 4916.6,166.51 4919.5,142 4920.3,135.38 4921.4,133.39 4919.5,127 4918.5,123.55 4917,120.13 4915.2,116.85", + lp="4722.5,178", + pos="e,4691.9,108.09 2551.6,251.68 2571.2,249.78 2591.4,248.08 2610.5,247 2666.8,243.8 4587.8,246.24 4641.5,229 4665.8,221.2 4674.1,217.1 \ +4688.5,196 4702.4,175.59 4698.6,166.51 4701.5,142 4702.3,135.38 4703.4,133.39 4701.5,127 4700.5,123.55 4699,120.13 4697.2,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2875.5,265", + pos="2657.5,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3006.5,265", + pos="2788.5,265", width=2.0762]; subject -> object [label=relation, - lp="4891.5,134.5", - pos="e,4878.6,107.23 4854.6,159.55 4855.8,149.57 4858.3,137.07 4863.5,127 4865.7,122.68 4868.6,118.52 4871.8,114.66"]; + lp="4673.5,134.5", + pos="e,4660.6,107.23 4636.6,159.55 4637.8,149.57 4640.3,137.07 4645.5,127 4647.7,122.68 4650.6,118.52 4653.8,114.66"]; relation [height=0.5, - pos="4841.5,18", + pos="4623.5,18", width=1.2999]; - subject -> relation [pos="e,4842.8,36.188 4852.2,159.79 4850.1,132.48 4846,78.994 4843.6,46.38", + subject -> relation [pos="e,4624.8,36.188 4634.2,159.79 4632.1,132.48 4628,78.994 4625.6,46.38", style=dotted]; "exon to transcript relationship_subject" [color=blue, height=0.5, label=exon, - pos="3131.5,265", + pos="2913.5,265", width=0.9027]; - object -> relation [pos="e,4854.3,35.54 4884,73.889 4877.1,64.939 4868.3,53.617 4860.5,43.584", + object -> relation [pos="e,4636.3,35.54 4666,73.889 4659.1,64.939 4650.3,53.617 4642.5,43.584", style=dotted]; "exon to transcript relationship_object" [color=blue, height=0.5, label=transcript, - pos="3239.5,265", + pos="3021.5,265", width=1.5887]; } diff --git a/graphviz/exon_to_transcript_relationship.svg b/graphviz/exon_to_transcript_relationship.svg index e0e11ee383..c6cefd5550 100644 --- a/graphviz/exon_to_transcript_relationship.svg +++ b/graphviz/exon_to_transcript_relationship.svg @@ -4,16 +4,16 @@ - + %3 - + exon to transcript relationship - -exon to transcript relationship + +exon to transcript relationship @@ -24,9 +24,9 @@ exon to transcript relationship->sequence feature relationship - - -is_a + + +is_a @@ -37,9 +37,9 @@ exon to transcript relationship->id - - -id + + +id @@ -50,9 +50,9 @@ exon to transcript relationship->iri - - -iri + + +iri @@ -63,9 +63,9 @@ exon to transcript relationship->name - - -name + + +name @@ -76,9 +76,9 @@ exon to transcript relationship->description - - -description + + +description @@ -89,9 +89,9 @@ exon to transcript relationship->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ exon to transcript relationship->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ exon to transcript relationship->negated - - -negated + + +negated @@ -128,9 +128,9 @@ exon to transcript relationship->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ exon to transcript relationship->publications - - -publications + + +publications @@ -154,344 +154,344 @@ exon to transcript relationship->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string exon to transcript relationship->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string exon to transcript relationship->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string exon to transcript relationship->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type exon to transcript relationship->timepoint - - -timepoint + + +timepoint original subject - -string + +string exon to transcript relationship->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie exon to transcript relationship->original predicate - - -original predicate + + +original predicate original object - -string + +string exon to transcript relationship->original object - - -original object + + +original object subject category - -ontology class + +ontology class exon to transcript relationship->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class exon to transcript relationship->object category - - -object category + + +object category subject closure - -string + +string exon to transcript relationship->subject closure - - -subject closure + + +subject closure object closure - -string + +string exon to transcript relationship->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class exon to transcript relationship->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class exon to transcript relationship->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string exon to transcript relationship->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string exon to transcript relationship->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string exon to transcript relationship->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string exon to transcript relationship->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source exon to transcript relationship->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type exon to transcript relationship->type - - -type + + +type category - -category + +category exon to transcript relationship->category - - -category + + +category subject - -subject + +subject exon to transcript relationship->subject - - -subject + + +subject object - -object + +object exon to transcript relationship->object - - -object + + +object association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + exon to transcript relationship_subject - -exon + +exon object->relation - - + + exon to transcript relationship_object - -transcript + +transcript diff --git a/graphviz/exposure_event_to_outcome_association.gv b/graphviz/exposure_event_to_outcome_association.gv index 044f7363a7..79307fe932 100644 --- a/graphviz/exposure_event_to_outcome_association.gv +++ b/graphviz/exposure_event_to_outcome_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,5734.4,283"]; + graph [bb="0,0,5476.4,283"]; node [label="\N"]; "exposure event to outcome association" [height=0.5, label="exposure event to outcome association", - pos="2911.4,265", + pos="2653.4,265", width=5.3079]; association [height=0.5, pos="62.394,178", width=1.7332]; "exposure event to outcome association" -> association [label=is_a, lp="493.39,221.5", - pos="e,107.14,190.56 2720.8,263.25 2227,261 914.2,252.88 479.39,229 325.59,220.55 286.37,221.09 134.39,196 128.71,195.06 122.81,193.93 \ -116.94,192.7"]; + pos="e,107.14,190.56 2463.3,262.88 2007.6,259.87 862.41,250.37 479.39,229 325.6,220.42 286.37,221.09 134.39,196 128.71,195.06 122.81,\ +193.93 116.94,192.7"]; "entity to outcome association mixin" [height=0.5, pos="319.39,178", width=4.8926]; "exposure event to outcome association" -> "entity to outcome association mixin" [label=uses, lp="647.89,221.5", - pos="e,395.31,194.3 2720.2,264.6 2247.8,265.51 1034.5,264.21 631.39,229 554.52,222.29 467.92,207.85 405.5,196.21"]; + pos="e,395.31,194.25 2462.2,264.15 2028.9,263.92 982.88,260.05 631.39,229 554.53,222.21 467.93,207.79 405.51,196.17"]; id [color=blue, height=0.5, label=string, @@ -26,8 +26,8 @@ digraph { "exposure event to outcome association" -> id [color=blue, label=id, lp="766.39,221.5", - pos="e,580.38,189.98 2721.3,262.94 2231.5,259.93 950.96,250.12 759.39,229 687.22,221.04 669.34,215.5 599.39,196 596.29,195.13 593.09,\ -194.17 589.89,193.15", + pos="e,580.38,189.98 2464,262.49 2017.7,258.65 925.17,247.47 759.39,229 687.23,220.96 669.34,215.5 599.39,196 596.29,195.13 593.09,194.17 \ +589.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -37,7 +37,7 @@ digraph { "exposure event to outcome association" -> iri [color=blue, label=iri, lp="873.39,221.5", - pos="e,685.31,190.16 2721.7,262.77 2249.5,259.43 1046.4,249.03 865.39,229 793.23,221.01 775.62,214.45 705.39,196 702.02,195.11 698.55,\ + pos="e,685.31,190.16 2462.2,264.7 2066.6,265.42 1169.7,263.07 865.39,229 793.24,220.92 775.62,214.45 705.39,196 702.02,195.11 698.55,\ 194.14 695.06,193.12", style=solid]; name [color=blue, @@ -48,7 +48,7 @@ digraph { "exposure event to outcome association" -> name [color=blue, label=name, lp="977.39,221.5", - pos="e,808.25,191.78 2721,263.24 2263.6,261.02 1128.4,253.15 957.39,229 908.92,222.16 855.05,206.78 817.81,194.88", + pos="e,808.25,191.75 2463.7,262.67 2052.2,259.41 1102.9,249.74 957.39,229 908.93,222.09 855.06,206.73 817.82,194.84", style=solid]; description [color=blue, height=0.5, @@ -58,7 +58,7 @@ digraph { "exposure event to outcome association" -> description [color=blue, label=description, lp="1093.9,221.5", - pos="e,952.77,194.4 2720.4,264.1 2279,263.81 1213.5,259.86 1053.4,229 1021.7,222.89 987.7,209.84 962.13,198.6", + pos="e,952.78,194.37 2462.8,263.46 2068.4,261.8 1188.1,255.19 1053.4,229 1021.7,222.84 987.71,209.79 962.14,198.57", style=solid]; "has attribute" [color=blue, height=0.5, @@ -68,7 +68,7 @@ digraph { "exposure event to outcome association" -> "has attribute" [color=blue, label="has attribute", lp="1232.4,221.5", - pos="e,1092.9,193.55 2720.4,264.17 2302.4,263.96 1331.9,260.09 1185.4,229 1156.1,222.79 1125,209.44 1101.9,198.1", + pos="e,1092.9,193.52 2463.1,263.41 2094.1,261.69 1306.8,254.99 1185.4,229 1156.1,222.74 1125,209.39 1101.9,198.07", style=solid]; subject [color=blue, height=0.5, @@ -78,7 +78,7 @@ digraph { "exposure event to outcome association" -> subject [color=blue, label=subject, lp="1359.4,221.5", - pos="e,1236.5,194.37 2720.8,263.53 2330.5,262.01 1465.8,255.65 1333.4,229 1302.9,222.87 1270.4,209.91 1245.8,198.72", + pos="e,1236.5,194.33 2463.7,262.61 2124.9,259.6 1440.8,250.87 1333.4,229 1303,222.8 1270.4,209.84 1245.9,198.67", style=solid]; predicate [color=blue, height=0.5, @@ -88,7 +88,7 @@ digraph { "exposure event to outcome association" -> predicate [color=blue, label=predicate, lp="1438.4,221.5", - pos="e,1378.4,196.14 2720.1,264.31 2327.1,264.31 1460.7,260.67 1404.4,229 1395,223.7 1387.9,214.33 1382.8,205.13", + pos="e,1378.4,196.12 2463.1,263.32 2124.8,261.45 1449.5,254.54 1404.4,229 1395,223.67 1387.9,214.3 1382.8,205.11", style=solid]; object [color=blue, height=0.5, @@ -98,7 +98,7 @@ digraph { "exposure event to outcome association" -> object [color=blue, label=object, lp="1517.4,178", - pos="e,1346,105.47 2724.3,261.32 2437.7,256.74 1902.9,246.21 1712.4,229 1615.2,220.23 1582.5,240.02 1495.4,196 1475.2,185.79 1478.1,172.77 \ + pos="e,1346,105.47 2465.8,261.48 2219.5,257.48 1800.2,248.09 1647.4,229 1578.8,220.43 1556.1,229.12 1495.4,196 1475.5,185.16 1478.1,172.77 \ 1459.4,160 1427.3,138.07 1387,120.64 1355.5,108.92", style=solid]; negated [color=blue, @@ -108,8 +108,8 @@ digraph { width=1.2999]; "exposure event to outcome association" -> negated [color=blue, label=negated, - lp="1822.4,221.5", - pos="e,1630,190.39 2722.1,262.55 2451.4,259.7 1967.1,251.55 1793.4,229 1739.6,222.02 1679.4,205.52 1639.6,193.37", + lp="1717.4,221.5", + pos="e,1616.7,194.16 2465.3,261.76 2205.6,257.96 1761,248.67 1688.4,229 1665.9,222.91 1642.9,210.58 1625.4,199.68", style=solid]; qualifiers [color=blue, height=0.5, @@ -118,8 +118,8 @@ digraph { width=2.1304]; "exposure event to outcome association" -> qualifiers [color=blue, label=qualifiers, - lp="1955.9,221.5", - pos="e,1778.3,193.2 2722.2,262.41 2479.2,259.49 2071.2,251.33 1922.4,229 1876.1,222.05 1824.8,207.75 1787.8,196.22", + lp="1796.9,221.5", + pos="e,1740.8,195.99 2466.1,261.34 2213.8,257.07 1792.7,247.25 1763.4,229 1754.8,223.63 1748.7,214.51 1744.6,205.52", style=solid]; publications [color=blue, height=0.5, @@ -128,8 +128,8 @@ digraph { width=1.7332]; "exposure event to outcome association" -> publications [color=blue, label=publications, - lp="2093.4,221.5", - pos="e,1928,193.08 2722.1,262.25 2508.3,259.23 2173.7,251.03 2049.4,229 2010.7,222.15 1968.4,208.15 1937.6,196.7", + lp="1882.4,221.5", + pos="e,1860.5,193.31 2464.2,262.39 2230.1,259.45 1859.7,251.29 1838.4,229 1828.3,218.5 1837.8,207.57 1851.5,198.61", style=solid]; "has evidence" [color=blue, height=0.5, @@ -138,239 +138,242 @@ digraph { width=2.0943]; "exposure event to outcome association" -> "has evidence" [color=blue, label="has evidence", - lp="2239.9,221.5", - pos="e,2083.8,194.09 2725.1,260.93 2547,256.91 2291.3,247.98 2193.4,229 2158.9,222.31 2121.4,209.1 2093.3,197.94", + lp="1979.9,221.5", + pos="e,1991.7,189.71 2466.3,261.24 2259.1,257.25 1951.6,248.13 1933.4,229 1928.8,224.17 1929.4,219.35 1933.4,214 1939.9,205.25 1960.2,\ +197.84 1982,192.13", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2251.4,178", - width=3.015]; + label=string, + pos="2181.4,178", + width=1.0652]; "exposure event to outcome association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2378.9,221.5", - pos="e,2267,195.95 2731.2,258.92 2569.8,253.47 2352.6,243.58 2314.4,229 2299.6,223.35 2285.5,212.89 2274.5,202.99", + lp="2110.9,221.5", + pos="e,2152.4,189.98 2471.1,259.51 2297.7,254.32 2061,244.46 2046.4,229 2000.8,180.74 1986.1,237.12 2133.4,196 2136.5,195.13 2139.7,194.17 \ +2142.9,193.15", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2486.4,178", - width=3.015]; + label=string, + pos="2276.4,178", + width=1.0652]; "exposure event to outcome association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2545.4,221.5", - pos="e,2462.2,195.77 2723.7,261.61 2604.6,258.08 2469.4,249.53 2450.4,229 2443,220.97 2447.2,211.37 2455,202.74", + lp="2277.4,221.5", + pos="e,2246.8,189.56 2464.9,261.96 2342.4,258.62 2202,250.14 2182.4,229 2177.9,224.11 2178.6,219.48 2182.4,214 2183.3,212.74 2211.9,202.19 \ +2237.3,193", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2721.4,178", - width=3.015]; + label=string, + pos="2371.4,178", + width=1.0652]; "exposure event to outcome association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2754.9,221.5", - pos="e,2672.2,194.17 2735.1,257.95 2695.6,252.79 2661.5,243.94 2648.4,229 2638,217.1 2647.7,206.69 2663.1,198.49", + lp="2491.9,221.5", + pos="e,2371.6,196.37 2483.7,256.63 2440.5,251.53 2401.6,243.06 2385.4,229 2378.8,223.29 2375.2,214.77 2373.3,206.36", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2903.4,178", + pos="2597.4,178", width=1.5346]; "exposure event to outcome association" -> timepoint [color=blue, label=timepoint, - lp="2901.4,221.5", - pos="e,2880.6,194.47 2881.8,247.2 2875.6,242.2 2869.9,236.11 2866.4,229 2861.7,219.42 2866.1,209.79 2873.4,201.57", + lp="2643.4,221.5", + pos="e,2598.3,196.31 2625.3,246.98 2618.9,241.92 2612.7,235.86 2608.4,229 2604.2,222.28 2601.5,214.16 2599.9,206.44", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="3015.4,178", + pos="2709.4,178", width=1.0652]; "exposure event to outcome association" -> "original subject" [color=blue, label="original subject", - lp="3015.4,221.5", - pos="e,2991.4,192.24 2926,246.75 2935.1,236.6 2947.3,223.86 2959.4,214 2966.6,208.17 2974.8,202.54 2982.7,197.56", + lp="2744.4,221.5", + pos="e,2699.3,195.84 2666.1,246.71 2670.1,241.11 2674.5,234.84 2678.4,229 2683.7,221.09 2689.2,212.33 2694.1,204.38", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3129.4,178", + pos="2835.4,178", width=1.5887]; "exposure event to outcome association" -> "original predicate" [color=blue, label="original predicate", - lp="3157.9,221.5", - pos="e,3114.2,195.85 3013,249.72 3033,244.74 3053.3,238.02 3071.4,229 3084.5,222.46 3097,212.32 3107.1,202.87", + lp="2882.9,221.5", + pos="e,2828.8,196.33 2761.5,250.02 2776.8,244.98 2791.6,238.17 2804.4,229 2812.7,223.06 2819.2,214.14 2824.1,205.48", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3243.4,178", + pos="2969.4,178", width=1.0652]; "exposure event to outcome association" -> "original object" [color=blue, label="original object", - lp="3285.9,221.5", - pos="e,3240.4,196.13 3044.4,251.99 3125,244.2 3213.9,234.52 3221.4,229 3229.1,223.36 3234.1,214.47 3237.4,205.74", + lp="3013.9,221.5", + pos="e,2967.4,196.05 2783,251.76 2859.7,244 2943.4,234.44 2950.4,229 2957.7,223.33 2962.1,214.55 2964.9,205.92", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3376.4,178", + pos="3102.4,178", width=2.1304]; "exposure event to outcome association" -> "subject category" [color=blue, label="subject category", - lp="3416.9,221.5", - pos="e,3369.3,195.96 3047.2,252.33 3068.7,250.52 3090.6,248.69 3111.4,247 3162.5,242.83 3296.9,254.43 3341.4,229 3351.1,223.48 3358.7,\ -214.08 3364.3,204.9", + lp="3144.9,221.5", + pos="e,3095.7,196.41 2789.8,252.38 2811.1,250.57 2832.8,248.73 2853.4,247 2901.4,242.96 3028,253.57 3069.4,229 3078.6,223.57 3085.7,214.48 \ +3090.9,205.53", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3547.4,178", + pos="3273.4,178", width=2.1304]; "exposure event to outcome association" -> "object category" [color=blue, label="object category", - lp="3562.9,221.5", - pos="e,3530.9,195.77 3044.2,252.04 3066.6,250.21 3089.7,248.45 3111.4,247 3193.3,241.52 3403.1,256.76 3480.4,229 3496.2,223.34 3511.3,\ -212.62 3523.2,202.56", + lp="3289.9,221.5", + pos="e,3257.5,195.75 2786.5,252.05 2808.8,250.23 2831.8,248.47 2853.4,247 2932.2,241.65 3134.3,256.32 3208.4,229 3223.8,223.32 3238.5,\ +212.6 3250.1,202.54", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3680.4,178", + pos="3406.4,178", width=1.0652]; "exposure event to outcome association" -> "subject closure" [color=blue, label="subject closure", - lp="3698.9,221.5", - pos="e,3664.6,194.71 3042.8,251.89 3065.7,250.06 3089.2,248.33 3111.4,247 3168.1,243.59 3569.5,249.72 3622.4,229 3630.3,225.91 3644.7,\ -213.49 3657.2,201.8", + lp="3428.9,221.5", + pos="e,3393.3,195.32 2784.8,251.91 2807.7,250.07 2831.2,248.34 2853.4,247 2908.4,243.66 3298.1,249.36 3349.4,229 3363.4,223.42 3376.3,\ +212.8 3386.3,202.77", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3776.4,178", + pos="3514.4,178", width=1.0652]; "exposure event to outcome association" -> "object closure" [color=blue, label="object closure", - lp="3818.4,221.5", - pos="e,3774,196.4 3042,251.82 3065.1,249.97 3089,248.27 3111.4,247 3147.1,244.98 3725.9,249.23 3755.4,229 3763.2,223.67 3768.1,214.84 \ -3771.2,206.08", + lp="3551.4,221.5", + pos="e,3510,196.03 2784,251.83 2807.1,249.98 2831,248.27 2853.4,247 2888.6,245.01 3457.4,247.48 3487.4,229 3496,223.68 3502.1,214.57 \ +3506.2,205.57", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3909.4,178", + pos="3647.4,178", width=2.1304]; "exposure event to outcome association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3976.9,221.5", - pos="e,3901.8,196.21 3041.5,251.78 3064.8,249.93 3088.8,248.23 3111.4,247 3153.6,244.71 3834.9,248.48 3872.4,229 3882.6,223.72 3890.7,\ -214.23 3896.7,204.93", + lp="3711.9,221.5", + pos="e,3638.2,196.26 2783.5,251.79 2806.8,249.93 2830.8,248.23 2853.4,247 2895.1,244.73 3567.7,247.1 3605.4,229 3616.3,223.74 3625.5,\ +214.11 3632.4,204.71", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="4098.4,178", + pos="3840.4,178", width=2.1304]; "exposure event to outcome association" -> "object category closure" [color=blue, label="object category closure", - lp="4166.9,221.5", - pos="e,4093.1,196.12 3040.9,251.73 3064.4,249.87 3088.6,248.18 3111.4,247 3137.9,245.62 4045.4,242.32 4068.4,229 4077.5,223.73 4084.2,\ -214.5 4088.8,205.4", + lp="3903.9,221.5", + pos="e,3832.8,196.22 2782.9,251.74 2806.4,249.87 2830.6,248.18 2853.4,247 2906.1,244.26 3756.5,253.2 3803.4,229 3813.6,223.75 3821.7,\ +214.26 3827.7,204.95", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4288.4,178", + pos="4030.4,178", width=1.0652]; "exposure event to outcome association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4338.4,221.5", - pos="e,4281.7,196.2 3040.4,251.72 3064,249.85 3088.4,248.16 3111.4,247 3143.1,245.4 4226.4,244.08 4254.4,229 4264.1,223.77 4271.6,214.42 \ -4277,205.2", + lp="4077.4,221.5", + pos="e,4022.4,195.77 2782.4,251.72 2806,249.85 2830.4,248.16 2853.4,247 2885,245.41 3963.1,243.09 3991.4,229 4002.1,223.66 4010.8,213.84 \ +4017.2,204.31", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4447.4,178", + pos="4189.4,178", width=1.0652]; "exposure event to outcome association" -> "object namespace" [color=blue, label="object namespace", - lp="4491.4,221.5", - pos="e,4440,195.75 3040.4,251.68 3064,249.81 3088.4,248.13 3111.4,247 3147.4,245.22 4378.3,245.47 4410.4,229 4420.7,223.7 4428.9,214.02 \ -4434.9,204.58", + lp="4231.4,221.5", + pos="e,4181.1,195.79 2782.4,251.68 2806,249.81 2830.4,248.13 2853.4,247 2889.4,245.22 4117.1,244.82 4149.4,229 4160.3,223.69 4169.1,213.87 \ +4175.7,204.33", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4598.4,178", + pos="4340.4,178", width=1.0652]; "exposure event to outcome association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4651.4,221.5", - pos="e,4590.4,195.78 3040.1,251.68 3063.8,249.8 3088.3,248.12 3111.4,247 3151.6,245.05 4523.4,246.87 4559.4,229 4570.1,223.68 4578.8,\ -213.86 4585.2,204.33", + lp="4393.4,221.5", + pos="e,4331.8,195.81 2782.1,251.68 2805.8,249.8 2830.3,248.12 2853.4,247 2893.5,245.05 4263.2,246.41 4299.4,229 4310.4,223.71 4319.4,\ +213.9 4326.2,204.35", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4769.4,178", + pos="4511.4,178", width=1.0652]; "exposure event to outcome association" -> "object label closure" [color=blue, label="object label closure", - lp="4817.9,221.5", - pos="e,4761.1,195.8 3039.9,251.67 3063.6,249.79 3088.2,248.11 3111.4,247 3156.3,244.85 4689,248.7 4729.4,229 4740.3,223.7 4749.1,213.89 \ -4755.7,204.35", + lp="4559.9,221.5", + pos="e,4503.1,195.8 2781.9,251.67 2805.6,249.79 2830.2,248.11 2853.4,247 2898.3,244.85 4431,248.7 4471.4,229 4482.3,223.7 4491.1,213.89 \ +4497.7,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4931.4,178", + pos="4673.4,178", width=2.347]; "exposure event to outcome association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4979.9,221.5", - pos="e,4922.8,196.3 3039.9,251.65 3063.6,249.77 3088.2,248.1 3111.4,247 3160.8,244.65 4846.9,250.64 4891.4,229 4902.1,223.78 4910.9,214.17 \ -4917.4,204.76", + lp="4721.9,221.5", + pos="e,4664.8,196.3 2781.9,251.65 2805.6,249.77 2830.2,248.1 2853.4,247 2902.8,244.65 4588.9,250.64 4633.4,229 4644.1,223.78 4652.9,214.17 \ +4659.4,204.76", style=solid]; type [height=0.5, - pos="5065.4,178", + pos="4807.4,178", width=0.86659]; "exposure event to outcome association" -> type [color=blue, label=type, - lp="5079.4,221.5", - pos="e,5066.2,196.19 3039.9,251.64 3063.6,249.76 3088.2,248.09 3111.4,247 3138.3,245.73 5032.3,245.8 5053.4,229 5060.2,223.55 5063.6,\ -214.93 5065.2,206.37", + lp="4821.4,221.5", + pos="e,4808.2,196.19 2781.9,251.64 2805.6,249.76 2830.2,248.09 2853.4,247 2880.3,245.73 4774.3,245.8 4795.4,229 4802.2,223.55 4805.6,\ +214.93 4807.2,206.37", style=solid]; category [height=0.5, - pos="5166.4,178", + pos="4908.4,178", width=1.4263]; "exposure event to outcome association" -> category [color=blue, label=category, - lp="5159.9,221.5", - pos="e,5150.8,195.26 3039.9,251.63 3063.6,249.76 3088.2,248.09 3111.4,247 3166.6,244.41 5047.1,246.64 5099.4,229 5115.6,223.54 5131.1,\ -212.51 5143.1,202.2", + lp="4901.9,221.5", + pos="e,4892.8,195.26 2781.9,251.63 2805.6,249.76 2830.2,248.09 2853.4,247 2908.6,244.41 4789.1,246.64 4841.4,229 4857.6,223.54 4873.1,\ +212.51 4885.1,202.2", style=solid]; "population context qualifier" [color=blue, height=0.5, label="population of individual organisms", - pos="5407.4,178", + pos="5149.4,178", width=4.7662]; "exposure event to outcome association" -> "population context qualifier" [color=blue, label="population context qualifier", - lp="5377.4,221.5", - pos="e,5353.5,195.22 3039.6,251.65 3063.4,249.76 3088.2,248.09 3111.4,247 3342.7,236.19 4965.5,256.75 5195.4,229 5246,222.9 5302,209.37 \ -5343.8,197.93", + lp="5119.4,221.5", + pos="e,5095.5,195.22 2781.6,251.65 2805.4,249.76 2830.2,248.09 2853.4,247 3084.7,236.19 4707.5,256.75 4937.4,229 4988,222.9 5044,209.37 \ +5085.8,197.93", style=solid]; "temporal context qualifier" [color=blue, height=0.5, label="time type", - pos="5652.4,178", + pos="5394.4,178", width=1.5346]; "exposure event to outcome association" -> "temporal context qualifier" [color=blue, label="temporal context qualifier", - lp="5640.9,221.5", - pos="e,5617.8,192.13 3039.6,251.63 3063.4,249.74 3088.2,248.07 3111.4,247 3242.9,240.92 5350.2,248.05 5480.4,229 5524.8,222.51 5573.8,\ -207.45 5608.1,195.55", + lp="5382.9,221.5", + pos="e,5359.8,192.13 2781.6,251.63 2805.4,249.74 2830.2,248.07 2853.4,247 2984.9,240.92 5092.2,248.05 5222.4,229 5266.8,222.51 5315.8,\ +207.45 5350.1,195.55", style=solid]; subject -> object [label=relation, lp="1289.4,134.5", @@ -385,11 +388,11 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="3158.4,265", + pos="2900.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3289.4,265", + pos="3031.4,265", width=2.0762]; } diff --git a/graphviz/exposure_event_to_outcome_association.svg b/graphviz/exposure_event_to_outcome_association.svg index c431af7d59..6a37d98ea5 100644 --- a/graphviz/exposure_event_to_outcome_association.svg +++ b/graphviz/exposure_event_to_outcome_association.svg @@ -4,16 +4,16 @@ - + %3 - + exposure event to outcome association - -exposure event to outcome association + +exposure event to outcome association @@ -24,7 +24,7 @@ exposure event to outcome association->association - + is_a @@ -37,8 +37,8 @@ exposure event to outcome association->entity to outcome association mixin - - + + uses @@ -50,7 +50,7 @@ exposure event to outcome association->id - + id @@ -63,7 +63,7 @@ exposure event to outcome association->iri - + iri @@ -76,8 +76,8 @@ exposure event to outcome association->name - - + + name @@ -89,8 +89,8 @@ exposure event to outcome association->description - - + + description @@ -102,8 +102,8 @@ exposure event to outcome association->has attribute - - + + has attribute @@ -115,8 +115,8 @@ exposure event to outcome association->subject - - + + subject @@ -128,8 +128,8 @@ exposure event to outcome association->predicate - - + + predicate @@ -141,7 +141,7 @@ exposure event to outcome association->object - + object @@ -154,9 +154,9 @@ exposure event to outcome association->negated - - -negated + + +negated @@ -167,9 +167,9 @@ exposure event to outcome association->qualifiers - - -qualifiers + + +qualifiers @@ -180,9 +180,9 @@ exposure event to outcome association->publications - - -publications + + +publications @@ -193,295 +193,295 @@ exposure event to outcome association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string exposure event to outcome association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string exposure event to outcome association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string exposure event to outcome association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type exposure event to outcome association->timepoint - - -timepoint + + +timepoint original subject - -string + +string exposure event to outcome association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie exposure event to outcome association->original predicate - - -original predicate + + +original predicate original object - -string + +string exposure event to outcome association->original object - - -original object + + +original object subject category - -ontology class + +ontology class exposure event to outcome association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class exposure event to outcome association->object category - - -object category + + +object category subject closure - -string + +string exposure event to outcome association->subject closure - - -subject closure + + +subject closure object closure - -string + +string exposure event to outcome association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class exposure event to outcome association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class exposure event to outcome association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string exposure event to outcome association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string exposure event to outcome association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string exposure event to outcome association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string exposure event to outcome association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source exposure event to outcome association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type exposure event to outcome association->type - - -type + + +type category - -category + +category exposure event to outcome association->category - - -category + + +category population context qualifier - -population of individual organisms + +population of individual organisms exposure event to outcome association->population context qualifier - - -population context qualifier + + +population context qualifier temporal context qualifier - -time type + +time type exposure event to outcome association->temporal context qualifier - - -temporal context qualifier + + +temporal context qualifier @@ -511,14 +511,14 @@ association_type - -string + +string association_category - -category type + +category type diff --git a/graphviz/exposure_event_to_phenotypic_feature_association.gv b/graphviz/exposure_event_to_phenotypic_feature_association.gv index 59958e173d..d604e0e30e 100644 --- a/graphviz/exposure_event_to_phenotypic_feature_association.gv +++ b/graphviz/exposure_event_to_phenotypic_feature_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,6258.4,283"]; + graph [bb="0,0,6000.4,283"]; node [label="\N"]; "exposure event to phenotypic feature association" [height=0.5, label="exposure event to phenotypic feature association", - pos="3379.4,265", + pos="3121.4,265", width=6.6439]; association [height=0.5, pos="62.394,178", width=1.7332]; "exposure event to phenotypic feature association" -> association [label=is_a, lp="570.39,221.5", - pos="e,107.12,190.68 3141.5,263.06 2556,260.43 1056.5,251.63 556.39,229 368.46,220.5 320.27,225.03 134.39,196 128.7,195.11 122.8,194.01 \ + pos="e,107.12,190.68 2884.1,262.72 2338,259.45 1004.9,249.57 556.39,229 368.46,220.38 320.27,225.03 134.39,196 128.7,195.11 122.8,194.01 \ 116.93,192.8"]; "entity to phenotypic feature association mixin" [height=0.5, pos="367.39,178", width=6.2286]; "exposure event to phenotypic feature association" -> "entity to phenotypic feature association mixin" [label=uses, lp="743.89,221.5", - pos="e,456.57,194.54 3140.2,264.67 2579.4,265.62 1192,264.19 727.39,229 638.76,222.29 538.66,207.82 466.55,196.17"]; + pos="e,456.94,194.57 2882,264.26 2361.5,264.2 1140.4,260.58 727.39,229 638.91,222.23 539,207.81 466.92,196.19"]; id [color=blue, height=0.5, label=string, @@ -26,8 +26,8 @@ digraph { "exposure event to phenotypic feature association" -> id [color=blue, label=id, lp="861.39,221.5", - pos="e,677.38,189.97 3141.3,263.31 2555.8,261.23 1077.2,253.58 854.39,229 783.09,221.13 765.47,215.35 696.39,196 693.29,195.13 690.09,\ -194.16 686.89,193.14", + pos="e,677.38,189.97 2883.7,262.89 2342.8,260.01 1051.5,250.9 854.39,229 783.1,221.08 765.47,215.35 696.39,196 693.29,195.13 690.09,194.16 \ +686.89,193.14", style=solid]; iri [color=blue, height=0.5, @@ -37,7 +37,7 @@ digraph { "exposure event to phenotypic feature association" -> iri [color=blue, label=iri, lp="958.39,221.5", - pos="e,782.7,190.05 3141.2,263.34 2571.8,261.38 1163.4,254.02 950.39,229 894.92,222.49 832.76,205.47 792.46,193.09", + pos="e,782.7,190.04 2883.5,262.89 2359.6,260.07 1137.7,251.16 950.39,229 894.92,222.44 832.77,205.43 792.46,193.07", style=solid]; name [color=blue, height=0.5, @@ -47,7 +47,7 @@ digraph { "exposure event to phenotypic feature association" -> name [color=blue, label=name, lp="1054.4,221.5", - pos="e,902.72,192.4 3140.4,264.19 2584.7,264.09 1237.9,260.54 1034.4,229 992.08,222.44 945.52,207.73 912.51,195.95", + pos="e,902.72,192.38 2882.6,263.7 2373.4,262.51 1212.4,256.76 1034.4,229 992.08,222.4 945.53,207.69 912.51,195.93", style=solid]; description [color=blue, height=0.5, @@ -57,7 +57,7 @@ digraph { "exposure event to phenotypic feature association" -> description [color=blue, label=description, lp="1157.9,221.5", - pos="e,1042.8,195.28 3141.4,263.19 2580.2,260.88 1214.2,252.85 1117.4,229 1094.1,223.26 1070,211.26 1051.5,200.46", + pos="e,1042.8,195.27 2883.9,262.68 2371.6,259.46 1201.6,249.84 1117.4,229 1094.1,223.24 1070,211.24 1051.5,200.44", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,7 +67,7 @@ digraph { "exposure event to phenotypic feature association" -> "has attribute" [color=blue, label="has attribute", lp="1277.4,221.5", - pos="e,1179,195.22 3140.5,264.04 2599.3,263.6 1319.3,259.33 1230.4,229 1214.2,223.48 1198.7,212.45 1186.7,202.15", + pos="e,1179,195.2 2882.8,263.47 2391.6,261.83 1307.1,255.26 1230.4,229 1214.2,223.46 1198.7,212.43 1186.7,202.14", style=solid]; predicate [color=blue, height=0.5, @@ -77,18 +77,18 @@ digraph { "exposure event to phenotypic feature association" -> predicate [color=blue, label=predicate, lp="1377.4,221.5", - pos="e,1317.4,196.16 3141.7,262.84 2612.9,259.86 1382.1,250.63 1343.4,229 1333.9,223.72 1326.9,214.36 1321.8,205.16", + pos="e,1317.4,196.15 2884.6,262.22 2408.3,258.25 1376.5,247.55 1343.4,229 1334,223.71 1326.9,214.35 1321.8,205.15", style=solid]; object [color=blue, height=0.5, label="named thing", - pos="5049.4,91", + pos="4791.4,91", width=1.9318]; "exposure event to phenotypic feature association" -> object [color=blue, label=object, lp="1456.4,178", - pos="e,4979.7,91.969 3141.2,263.07 2736.7,260.85 1931.6,253.4 1649.4,229 1549.4,220.35 1364.1,231.63 1434.4,160 1498.5,94.718 4444.1,\ -91.943 4969.6,91.968", + pos="e,4721.8,92.072 2882.6,263.7 2517.6,262.37 1838,256.16 1596.4,229 1518.6,220.26 1379.6,215.89 1434.4,160 1493.6,99.558 4209,92.817 \ +4711.8,92.086", style=solid]; negated [color=blue, height=0.5, @@ -97,8 +97,8 @@ digraph { width=1.2999]; "exposure event to phenotypic feature association" -> negated [color=blue, label=negated, - lp="1757.4,221.5", - pos="e,1568.2,190.48 3143.7,261.77 2720.9,257.36 1864.5,246.4 1728.4,229 1675.8,222.28 1617.1,205.84 1578.2,193.64", + lp="1672.4,221.5", + pos="e,1558.5,193.53 2882.6,263.63 2495.1,262.23 1760.3,255.99 1643.4,229 1616.5,222.8 1588.3,209.64 1567.3,198.37", style=solid]; qualifiers [color=blue, height=0.5, @@ -107,8 +107,8 @@ digraph { width=2.1304]; "exposure event to phenotypic feature association" -> qualifiers [color=blue, label=qualifiers, - lp="1896.9,221.5", - pos="e,1717.4,193.23 3144.4,261.63 2750.1,257.2 1986.2,246.5 1863.4,229 1816.4,222.31 1764.4,207.91 1727,196.28", + lp="1760.9,221.5", + pos="e,1687.4,195.84 2884.3,262.5 2500.3,259.44 1779.7,250.81 1727.4,229 1714.4,223.59 1702.9,213.34 1693.9,203.52", style=solid]; publications [color=blue, height=0.5, @@ -117,8 +117,8 @@ digraph { width=1.7332]; "exposure event to phenotypic feature association" -> publications [color=blue, label=publications, - lp="2042.4,221.5", - pos="e,1868.3,192.88 3144.5,261.46 2779.9,257.01 2107.9,246.55 1998.4,229 1956.8,222.33 1911,208 1878.1,196.38", + lp="1846.4,221.5", + pos="e,1812.5,195.16 2885.5,261.88 2511.2,257.94 1821,248.11 1802.4,229 1795,221.37 1798.7,211.57 1805.7,202.67", style=solid]; "has evidence" [color=blue, height=0.5, @@ -127,333 +127,335 @@ digraph { width=2.0943]; "exposure event to phenotypic feature association" -> "has evidence" [color=blue, label="has evidence", - lp="2201.9,221.5", - pos="e,2026.5,193.55 3140.3,264.58 2838.9,264.03 2338.2,258.45 2155.4,229 2114.4,222.39 2069.3,208.49 2036.4,197.02", + lp="1945.9,221.5", + pos="e,1935.1,190.83 2887,261.37 2536.9,256.87 1916.4,246.46 1899.4,229 1885,214.14 1902.3,202.43 1925.3,194.08", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2190.4,178", - width=3.015]; + label=string, + pos="2120.4,178", + width=1.0652]; "exposure event to phenotypic feature association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2357.9,221.5", - pos="e,2216.8,195.64 3144.2,261.62 2849.5,257.84 2373.3,248.74 2293.4,229 2269.6,223.12 2244.8,211.28 2225.5,200.6", + lp="2063.9,221.5", + pos="e,2091.4,189.8 2882.1,264.9 2561.7,264.91 2029.6,260.18 1999.4,229 1994.8,224.21 1995.3,219.25 1999.4,214 2020,187.69 2040.4,205.59 \ +2072.4,196 2075.5,195.07 2078.7,194.07 2081.9,193.02", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2425.4,178", - width=3.015]; + label=string, + pos="2215.4,178", + width=1.0652]; "exposure event to phenotypic feature association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2529.4,221.5", - pos="e,2423.5,196.48 3142.1,262.57 2870.9,259.84 2460.8,251.93 2434.4,229 2428,223.41 2425.1,214.91 2424,206.5", + lp="2230.4,221.5", + pos="e,2186.3,189.93 2882.7,263.74 2599.2,262.22 2161,255.56 2135.4,229 2130.8,224.2 2131.7,219.58 2135.4,214 2138,209.97 2157.8,201.3 \ +2177,193.6", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2660.4,178", - width=3.015]; + label=string, + pos="2310.4,178", + width=1.0652]; "exposure event to phenotypic feature association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2738.9,221.5", - pos="e,2640.7,196.14 3146.9,260.78 2934.3,256.66 2650.2,247.68 2632.4,229 2625.5,221.8 2628.3,212.59 2634.2,204.05", + lp="2451.9,221.5", + pos="e,2317.4,196.09 2882.6,263.77 2672,261.85 2391.7,254.45 2345.4,229 2335.6,223.64 2328,214.27 2322.4,205.07", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2842.4,178", + pos="2536.4,178", width=1.5346]; "exposure event to phenotypic feature association" -> timepoint [color=blue, label=timepoint, - lp="2895.4,221.5", - pos="e,2843.9,196.19 3149.5,259.98 3021.9,255.73 2884.2,246.98 2860.4,229 2853.1,223.49 2848.7,214.74 2846.2,206.1", + lp="2615.4,221.5", + pos="e,2546.4,196.1 2902.2,257.72 2765.3,252.43 2609.6,243.36 2580.4,229 2569.2,223.48 2559.6,213.68 2552.2,204.21", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2954.4,178", + pos="2648.4,178", width=1.0652]; "exposure event to phenotypic feature association" -> "original subject" [color=blue, label="original subject", - lp="2994.4,221.5", - pos="e,2941.9,195.19 3152.7,259.25 3052.7,254.75 2954.1,246 2938.4,229 2932.1,222.22 2933.3,212.97 2937.1,204.27", + lp="2720.4,221.5", + pos="e,2649.2,196.11 2900.8,258.03 2793.8,253.16 2683.9,244.45 2664.4,229 2657.3,223.39 2653.3,214.63 2651.1,205.99", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3068.4,178", + pos="2774.4,178", width=1.5887]; "exposure event to phenotypic feature association" -> "original predicate" [color=blue, label="original predicate", - lp="3121.9,221.5", - pos="e,3058.6,195.75 3192.2,253.77 3127.5,248.29 3068.5,240.29 3058.4,229 3052.6,222.56 3052.7,213.75 3055,205.31", + lp="2853.9,221.5", + pos="e,2775.2,196.02 2940.2,253.2 2869.9,247.44 2803.1,239.37 2790.4,229 2783.4,223.29 2779.4,214.5 2777.2,205.87", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3182.4,178", + pos="2903.4,178", width=1.0652]; "exposure event to phenotypic feature association" -> "original object" [color=blue, label="original object", - lp="3250.9,221.5", - pos="e,3183.9,196.25 3257.1,249.46 3231.5,244.34 3209.3,237.63 3199.4,229 3192.7,223.17 3188.7,214.61 3186.2,206.22", + lp="2987.9,221.5", + pos="e,2910.3,196.01 3004.4,249.22 2975.1,243.89 2948.6,237.15 2936.4,229 2927.5,223.1 2920.5,213.92 2915.2,205.02", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3315.4,178", + pos="3036.4,178", width=2.1304]; "exposure event to phenotypic feature association" -> "subject category" [color=blue, label="subject category", - lp="3368.9,221.5", - pos="e,3308.1,196.39 3328.7,247.39 3321,242.65 3314.1,236.63 3309.4,229 3305.2,222.28 3304.8,214.07 3305.9,206.26", + lp="3110.9,221.5", + pos="e,3038.1,196.38 3074.3,247.15 3065.8,242.36 3057.6,236.38 3051.4,229 3046,222.56 3042.5,214.22 3040.3,206.2", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3486.4,178", + pos="3207.4,178", width=2.1304]; "exposure event to phenotypic feature association" -> "object category" [color=blue, label="object category", - lp="3501.9,221.5", - pos="e,3468,195.66 3404.1,246.98 3412,241.4 3420.7,235.07 3428.4,229 3439.1,220.58 3450.6,210.87 3460.4,202.27", + lp="3238.9,221.5", + pos="e,3196.6,196.26 3148.3,247.08 3155.8,241.74 3163.8,235.52 3170.4,229 3177.8,221.69 3184.9,212.79 3190.9,204.54", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3619.4,178", + pos="3340.4,178", width=1.0652]; "exposure event to phenotypic feature association" -> "subject closure" [color=blue, label="subject closure", - lp="3638.9,221.5", - pos="e,3605.2,195.02 3502.2,249.49 3522.5,244.54 3543,237.9 3561.4,229 3574.9,222.45 3587.8,211.92 3598,202.21", + lp="3370.9,221.5", + pos="e,3330.8,195.52 3249,249.63 3266.3,244.62 3283.3,237.92 3298.4,229 3308.9,222.82 3317.9,213.05 3324.9,203.78", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3715.4,178", + pos="3453.4,178", width=1.0652]; "exposure event to phenotypic feature association" -> "object closure" [color=blue, label="object closure", - lp="3756.4,221.5", - pos="e,3712.8,196.12 3550.2,252.39 3617.4,246.43 3681.8,238.43 3694.4,229 3702,223.35 3706.8,214.45 3709.9,205.72", + lp="3492.4,221.5", + pos="e,3449.7,196.17 3287.3,252 3353.4,245.94 3416.8,237.97 3429.4,229 3437.3,223.4 3442.6,214.52 3446.3,205.79", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3848.4,178", + pos="3586.4,178", width=2.1304]; "exposure event to phenotypic feature association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3914.9,221.5", - pos="e,3840.3,195.98 3545.8,252.03 3664.6,243.25 3804.4,232.3 3810.4,229 3820.5,223.44 3828.8,213.91 3835,204.64", + lp="3651.9,221.5", + pos="e,3577.7,195.99 3286.1,251.93 3403,243.11 3540.4,232.17 3546.4,229 3556.8,223.46 3565.5,213.92 3572,204.65", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="4037.4,178", + pos="3779.4,178", width=2.1304]; "exposure event to phenotypic feature association" -> "object category closure" [color=blue, label="object category closure", - lp="4104.9,221.5", - pos="e,4031.7,196.03 3546.8,252.1 3574.1,250.29 3602,248.53 3628.4,247 3670.4,244.57 3970.2,250.32 4006.4,229 4015.5,223.62 4022.4,214.37 \ -4027.3,205.28", + lp="3843.9,221.5", + pos="e,3772,196.09 3288.8,252.11 3316.1,250.31 3344,248.54 3370.4,247 3411.8,244.59 3706.9,248.8 3743.4,229 3753.4,223.58 3761.3,214.07 \ +3767.1,204.78", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4227.4,178", + pos="3969.4,178", width=1.0652]; "exposure event to phenotypic feature association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4277.4,221.5", - pos="e,4220.4,196.15 3544.1,251.91 3572.2,250.09 3601.1,248.37 3628.4,247 3659.7,245.43 4164.8,243.92 4192.4,229 4202.2,223.71 4209.8,\ -214.34 4215.4,205.14", + lp="4016.4,221.5", + pos="e,3961.7,195.69 3286.1,251.91 3314.2,250.09 3343.1,248.37 3370.4,247 3401.5,245.44 3903.7,243.3 3931.4,229 3941.8,223.62 3950.2,\ +213.93 3956.4,204.5", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4386.4,178", + pos="4128.4,178", width=1.0652]; "exposure event to phenotypic feature association" -> "object namespace" [color=blue, label="object namespace", - lp="4430.4,221.5", - pos="e,4379,195.71 3542.7,251.83 3571.3,250 3600.7,248.29 3628.4,247 3668.4,245.13 4313.8,247.48 4349.4,229 4359.7,223.64 4367.9,213.95 \ -4373.9,204.52", + lp="4170.4,221.5", + pos="e,4120.1,195.74 3284.7,251.84 3313.3,250 3342.7,248.29 3370.4,247 3410.3,245.14 4052.7,246.73 4088.4,229 4099.2,223.63 4108.1,213.8 \ +4114.7,204.27", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4537.4,178", + pos="4279.4,178", width=1.0652]; "exposure event to phenotypic feature association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4590.4,221.5", - pos="e,4529.4,195.75 3542.1,251.78 3570.8,249.94 3600.5,248.24 3628.4,247 3676.7,244.85 4455.2,250.66 4498.4,229 4509.1,223.64 4517.7,\ -213.81 4524.1,204.28", + lp="4330.4,221.5", + pos="e,4270.8,195.77 3284.1,251.78 3312.8,249.94 3342.5,248.24 3370.4,247 3418.6,244.86 4195,250.08 4238.4,229 4249.4,223.67 4258.4,213.84 \ +4265.2,204.31", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4657.4,178", + pos="4399.4,178", width=1.0652]; "exposure event to phenotypic feature association" -> "object label closure" [color=blue, label="object label closure", - lp="4743.9,221.5", - pos="e,4667.7,195.5 3541.4,251.74 3570.4,249.89 3600.3,248.2 3628.4,247 3657.3,245.77 4648.1,249.61 4668.4,229 4674.6,222.64 4674.3,213.6 \ -4671.6,204.94", + lp="4483.9,221.5", + pos="e,4408.8,195.54 3283.4,251.74 3312.4,249.89 3342.3,248.2 3370.4,247 3399.2,245.77 4388.2,249.57 4408.4,229 4414.6,222.69 4414.6,\ +213.66 4412.2,205", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4798.4,178", + pos="4540.4,178", width=2.347]; "exposure event to phenotypic feature association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4891.9,221.5", - pos="e,4813.2,196.2 3541.1,251.71 3570.1,249.86 3600.1,248.18 3628.4,247 3661.4,245.62 4794.2,252.53 4817.4,229 4823.9,222.42 4822.5,\ -213.41 4818.3,204.84", + lp="4631.9,221.5", + pos="e,4553.9,195.8 3283.1,251.71 3312.1,249.86 3342.1,248.18 3370.4,247 3403.3,245.63 4534.3,252.49 4557.4,229 4563.8,222.48 4562.6,\ +213.43 4558.8,204.83", style=solid]; type [height=0.5, - pos="4932.4,178", + pos="4674.4,178", width=0.86659]; "exposure event to phenotypic feature association" -> type [color=blue, label=type, - lp="4986.4,221.5", - pos="e,4951.1,192.56 3540.7,251.69 3569.9,249.84 3600,248.16 3628.4,247 3647,246.24 4952.4,242.22 4965.4,229 4974,220.33 4967.8,209.12 \ -4958.5,199.52", + lp="4726.4,221.5", + pos="e,4692.4,192.88 3282.7,251.69 3311.9,249.84 3342,248.16 3370.4,247 3388.9,246.24 4692.4,242.2 4705.4,229 4713.7,220.62 4708.2,209.66 \ +4699.7,200.14", style=solid]; category [height=0.5, - pos="5033.4,178", + pos="4775.4,178", width=1.4263]; "exposure event to phenotypic feature association" -> category [color=blue, label=category, - lp="5051.9,221.5", - pos="e,5029.1,196.09 3540.7,251.68 3569.9,249.83 3600,248.15 3628.4,247 3666.6,245.45 4973.6,248.82 5006.4,229 5015.1,223.75 5021.1,214.65 \ -5025.3,205.64", + lp="4792.9,221.5", + pos="e,4770.4,196.13 3282.7,251.68 3311.9,249.83 3342,248.15 3370.4,247 3408.6,245.45 4713.4,248.3 4746.4,229 4755.4,223.74 4761.9,214.51 \ +4766.4,205.4", style=solid]; subject [height=0.5, - pos="5147.4,178", + pos="4889.4,178", width=1.2277]; "exposure event to phenotypic feature association" -> subject [color=blue, label=subject, - lp="5139.4,221.5", - pos="e,5133.5,195.46 3540.4,251.69 3569.7,249.83 3599.9,248.15 3628.4,247 3668.9,245.37 5049.4,243.03 5087.4,229 5102.1,223.56 5115.8,\ -212.8 5126.4,202.65", + lp="4881.4,221.5", + pos="e,4875.2,195.46 3282.4,251.69 3311.7,249.83 3341.9,248.15 3370.4,247 3410.9,245.37 4790.3,242.87 4828.4,229 4843.3,223.57 4857.2,\ +212.81 4868,202.66", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="5294.4,178", + pos="5036.4,178", width=2.3651]; "exposure event to phenotypic feature association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="5287.4,221.5", - pos="e,5264,194.83 3540.4,251.67 3569.7,249.81 3599.9,248.14 3628.4,247 3713.9,243.58 5085.4,245.68 5169.4,229 5199.1,223.09 5230.9,210.32 \ -5254.9,199.17", + lp="5029.4,221.5", + pos="e,5006,194.83 3282.4,251.67 3311.7,249.81 3341.9,248.14 3370.4,247 3455.9,243.58 4827.4,245.68 4911.4,229 4941.1,223.09 4972.9,210.32 \ +4996.9,199.17", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="5473.4,178", + pos="5215.4,178", width=2.1123]; "exposure event to phenotypic feature association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="5466.4,221.5", - pos="e,5445.9,194.84 3540.1,251.66 3569.4,249.8 3599.8,248.12 3628.4,247 3724.5,243.22 5265.4,249.22 5359.4,229 5386.6,223.15 5415.2,\ -210.56 5437,199.48", + lp="5208.4,221.5", + pos="e,5187.9,194.84 3282.1,251.66 3311.4,249.8 3341.8,248.12 3370.4,247 3466.5,243.22 5007.4,249.22 5101.4,229 5128.6,223.15 5157.2,\ +210.56 5179,199.48", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="5603.4,178", + pos="5345.4,178", width=1.011]; "exposure event to phenotypic feature association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="5612.9,221.5", - pos="e,5587.5,194.3 3540.1,251.64 3569.4,249.78 3599.8,248.11 3628.4,247 3681.2,244.95 5481,245.04 5531.4,229 5549.3,223.3 5566.7,211.48 \ -5579.9,200.76", + lp="5354.9,221.5", + pos="e,5329.5,194.3 3282.1,251.64 3311.4,249.78 3341.8,248.11 3370.4,247 3423.2,244.95 5223,245.04 5273.4,229 5291.3,223.3 5308.7,211.48 \ +5321.9,200.76", style=solid]; "sex qualifier" [color=blue, height=0.5, label="biological sex", - pos="5731.4,178", + pos="5473.4,178", width=2.0401]; "exposure event to phenotypic feature association" -> "sex qualifier" [color=blue, label="sex qualifier", - lp="5739.4,221.5", - pos="e,5716.2,195.98 3540.1,251.63 3569.4,249.76 3599.8,248.1 3628.4,247 3685,244.82 5615,247.89 5668.4,229 5683.4,223.68 5697.6,213.15 \ -5708.7,203.12", + lp="5481.4,221.5", + pos="e,5458.2,195.98 3282.1,251.63 3311.4,249.76 3341.8,248.1 3370.4,247 3427,244.82 5357,247.89 5410.4,229 5425.4,223.68 5439.6,213.15 \ +5450.7,203.12", style=solid]; "has count" [color=blue, height=0.5, label=integer, - pos="5867.4,178", + pos="5609.4,178", width=1.2277]; "exposure event to phenotypic feature association" -> "has count" [color=blue, label="has count", - lp="5855.4,221.5", - pos="e,5849.1,194.57 3539.7,251.64 3569.2,249.77 3599.7,248.1 3628.4,247 3688.3,244.71 5729.8,245.77 5787.4,229 5806.8,223.33 5826.2,\ -211.47 5841,200.71", + lp="5597.4,221.5", + pos="e,5591.1,194.57 3281.7,251.64 3311.2,249.77 3341.7,248.1 3370.4,247 3430.3,244.71 5471.8,245.77 5529.4,229 5548.8,223.33 5568.2,\ +211.47 5583,200.71", style=solid]; "has total" [color=blue, height=0.5, label=integer, - pos="5973.4,178", + pos="5715.4,178", width=1.2277]; "exposure event to phenotypic feature association" -> "has total" [color=blue, label="has total", - lp="5958.9,221.5", - pos="e,5955.4,194.57 3539.7,251.63 3569.2,249.76 3599.7,248.09 3628.4,247 3691.3,244.61 5834,246.76 5894.4,229 5913.7,223.33 5932.8,211.47 \ -5947.3,200.71", + lp="5700.9,221.5", + pos="e,5697.4,194.57 3281.7,251.63 3311.2,249.76 3341.7,248.09 3370.4,247 3433.3,244.61 5576,246.76 5636.4,229 5655.7,223.33 5674.8,211.47 \ +5689.3,200.71", style=solid]; "has quotient" [color=blue, height=0.5, label=double, - pos="6077.4,178", + pos="5819.4,178", width=1.1735]; "exposure event to phenotypic feature association" -> "has quotient" [color=blue, label="has quotient", - lp="6073.4,221.5", - pos="e,6058.7,194.34 3539.7,251.62 3569.2,249.75 3599.7,248.09 3628.4,247 3694.1,244.51 5931.1,246.84 5994.4,229 6014.6,223.31 6034.8,\ -211.32 6050.2,200.51", + lp="5815.4,221.5", + pos="e,5800.7,194.34 3281.7,251.62 3311.2,249.75 3341.7,248.09 3370.4,247 3436.1,244.51 5673.1,246.84 5736.4,229 5756.6,223.31 5776.8,\ +211.32 5792.2,200.51", style=solid]; "has percentage" [color=blue, height=0.5, label=double, - pos="6184.4,178", + pos="5926.4,178", width=1.1735]; "exposure event to phenotypic feature association" -> "has percentage" [color=blue, label="has percentage", - lp="6203.4,221.5", - pos="e,6170.4,195 3539.7,251.61 3569.2,249.74 3599.7,248.08 3628.4,247 3697.6,244.39 6057.1,252.3 6122.4,229 6137.7,223.54 6152,212.56 \ -6163,202.28", + lp="5945.4,221.5", + pos="e,5912.4,195 3281.7,251.61 3311.2,249.74 3341.7,248.08 3370.4,247 3439.6,244.39 5799.1,252.3 5864.4,229 5879.7,223.54 5894,212.56 \ +5905,202.28", style=solid]; relation [height=0.5, - pos="5098.4,18", + pos="4840.4,18", width=1.2999]; - object -> relation [pos="e,5086.9,35.705 5061,73.174 5067,64.509 5074.4,53.768 5081,44.141", + object -> relation [pos="e,4828.9,35.705 4803,73.174 4809,64.509 4816.4,53.768 4823,44.141", style=dotted]; association_type [color=blue, height=0.5, label=string, - pos="3675.4,265", + pos="3417.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3806.4,265", + pos="3548.4,265", width=2.0762]; subject -> object [label=relation, - lp="5105.4,134.5", - pos="e,5055.8,108.97 5114.9,165.59 5102.1,159.94 5088,152.13 5077.4,142 5070.4,135.31 5064.7,126.48 5060.3,118.1"]; - subject -> relation [pos="e,5109.6,35.828 5146,159.99 5143.9,139.02 5139,102.55 5128.4,73 5124.9,63.258 5119.8,53.189 5114.8,44.423", + lp="4847.4,134.5", + pos="e,4797.8,108.97 4856.9,165.59 4844.1,159.94 4830,152.13 4819.4,142 4812.4,135.31 4806.7,126.48 4802.3,118.1"]; + subject -> relation [pos="e,4851.6,35.828 4888,159.99 4885.9,139.02 4881,102.55 4870.4,73 4866.9,63.258 4861.8,53.189 4856.8,44.423", style=dotted]; "exposure event to phenotypic feature association_subject" [color=blue, height=0.5, label="exposure event", - pos="3981.4,265", + pos="3723.4,265", width=2.2748]; } diff --git a/graphviz/exposure_event_to_phenotypic_feature_association.svg b/graphviz/exposure_event_to_phenotypic_feature_association.svg index 93c8dd99a3..e65e4a0999 100644 --- a/graphviz/exposure_event_to_phenotypic_feature_association.svg +++ b/graphviz/exposure_event_to_phenotypic_feature_association.svg @@ -4,16 +4,16 @@ - + %3 - + exposure event to phenotypic feature association - -exposure event to phenotypic feature association + +exposure event to phenotypic feature association @@ -24,7 +24,7 @@ exposure event to phenotypic feature association->association - + is_a @@ -37,8 +37,8 @@ exposure event to phenotypic feature association->entity to phenotypic feature association mixin - - + + uses @@ -50,7 +50,7 @@ exposure event to phenotypic feature association->id - + id @@ -63,8 +63,8 @@ exposure event to phenotypic feature association->iri - - + + iri @@ -76,8 +76,8 @@ exposure event to phenotypic feature association->name - - + + name @@ -89,8 +89,8 @@ exposure event to phenotypic feature association->description - - + + description @@ -102,8 +102,8 @@ exposure event to phenotypic feature association->has attribute - - + + has attribute @@ -115,21 +115,21 @@ exposure event to phenotypic feature association->predicate - - + + predicate object - -named thing + +named thing exposure event to phenotypic feature association->object - - + + object @@ -141,9 +141,9 @@ exposure event to phenotypic feature association->negated - - -negated + + +negated @@ -154,9 +154,9 @@ exposure event to phenotypic feature association->qualifiers - - -qualifiers + + +qualifiers @@ -167,9 +167,9 @@ exposure event to phenotypic feature association->publications - - -publications + + +publications @@ -180,429 +180,429 @@ exposure event to phenotypic feature association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string exposure event to phenotypic feature association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string exposure event to phenotypic feature association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string exposure event to phenotypic feature association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type exposure event to phenotypic feature association->timepoint - - -timepoint + + +timepoint original subject - -string + +string exposure event to phenotypic feature association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie exposure event to phenotypic feature association->original predicate - - -original predicate + + +original predicate original object - -string + +string exposure event to phenotypic feature association->original object - - -original object + + +original object subject category - -ontology class + +ontology class exposure event to phenotypic feature association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class exposure event to phenotypic feature association->object category - - -object category + + +object category subject closure - -string + +string exposure event to phenotypic feature association->subject closure - - -subject closure + + +subject closure object closure - -string + +string exposure event to phenotypic feature association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class exposure event to phenotypic feature association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class exposure event to phenotypic feature association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string exposure event to phenotypic feature association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string exposure event to phenotypic feature association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string exposure event to phenotypic feature association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string exposure event to phenotypic feature association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source exposure event to phenotypic feature association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type exposure event to phenotypic feature association->type - - -type + + +type category - -category + +category exposure event to phenotypic feature association->category - - -category + + +category subject - -subject + +subject exposure event to phenotypic feature association->subject - - -subject + + +subject frequency qualifier - -frequency value + +frequency value exposure event to phenotypic feature association->frequency qualifier - - -frequency qualifier + + +frequency qualifier severity qualifier - -severity value + +severity value exposure event to phenotypic feature association->severity qualifier - - -severity qualifier + + +severity qualifier onset qualifier - -onset + +onset exposure event to phenotypic feature association->onset qualifier - - -onset qualifier + + +onset qualifier sex qualifier - -biological sex + +biological sex exposure event to phenotypic feature association->sex qualifier - - -sex qualifier + + +sex qualifier has count - -integer + +integer exposure event to phenotypic feature association->has count - - -has count + + +has count has total - -integer + +integer exposure event to phenotypic feature association->has total - - -has total + + +has total has quotient - -double + +double exposure event to phenotypic feature association->has quotient - - -has quotient + + +has quotient has percentage - -double + +double exposure event to phenotypic feature association->has percentage - - -has percentage + + +has percentage relation - -relation + +relation object->relation - - + + association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation subject->relation - - + + exposure event to phenotypic feature association_subject - -exposure event + +exposure event diff --git a/graphviz/functional_association.gv b/graphviz/functional_association.gv index 69f594afaa..86a9d887d7 100644 --- a/graphviz/functional_association.gv +++ b/graphviz/functional_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4788.4,283"]; + graph [bb="0,0,4570.4,283"]; node [label="\N"]; "functional association" [height=0.5, label="functional association", - pos="2492.4,265", + pos="2274.4,265", width=3.1053]; association [height=0.5, pos="62.394,178", width=1.7332]; "functional association" -> association [label=is_a, - lp="281.39,221.5", - pos="e,103.12,191.79 2380.6,263.71 1958.9,262.4 477.37,255.91 267.39,229 213.85,222.14 154.03,206.61 112.9,194.67"]; + lp="280.39,221.5", + pos="e,102.91,191.77 2162.9,263.51 1768.6,261.57 454.14,253.33 266.39,229 213.11,222.09 153.58,206.57 112.65,194.64"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "functional association" -> id [color=blue, label=id, - lp="398.39,221.5", - pos="e,210.38,190 2381,263.35 1975.2,260.8 589.15,250.6 391.39,229 318.35,221.02 300.2,215.65 229.39,196 226.29,195.14 223.09,194.17 \ -219.89,193.16", + lp="396.39,221.5", + pos="e,210.38,189.98 2162.9,263.13 1784.8,260.02 564.95,248.56 389.39,229 317.23,220.96 299.34,215.5 229.39,196 226.29,195.13 223.09,\ +194.17 219.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "functional association" -> iri [color=blue, label=iri, - lp="515.39,221.5", - pos="e,315.29,190.23 2381.2,263.16 1990.3,260.04 693.38,248.34 507.39,229 429.97,220.95 410.81,215.26 335.39,196 332.02,195.14 328.54,\ -194.18 325.05,193.17", + lp="509.39,221.5", + pos="e,315.3,190.2 2162.5,264.37 1825.9,265.09 825.36,264.12 501.39,229 426.61,220.89 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ +325.06,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "functional association" -> name [color=blue, label=name, - lp="627.39,221.5", - pos="e,440.01,191.15 2380.9,263.31 2002.7,260.79 782.66,251.03 607.39,229 552.58,222.11 491.21,206.11 449.83,194.05", + lp="617.39,221.5", + pos="e,439.19,191.41 2162.9,263.15 1813.1,260.26 751.28,249.86 597.39,229 545.74,222 488.1,206.31 448.78,194.36", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "functional association" -> description [color=blue, label=description, - lp="755.89,221.5", - pos="e,588.8,193.65 2380.6,263.59 2016.6,262.01 878.85,255.01 715.39,229 675.03,222.58 630.79,208.66 598.44,197.14", + lp="739.89,221.5", + pos="e,586.19,194.12 2162.9,263.47 1827.4,261.62 842.08,254.08 699.39,229 663.52,222.69 624.55,209.24 595.6,197.88", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "functional association" -> "has attribute" [color=blue, label="has attribute", - lp="913.39,221.5", - pos="e,729.98,191.75 2380.9,263.31 2038.3,260.94 1014.7,251.99 866.39,229 822.26,222.16 773.51,207 739.58,195.15", + lp="887.39,221.5", + pos="e,726.83,192.67 2162.9,263.26 1848.4,260.9 968.81,252.28 840.39,229 804.17,222.43 764.8,208.24 736.39,196.65", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "functional association" -> predicate [color=blue, label=predicate, - lp="1074.4,221.5", - pos="e,887.81,193.09 2380.5,264.56 2086.8,265.52 1298.6,264.58 1040.4,229 991.17,222.22 936.47,207.65 897.4,195.99", + lp="1031.4,221.5", + pos="e,880.43,194.06 2163.3,262.79 1873.8,259.36 1110.3,248.58 997.39,229 960.25,222.56 919.77,209.02 889.78,197.66", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "functional association" -> negated [color=blue, label=negated, - lp="1220.4,221.5", - pos="e,1022.3,190.23 2380.5,263.73 2108.8,262.65 1419.9,257.11 1191.4,229 1135.6,222.13 1072.9,205.38 1032,193.16", + lp="1151.4,221.5", + pos="e,1015.6,192.51 2163.5,262.67 1894.6,259.16 1222.6,248.53 1122.4,229 1088.3,222.36 1051.5,208.2 1024.9,196.64", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "functional association" -> qualifiers [color=blue, label=qualifiers, - lp="1356.9,221.5", - pos="e,1171.6,193.02 2380.7,263.8 2129.4,262.84 1525.2,257.53 1323.4,229 1274.6,222.11 1220.5,207.65 1181.6,196.05", + lp="1254.9,221.5", + pos="e,1151.6,195.39 2163.2,263.17 1910.9,260.88 1310.3,252.96 1221.4,229 1199.7,223.15 1177.4,211.43 1160.1,200.81", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "functional association" -> publications [color=blue, label=publications, - lp="1499.4,221.5", - pos="e,1321.9,192.66 2380.5,263.78 2150.2,262.75 1630.6,257.25 1455.4,229 1412.5,222.09 1365.3,207.61 1331.5,196.01", + lp="1346.4,221.5", + pos="e,1286.4,196.26 2162.9,263.35 1914.8,261.44 1336.4,254.29 1302.4,229 1295.1,223.57 1290.9,214.84 1288.5,206.19", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,263 +110,264 @@ digraph { width=2.0943]; "functional association" -> "has evidence" [color=blue, label="has evidence", - lp="1652.9,221.5", - pos="e,1479.4,193.55 2380.9,263.13 2177.1,260.95 1752,253.53 1606.4,229 1566,222.2 1521.6,208.38 1489.1,196.99", + lp="1444.9,221.5", + pos="e,1413.8,194.93 2162.6,263.6 1932.3,262.22 1424.4,256.11 1398.4,229 1390,220.25 1395.9,210.18 1405.7,201.37", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1643.4,178", - width=3.015]; + label=string, + pos="1573.4,178", + width=1.0652]; "functional association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1802.9,221.5", - pos="e,1667.9,195.78 2380.5,264.75 2200.7,264.96 1856,260.97 1738.4,229 1716.6,223.09 1694.2,211.61 1676.7,201.13", + lp="1562.9,221.5", + pos="e,1543.3,189.28 2163.1,262.99 1953.9,260.53 1521,252.61 1498.4,229 1493.8,224.18 1494.8,219.62 1498.4,214 1502.8,207.12 1518,199.47 \ +1533.6,193.08", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1878.4,178", - width=3.015]; + label=string, + pos="1668.4,178", + width=1.0652]; "functional association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1972.4,221.5", - pos="e,1872.6,196 2382.4,261.61 2210.1,257.32 1894.4,247.04 1877.4,229 1871.6,222.9 1870.4,214.27 1871,205.9", + lp="1729.4,221.5", + pos="e,1648.1,193.48 2164.2,261.87 1986,257.87 1652.3,247.9 1634.4,229 1626.3,220.46 1631.8,209.82 1640.6,200.55", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2113.4,178", - width=3.015]; + label=string, + pos="1810.4,178", + width=1.0652]; "functional association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2180.9,221.5", - pos="e,2087.6,195.53 2381.8,262.33 2265,259.38 2094.9,251.28 2074.4,229 2066.7,220.62 2071.6,210.86 2080.1,202.2", + lp="1949.9,221.5", + pos="e,1816.9,195.93 2166.5,260.14 2047.9,255.13 1870.6,245.07 1843.4,229 1834,223.44 1826.8,214.03 1821.5,204.86", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2295.4,178", + pos="2037.4,178", width=1.5346]; "functional association" -> timepoint [color=blue, label=timepoint, - lp="2332.4,221.5", - pos="e,2291.1,196.26 2391.1,257.32 2350.5,252.38 2310.3,243.82 2297.4,229 2292,222.83 2290.3,214.43 2290.3,206.27", + lp="2112.4,221.5", + pos="e,2046.6,196.08 2184.5,254.24 2141.6,248.35 2095.7,239.86 2077.4,229 2067.4,223.06 2058.9,213.63 2052.3,204.55", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2407.4,178", + pos="2149.4,178", width=1.0652]; "functional association" -> "original subject" [color=blue, label="original subject", - lp="2430.4,221.5", - pos="e,2387.4,193.75 2407.2,253.21 2394.4,247.87 2382.7,240.13 2374.4,229 2367.7,220.01 2372.5,209.73 2380.3,200.83", + lp="2214.4,221.5", + pos="e,2148.2,196.23 2194,252.37 2180.6,247.15 2167.9,239.68 2158.4,229 2152.9,222.8 2150.2,214.39 2149,206.23", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2521.4,178", + pos="2274.4,178", width=1.5887]; "functional association" -> "original predicate" [color=blue, label="original predicate", - lp="2556.9,221.5", - pos="e,2504.6,195.4 2490.1,246.84 2489.4,236.95 2489.6,224.45 2493.4,214 2494.7,210.42 2496.5,206.94 2498.6,203.64", + lp="2337.9,221.5", + pos="e,2274.4,196.18 2274.4,246.8 2274.4,235.16 2274.4,219.55 2274.4,206.24", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2635.4,178", + pos="2403.4,178", width=1.0652]; "functional association" -> "original object" [color=blue, label="original object", - lp="2681.9,221.5", - pos="e,2634.3,196.46 2578.3,253.37 2593.8,248.09 2608.8,240.34 2620.4,229 2626.5,223.04 2630.2,214.69 2632.3,206.52", + lp="2459.9,221.5", + pos="e,2407.8,195.99 2348.7,251.55 2372.7,245.93 2395.1,238.4 2402.4,229 2407.4,222.62 2408.9,214.26 2408.7,206.21", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2768.4,178", + pos="2536.4,178", width=2.1304]; "functional association" -> "subject category" [color=blue, label="subject category", - lp="2811.9,221.5", - pos="e,2762.2,196.16 2573.6,252.6 2644.6,242.61 2736.5,229.58 2737.4,229 2746.2,223.28 2752.9,214.13 2757.8,205.22", + lp="2586.9,221.5", + pos="e,2533.7,196.01 2355.3,252.49 2425,242.53 2514.6,229.63 2515.4,229 2522.8,223.28 2527.6,214.49 2530.7,205.86", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2939.4,178", + pos="2707.4,178", width=2.1304]; "functional association" -> "object category" [color=blue, label="object category", - lp="2956.9,221.5", - pos="e,2923.7,195.65 2571.1,252.12 2585.1,250.23 2599.7,248.43 2613.4,247 2671.4,240.94 2820.9,249.88 2875.4,229 2890.4,223.24 2904.8,\ -212.66 2916.1,202.71", + lp="2728.9,221.5", + pos="e,2693.4,196.12 2353.1,252.15 2367.1,250.25 2381.7,248.45 2395.4,247 2451.9,241.04 2598,250.87 2650.4,229 2663.9,223.35 2676.5,213.12 \ +2686.4,203.39", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3072.4,178", + pos="2840.4,178", width=1.0652]; "functional association" -> "subject closure" [color=blue, label="subject closure", - lp="3093.9,221.5", - pos="e,3059.6,195.27 2570.1,251.98 2584.4,250.07 2599.3,248.3 2613.4,247 2658,242.88 2974.9,245.91 3016.4,229 3030.2,223.36 3042.9,212.73 \ -3052.7,202.72", + lp="2864.9,221.5", + pos="e,2828.8,195.25 2352.1,251.99 2366.4,250.08 2381.3,248.31 2395.4,247 2438.9,242.95 2748.2,246.25 2788.4,229 2801.5,223.38 2813.2,\ +212.9 2822.2,202.98", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3172.4,178", + pos="2953.4,178", width=1.0652]; "functional association" -> "object closure" [color=blue, label="object closure", - lp="3214.4,221.5", - pos="e,3170.3,196.35 2569.4,251.93 2584,250 2599.1,248.24 2613.4,247 2643.2,244.41 3127.9,246.21 3152.4,229 3160.1,223.62 3164.8,214.78 \ -3167.7,206.02", + lp="2988.4,221.5", + pos="e,2948,196.06 2351.4,251.94 2366,250.01 2381.1,248.24 2395.4,247 2424.6,244.45 2898.1,243.89 2923.4,229 2932.5,223.66 2939.1,214.42 \ +2943.8,205.32", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3305.4,178", + pos="3086.4,178", width=2.1304]; "functional association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3372.9,221.5", - pos="e,3297.7,196.19 2569.4,251.87 2584,249.94 2599.1,248.19 2613.4,247 2649.7,243.96 3236.1,245.83 3268.4,229 3278.6,223.7 3286.6,214.21 \ -3292.6,204.91", + lp="3148.9,221.5", + pos="e,3076.5,196.26 2351.4,251.87 2366,249.94 2381.1,248.2 2395.4,247 2431.2,243.99 3009.8,244.27 3042.4,229 3053.7,223.68 3063.3,213.92 \ +3070.7,204.42", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3497.4,178", + pos="3279.4,178", width=2.1304]; "functional association" -> "object category closure" [color=blue, label="object category closure", - lp="3563.9,221.5", - pos="e,3491.1,196.16 2569.1,251.83 2583.7,249.9 2599,248.16 2613.4,247 2660.5,243.2 3423,251.85 3464.4,229 3474,223.72 3481.2,214.36 \ -3486.5,205.16", + lp="3341.9,221.5", + pos="e,3271.1,196.24 2351.1,251.84 2365.7,249.9 2381,248.16 2395.4,247 2442.2,243.23 3198.4,250.05 3240.4,229 3250.8,223.76 3259.3,214.28 \ +3265.7,204.97", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3687.4,178", + pos="3469.4,178", width=1.0652]; "functional association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3736.4,221.5", - pos="e,3680.3,195.73 2568.7,251.83 2583.5,249.89 2598.9,248.14 2613.4,247 2670.9,242.48 3600.3,255.74 3651.4,229 3661.6,223.66 3669.6,\ -213.98 3675.4,204.54", + lp="3515.4,221.5", + pos="e,3461.1,195.77 2350.7,251.83 2365.5,249.89 2380.9,248.14 2395.4,247 2452.7,242.49 3377.8,254.34 3429.4,229 3440.2,223.67 3449.1,\ +213.85 3455.7,204.31", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3846.4,178", + pos="3628.4,178", width=1.0652]; "functional association" -> "object namespace" [color=blue, label="object namespace", - lp="3890.4,221.5", - pos="e,3838.7,195.76 2568.7,251.81 2583.5,249.86 2598.9,248.12 2613.4,247 2646.5,244.44 3778.8,243.98 3808.4,229 3818.9,223.71 3827.2,\ -214.03 3833.4,204.59", + lp="3669.4,221.5", + pos="e,3619.8,195.79 2350.7,251.81 2365.5,249.86 2380.9,248.12 2395.4,247 2461.4,241.88 3527.7,257.78 3587.4,229 3598.4,223.7 3607.4,\ +213.88 3614.2,204.34", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3997.4,178", + pos="3779.4,178", width=1.0652]; "functional association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4050.4,221.5", - pos="e,3989.4,195.78 2568.7,251.79 2583.5,249.84 2598.9,248.11 2613.4,247 2650.6,244.15 3924.9,245.62 3958.4,229 3969.1,223.68 3977.8,\ -213.86 3984.2,204.32", + lp="3831.4,221.5", + pos="e,3770.5,195.81 2350.7,251.79 2365.5,249.84 2380.9,248.11 2395.4,247 2432.6,244.15 3703.7,244.97 3737.4,229 3748.5,223.72 3757.8,\ +213.91 3764.7,204.36", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4168.4,178", + pos="3950.4,178", width=1.0652]; "functional association" -> "object label closure" [color=blue, label="object label closure", - lp="4216.9,221.5", - pos="e,4160.1,195.8 2568.7,251.77 2583.5,249.83 2598.9,248.1 2613.4,247 2655.4,243.82 4090.6,247.46 4128.4,229 4139.3,223.7 4148.1,213.88 \ -4154.7,204.34", + lp="3998.9,221.5", + pos="e,3941.8,195.81 2350.7,251.77 2365.5,249.83 2380.9,248.1 2395.4,247 2437.3,243.82 3871.5,247.22 3909.4,229 3920.4,223.71 3929.4,\ +213.9 3936.2,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4330.4,178", + pos="4112.4,178", width=2.347]; "functional association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4378.9,221.5", - pos="e,4321.8,196.3 2568.4,251.8 2583.3,249.84 2598.8,248.1 2613.4,247 2659.8,243.5 4248.5,249.41 4290.4,229 4301.1,223.78 4309.9,214.17 \ -4316.4,204.75", + lp="4160.9,221.5", + pos="e,4103.8,196.3 2350.4,251.8 2365.3,249.84 2380.8,248.1 2395.4,247 2441.8,243.5 4030.5,249.41 4072.4,229 4083.1,223.78 4091.9,214.17 \ +4098.4,204.75", style=solid]; type [height=0.5, - pos="4464.4,178", + pos="4246.4,178", width=0.86659]; "functional association" -> type [color=blue, label=type, - lp="4478.4,221.5", - pos="e,4465.2,196.18 2568.4,251.79 2583.3,249.83 2598.8,248.09 2613.4,247 2638.9,245.09 4432.4,244.91 4452.4,229 4459.2,223.54 4462.6,\ -214.93 4464.1,206.37", + lp="4260.4,221.5", + pos="e,4247.2,196.18 2350.4,251.79 2365.3,249.83 2380.8,248.09 2395.4,247 2420.9,245.09 4214.4,244.91 4234.4,229 4241.2,223.54 4244.6,\ +214.93 4246.1,206.37", style=solid]; category [height=0.5, - pos="4565.4,178", + pos="4347.4,178", width=1.4263]; "functional association" -> category [color=blue, label=category, - lp="4558.9,221.5", - pos="e,4549.8,195.26 2568.4,251.78 2583.3,249.83 2598.8,248.09 2613.4,247 2665.6,243.1 4448.8,245.74 4498.4,229 4514.6,223.53 4530.1,\ -212.51 4542.1,202.2", + lp="4340.9,221.5", + pos="e,4331.8,195.26 2350.4,251.78 2365.3,249.83 2380.8,248.09 2395.4,247 2447.6,243.1 4230.8,245.74 4280.4,229 4296.6,223.53 4312.1,\ +212.51 4324.1,202.2", style=solid]; subject [height=0.5, - pos="4679.4,178", + pos="4461.4,178", width=1.2277]; "functional association" -> subject [color=blue, label=subject, - lp="4655.4,221.5", - pos="e,4660.1,194.33 2568.4,251.78 2583.3,249.82 2598.8,248.09 2613.4,247 2723.2,238.83 4488.3,258.4 4594.4,229 4615.1,223.25 4636,211.09 \ -4651.9,200.2", + lp="4437.4,221.5", + pos="e,4442.1,194.33 2350.4,251.78 2365.3,249.82 2380.8,248.09 2395.4,247 2505.2,238.83 4270.3,258.4 4376.4,229 4397.1,223.25 4418,211.09 \ +4433.9,200.2", style=solid]; object [height=0.5, - pos="4722.4,91", + pos="4504.4,91", width=1.0832]; "functional association" -> object [color=blue, label=object, - lp="4766.4,178", - pos="e,4735.8,108.09 2568.4,251.77 2583.3,249.82 2598.8,248.08 2613.4,247 2670.8,242.74 4630.6,246.58 4685.4,229 4709.7,221.2 4718,217.1 \ -4732.4,196 4746.3,175.59 4742.5,166.51 4745.4,142 4746.2,135.38 4747.3,133.39 4745.4,127 4744.4,123.55 4742.9,120.13 4741.1,116.85", + lp="4548.4,178", + pos="e,4517.8,108.09 2350.4,251.77 2365.3,249.82 2380.8,248.08 2395.4,247 2452.8,242.74 4412.6,246.58 4467.4,229 4491.7,221.2 4500,217.1 \ +4514.4,196 4528.3,175.59 4524.5,166.51 4527.4,142 4528.2,135.38 4529.3,133.39 4527.4,127 4526.4,123.55 4524.9,120.13 4523.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2660.4,265", + pos="2442.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2791.4,265", + pos="2573.4,265", width=2.0762]; subject -> object [label=relation, - lp="4717.4,134.5", - pos="e,4704.5,107.23 4680.5,159.55 4681.7,149.57 4684.2,137.07 4689.4,127 4691.6,122.68 4694.5,118.52 4697.7,114.66"]; + lp="4499.4,134.5", + pos="e,4486.5,107.23 4462.5,159.55 4463.7,149.57 4466.2,137.07 4471.4,127 4473.6,122.68 4476.5,118.52 4479.7,114.66"]; relation [height=0.5, - pos="4667.4,18", + pos="4449.4,18", width=1.2999]; - subject -> relation [pos="e,4668.7,36.188 4678.1,159.79 4676,132.48 4672,78.994 4669.5,46.38", + subject -> relation [pos="e,4450.7,36.188 4460.1,159.79 4458,132.48 4454,78.994 4451.5,46.38", style=dotted]; "functional association_subject" [color=blue, height=0.5, label="macromolecular machine mixin", - pos="3040.4,265", + pos="2822.4,265", width=4.3329]; - object -> relation [pos="e,4680.2,35.54 4709.9,73.889 4703,64.939 4694.2,53.617 4686.4,43.584", + object -> relation [pos="e,4462.2,35.54 4491.9,73.889 4485,64.939 4476.2,53.617 4468.4,43.584", style=dotted]; "functional association_object" [color=blue, height=0.5, label="ontology class", - pos="3291.4,265", + pos="3073.4,265", width=2.1304]; } diff --git a/graphviz/functional_association.svg b/graphviz/functional_association.svg index 9dfe113a46..51165a78e8 100644 --- a/graphviz/functional_association.svg +++ b/graphviz/functional_association.svg @@ -4,16 +4,16 @@ - + %3 - + functional association - -functional association + +functional association @@ -24,9 +24,9 @@ functional association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ functional association->id - - -id + + +id @@ -50,9 +50,9 @@ functional association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ functional association->name - - -name + + +name @@ -76,9 +76,9 @@ functional association->description - - -description + + +description @@ -89,9 +89,9 @@ functional association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ functional association->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ functional association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ functional association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ functional association->publications - - -publications + + +publications @@ -154,344 +154,344 @@ functional association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string functional association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string functional association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string functional association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type functional association->timepoint - - -timepoint + + +timepoint original subject - -string + +string functional association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie functional association->original predicate - - -original predicate + + +original predicate original object - -string + +string functional association->original object - - -original object + + +original object subject category - -ontology class + +ontology class functional association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class functional association->object category - - -object category + + +object category subject closure - -string + +string functional association->subject closure - - -subject closure + + +subject closure object closure - -string + +string functional association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class functional association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class functional association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string functional association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string functional association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string functional association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string functional association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source functional association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type functional association->type - - -type + + +type category - -category + +category functional association->category - - -category + + +category subject - -subject + +subject functional association->subject - - -subject + + +subject object - -object + +object functional association->object - - -object + + +object association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + functional association_subject - -macromolecular machine mixin + +macromolecular machine mixin object->relation - - + + functional association_object - -ontology class + +ontology class diff --git a/graphviz/gene_as_a_model_of_disease_association.gv b/graphviz/gene_as_a_model_of_disease_association.gv index 671104200d..d1735ce422 100644 --- a/graphviz/gene_as_a_model_of_disease_association.gv +++ b/graphviz/gene_as_a_model_of_disease_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,6122.8,283"]; + graph [bb="0,0,6870,283"]; node [label="\N"]; "gene as a model of disease association" [height=0.5, label="gene as a model of disease association", - pos="3369.8,265", + pos="3656.8,265", width=5.2718]; "gene to disease association" [height=0.5, pos="137.79,178", width=3.8274]; "gene as a model of disease association" -> "gene to disease association" [label=is_a, lp="776.79,221.5", - pos="e,234.59,190.84 3181.1,262.83 2664.5,259.41 1233.8,248.41 762.79,229 550.02,220.23 496.84,215.57 284.79,196 271.84,194.81 258.27,\ -193.42 244.83,191.96"]; + pos="e,234.59,190.84 3467.6,263.12 2912.1,260.31 1292,250.45 762.79,229 550.01,220.38 496.84,215.57 284.79,196 271.84,194.81 258.27,193.42 \ +244.83,191.96"]; "model to disease association mixin" [height=0.5, pos="465.79,178", width=4.7843]; "gene as a model of disease association" -> "model to disease association mixin" [label=uses, lp="994.29,221.5", - pos="e,573.46,192.13 3180.6,263.26 2693.5,261.01 1404.9,252.94 977.79,229 842.3,221.41 687.28,205.21 583.64,193.3"]; + pos="e,572.97,192.12 3467.2,263.6 2939.8,262.17 1462.8,255.8 977.79,229 842.08,221.5 686.78,205.25 583.15,193.3"]; "entity to disease association mixin" [height=0.5, pos="826.79,178", width=4.7482]; "gene as a model of disease association" -> "entity to disease association mixin" [label=uses, lp="1149.3,221.5", - pos="e,900.91,194.23 3179.7,264.6 2714.3,265.5 1527.5,264.15 1132.8,229 1057.2,222.27 972.15,207.8 910.91,196.15"]; + pos="e,900.91,194.27 3467.7,263 2921,259.86 1362.5,249.25 1132.8,229 1057.2,222.34 972.15,207.86 910.91,196.19"]; id [color=blue, height=0.5, label=string, @@ -32,7 +32,7 @@ digraph { "gene as a model of disease association" -> id [color=blue, label=id, lp="1266.8,221.5", - pos="e,1082.8,189.97 3181.2,262.91 2699.3,259.85 1447.3,249.95 1259.8,229 1188.5,221.04 1170.9,215.35 1101.8,196 1098.7,195.13 1095.5,\ + pos="e,1082.8,189.97 3467.8,263.32 2940.3,261.13 1476.2,252.96 1259.8,229 1188.5,221.11 1170.9,215.35 1101.8,196 1098.7,195.13 1095.5,\ 194.16 1092.3,193.14", style=solid]; iri [color=blue, @@ -42,8 +42,9 @@ digraph { width=1.2277]; "gene as a model of disease association" -> iri [color=blue, label=iri, - lp="1363.8,221.5", - pos="e,1188.1,190.02 3180.9,262.89 2714.6,259.85 1533.5,250.13 1355.8,229 1300.3,222.4 1238.2,205.4 1197.9,193.05", + lp="1371.8,221.5", + pos="e,1187.7,190.13 3467.8,263.21 2956.3,260.78 1569.6,252.12 1363.8,229 1293.4,221.09 1276.3,214.18 1207.8,196 1204.4,195.11 1200.9,\ +194.12 1197.5,193.1", style=solid]; name [color=blue, height=0.5, @@ -52,8 +53,8 @@ digraph { width=1.5707]; "gene as a model of disease association" -> name [color=blue, label=name, - lp="1459.8,221.5", - pos="e,1308.1,192.37 3180.4,263.51 2727.8,261.93 1608.2,255.37 1439.8,229 1397.5,222.37 1350.9,207.67 1317.9,195.91", + lp="1473.8,221.5", + pos="e,1309.7,191.92 3467.1,263.75 2969.2,262.71 1649.7,257.29 1453.8,229 1407.1,222.26 1355.4,207.06 1319.5,195.18", style=solid]; description [color=blue, height=0.5, @@ -62,8 +63,8 @@ digraph { width=2.0943]; "gene as a model of disease association" -> description [color=blue, label=description, - lp="1563.3,221.5", - pos="e,1448.2,195.26 3181.5,262.69 2727.2,259.22 1602.1,248.7 1522.8,229 1499.5,223.22 1475.4,211.22 1456.9,200.42", + lp="1586.3,221.5", + pos="e,1453.4,194.79 3468.2,262.77 2968,259.25 1638.9,248.15 1545.8,229 1516.8,223.04 1486,210.36 1462.6,199.27", style=solid]; "has attribute" [color=blue, height=0.5, @@ -72,343 +73,429 @@ digraph { width=1.4443]; "gene as a model of disease association" -> "has attribute" [color=blue, label="has attribute", - lp="1682.8,221.5", - pos="e,1584.4,195.2 3180.5,263.28 2745.7,261.2 1707.7,253.68 1635.8,229 1619.6,223.45 1604.1,212.42 1592.1,202.13", - style=solid]; - predicate [color=blue, - height=0.5, - label="predicate type", - pos="1716.8,178", - width=2.1665]; - "gene as a model of disease association" -> predicate [color=blue, - label=predicate, - lp="1782.8,221.5", - pos="e,1722.8,196.14 3179.8,264.65 2765,265.43 1810.2,263.45 1748.8,229 1739.4,223.7 1732.3,214.34 1727.2,205.14", - style=solid]; - object [color=blue, - height=0.5, - label="named thing", - pos="5508.8,91", - width=1.9318]; - "gene as a model of disease association" -> object [color=blue, - label=object, - lp="1861.8,178", - pos="e,5439.3,91.949 3182.9,261.84 2874.2,257.8 2271.1,247.76 2058.8,229 1957.1,220.02 1768.3,232.83 1839.8,160 1904.9,93.7 4899.2,91.768 \ -5429.1,91.946", + lp="1718.8,221.5", + pos="e,1592.6,194.29 3468.2,262.87 2989.3,259.72 1758.1,249.63 1671.8,229 1646.9,223.05 1621,210.46 1601.4,199.4", style=solid]; negated [color=blue, height=0.5, label=boolean, - pos="1939.8,178", + pos="1685.8,178", width=1.2999]; "gene as a model of disease association" -> negated [color=blue, label=negated, - lp="2169.8,221.5", - pos="e,1974.5,190.32 3180.9,263.09 2887.5,260.92 2336,253.61 2140.8,229 2086,222.1 2024.7,205.5 1984.3,193.31", + lp="1851.8,221.5", + pos="e,1714.1,192.49 3467.1,263.92 3030.7,263.24 1980.8,258.5 1822.8,229 1788.1,222.53 1750.6,208.28 1723.6,196.64", style=solid]; qualifiers [color=blue, height=0.5, label="ontology class", - pos="2080.8,178", + pos="1826.8,178", width=2.1304]; "gene as a model of disease association" -> qualifiers [color=blue, label=qualifiers, - lp="2304.3,221.5", - pos="e,2123.2,193.12 3180.8,263.12 2914.1,260.99 2440.6,253.73 2270.8,229 2223.4,222.1 2170.8,207.72 2133,196.15", + lp="1956.3,221.5", + pos="e,1850.4,195.24 3468.5,262.5 3034.8,258.75 1996.5,247.83 1922.8,229 1900.3,223.26 1877.2,211.42 1859.3,200.71", style=solid]; publications [color=blue, height=0.5, label=publication, - pos="2237.8,178", + pos="1983.8,178", width=1.7332]; "gene as a model of disease association" -> publications [color=blue, label=publications, - lp="2443.8,221.5", - pos="e,2273.2,192.88 3181,263.07 2942.2,260.88 2544.6,253.53 2399.8,229 2359.3,222.14 2314.8,207.9 2282.7,196.37", + lp="2049.8,221.5", + pos="e,1986.6,196.44 3468.2,262.64 3041.4,259.22 2035.8,249.05 2005.8,229 1997.9,223.72 1992.8,214.91 1989.5,206.14", style=solid]; "has evidence" [color=blue, height=0.5, label="evidence type", - pos="2393.8,178", + pos="2139.8,178", width=2.0943]; "gene as a model of disease association" -> "has evidence" [color=blue, label="has evidence", - lp="2593.3,221.5", - pos="e,2429.9,193.89 3182.7,261.96 2978.2,258.68 2664.2,250.27 2546.8,229 2509.7,222.28 2469.2,208.76 2439.2,197.47", + lp="2148.3,221.5", + pos="e,2115.2,195.13 3468,263.16 3058.9,260.9 2125.4,253.1 2101.8,229 2093.7,220.76 2098.8,210.79 2107.5,201.94", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2595.8,178", - width=3.015]; + label=string, + pos="2271.8,178", + width=1.0652]; "gene as a model of disease association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2737.3,221.5", - pos="e,2615.2,195.77 3187.9,259.76 2997.8,254.54 2720.5,244.44 2672.8,229 2655,223.23 2637.3,212.21 2623.3,201.98", + lp="2266.3,221.5", + pos="e,2242.9,189.84 3468.1,262.86 3079.4,260.05 2223.6,251.34 2201.8,229 2197.1,224.23 2198.3,219.67 2201.8,214 2205.7,207.6 2219.4,\ +200.19 2233.6,193.84", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2830.8,178", - width=3.015]; + label=string, + pos="2366.8,178", + width=1.0652]; "gene as a model of disease association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2904.8,221.5", - pos="e,2815.1,195.98 3191.8,258.69 3032.9,253.05 2823,243.01 2809.8,229 2803.4,222.18 2805.1,213.11 2809.6,204.57", + lp="2433.8,221.5", + pos="e,2348.8,194.35 3468.8,262.37 3109.4,258.79 2358.2,248.94 2338.8,229 2331.3,221.28 2335.1,211.15 2342.1,202.02", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="3065.8,178", - width=3.015]; + label=string, + pos="2508.8,178", + width=1.0652]; "gene as a model of disease association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="3114.3,221.5", - pos="e,3027.4,194.99 3196.7,257.59 3110.3,252.55 3021.3,243.83 3007.8,229 2998.6,218.83 3006.2,208.72 3018.7,200.28", + lp="2656.3,221.5", + pos="e,2517.4,195.72 3469.2,262.09 3164.1,258.42 2590.2,248.9 2549.8,229 2538.8,223.61 2529.8,213.78 2523,204.25", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="3247.8,178", + pos="2735.8,178", width=1.5346]; "gene as a model of disease association" -> timepoint [color=blue, label=timepoint, - lp="3262.8,221.5", - pos="e,3233.2,195.52 3273.6,249.47 3252.5,244.29 3234.5,237.54 3227.8,229 3222.1,221.76 3223.8,212.7 3227.9,204.28", + lp="2822.8,221.5", + pos="e,2747.8,195.77 3467.6,263.48 3230.7,261.72 2848.4,254.85 2787.8,229 2774.9,223.5 2763.3,213.23 2754.4,203.43", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="3359.8,178", + pos="2847.8,178", width=1.0652]; "gene as a model of disease association" -> "original subject" [color=blue, label="original subject", - lp="3359.8,221.5", - pos="e,3331.1,190.29 3323,247.53 3315.3,242.75 3308.4,236.67 3303.8,229 3295.8,215.65 3307.4,203.87 3322.2,195.09", + lp="2930.8,221.5", + pos="e,2852.2,195.97 3473.3,260.32 3250.1,255.17 2899.8,244.66 2874.8,229 2866.2,223.61 2860.1,214.49 2856,205.49", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3473.8,178", + pos="2972.8,178", width=1.5887]; "gene as a model of disease association" -> "original predicate" [color=blue, label="original predicate", - lp="3497.3,221.5", - pos="e,3455.5,195.28 3392.9,246.83 3400.3,241.23 3408.5,234.94 3415.8,229 3426.5,220.35 3438,210.53 3447.9,201.9", + lp="3069.3,221.5", + pos="e,2979.2,196.03 3468.6,262.45 3290.7,259.6 3045.2,251.57 3005.8,229 2996.3,223.57 2989.1,214.18 2983.8,205", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3587.8,178", + pos="3101.8,178", width=1.0652]; "gene as a model of disease association" -> "original object" [color=blue, label="original object", - lp="3629.3,221.5", - pos="e,3584.3,195.93 3492.2,251.19 3523.7,245.89 3552.3,238.66 3564.8,229 3572.4,223.14 3577.5,214.2 3581,205.49", + lp="3211.3,221.5", + pos="e,3115.2,195.15 3468,262.93 3351.5,259.92 3214.3,251.45 3159.8,229 3145.7,223.19 3132.6,212.54 3122.4,202.56", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3720.8,178", + pos="3234.8,178", width=2.1304]; "gene as a model of disease association" -> "subject category" [color=blue, label="subject category", - lp="3761.3,221.5", - pos="e,3713,196.33 3500.5,251.9 3583.4,243.83 3676.5,233.85 3684.8,229 3694.3,223.42 3702.1,214.17 3707.9,205.14", + lp="3347.3,221.5", + pos="e,3247.6,195.99 3480.9,258.11 3403.5,253.33 3322.4,244.67 3287.8,229 3275.1,223.23 3263.4,213.13 3254.4,203.51", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3891.8,178", + pos="3405.8,178", width=2.1304]; "gene as a model of disease association" -> "object category" [color=blue, label="object category", - lp="3907.3,221.5", - pos="e,3875.3,195.65 3504.1,252.25 3525.7,250.44 3547.9,248.63 3568.8,247 3625.6,242.57 3771.3,248.86 3824.8,229 3840.5,223.17 3855.6,\ -212.44 3867.6,202.41", + lp="3476.3,221.5", + pos="e,3406.4,196.34 3504.6,254.19 3467.7,249.01 3434.8,241.09 3420.8,229 3414.2,223.27 3410.4,214.73 3408.3,206.33", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="4024.8,178", + pos="3538.8,178", width=1.0652]; "gene as a model of disease association" -> "subject closure" [color=blue, label="subject closure", - lp="4043.3,221.5", - pos="e,4009,194.69 3501.4,252.01 3523.9,250.18 3547,248.42 3568.8,247 3613,244.12 3925.7,245.35 3966.8,229 3974.7,225.87 3989.1,213.45 \ -4001.6,201.77", + lp="3596.3,221.5", + pos="e,3535.3,196.01 3567.2,249.12 3557.4,244.15 3548.6,237.6 3541.8,229 3536.8,222.64 3535,214.28 3534.8,206.23", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="4120.8,178", + pos="3651.8,178", width=1.0652]; "gene as a model of disease association" -> "object closure" [color=blue, label="object closure", - lp="4161.8,221.5", - pos="e,4118.3,196.38 3500,251.91 3522.9,250.06 3546.5,248.33 3568.8,247 3598.3,245.24 4075.5,245.75 4099.8,229 4107.6,223.64 4112.5,214.81 \ -4115.6,206.05", + lp="3704.8,221.5", + pos="e,3652.8,196.18 3655.8,246.8 3655.1,235.16 3654.2,219.55 3653.4,206.24", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="4253.8,178", + pos="3784.8,178", width=2.1304]; "gene as a model of disease association" -> "subject category closure" [color=blue, label="subject category closure", - lp="4320.3,221.5", - pos="e,4245.8,196.2 3499.5,251.84 3522.6,249.98 3546.4,248.27 3568.8,247 3604.7,244.97 4183.8,245.42 4215.8,229 4226.1,223.72 4234.4,\ -214.22 4240.5,204.92", + lp="3857.3,221.5", + pos="e,3779.1,196.41 3725.2,248.11 3736.9,243.29 3748.3,237.05 3757.8,229 3765.1,222.78 3770.8,214.06 3775,205.64", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="4442.8,178", + pos="3977.8,178", width=2.1304]; "gene as a model of disease association" -> "object category closure" [color=blue, label="object category closure", - lp="4510.3,221.5", - pos="e,4437.1,196.13 3498.7,251.78 3522,249.91 3546.1,248.21 3568.8,247 3615.6,244.51 4371.1,252.22 4411.8,229 4421,223.74 4427.8,214.51 \ -4432.7,205.41", + lp="4047.3,221.5", + pos="e,3972.4,196.22 3797,252.82 3865.3,246.36 3935.4,237.79 3948.8,229 3957.3,223.41 3963.6,214.41 3968.1,205.57", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4632.8,178", + pos="4167.8,178", width=1.0652]; "gene as a model of disease association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4682.8,221.5", - pos="e,4625.8,196.2 3498.4,251.73 3521.8,249.86 3546,248.17 3568.8,247 3597.3,245.53 4572.5,242.42 4597.8,229 4607.6,223.78 4615.3,214.43 \ -4620.9,205.21", + lp="4218.8,221.5", + pos="e,4161.4,195.99 3790.6,252.19 3812.4,250.37 3834.7,248.58 3855.8,247 3886.8,244.68 4107.9,244.59 4134.8,229 4144.2,223.52 4151.5,\ +214.12 4156.7,204.94", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4791.8,178", + pos="4326.8,178", width=1.0652]; "gene as a model of disease association" -> "object namespace" [color=blue, label="object namespace", - lp="4835.8,221.5", - pos="e,4784.4,195.75 3498.2,251.7 3521.6,249.83 3545.9,248.15 3568.8,247 3601.7,245.35 4725.5,244.05 4754.8,229 4765.1,223.69 4773.3,\ -214.01 4779.3,204.57", + lp="4371.8,221.5", + pos="e,4319.4,196.12 3787.9,251.98 3810.5,250.14 3833.8,248.39 3855.8,247 3904.1,243.94 4248.2,251.94 4290.8,229 4300.8,223.62 4308.7,\ +214.11 4314.5,204.82", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4942.8,178", + pos="4437.8,178", width=1.0652]; "gene as a model of disease association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4995.8,221.5", - pos="e,4934.8,195.78 3497.9,251.69 3521.4,249.82 3545.8,248.13 3568.8,247 3605.8,245.17 4870.6,245.5 4903.8,229 4914.5,223.68 4923.2,\ -213.86 4929.6,204.32", + lp="4520.8,221.5", + pos="e,4444.1,196.07 3786.8,251.87 3809.8,250.02 3833.5,248.3 3855.8,247 3888.2,245.12 4417.2,252.3 4439.8,229 4445.6,222.97 4446.8,214.36 \ +4445.9,205.98", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="5113.8,178", + pos="4532.8,178", width=1.0652]; "gene as a model of disease association" -> "object label closure" [color=blue, label="object label closure", - lp="5162.3,221.5", - pos="e,5105.5,195.8 3497.6,251.69 3521.3,249.81 3545.8,248.12 3568.8,247 3610.5,244.97 5036.2,247.34 5073.8,229 5084.6,223.7 5093.5,213.88 \ -5100.1,204.34", + lp="4673.3,221.5", + pos="e,4563.2,188.94 3786,251.81 3809.2,249.95 3833.2,248.24 3855.8,247 3876.4,245.87 4584.4,243.77 4598.8,229 4612.3,215.2 4593.5,202.13 \ +4572.6,192.82", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="5257.8,178", + pos="4673.8,178", width=2.347]; "gene as a model of disease association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="5318.3,221.5", - pos="e,5255,196.48 3497.6,251.66 3521.3,249.79 3545.8,248.11 3568.8,247 3591.9,245.89 5216.5,241.76 5235.8,229 5243.7,223.76 5248.8,214.96 \ -5252.1,206.18", + lp="4821.3,221.5", + pos="e,4719.8,193.15 3785.7,251.76 3809,249.89 3833.1,248.2 3855.8,247 3880.5,245.7 4729.5,246.68 4746.8,229 4758.6,216.9 4746.7,205.95 \ +4729.3,197.4", style=solid]; type [height=0.5, - pos="5391.8,178", + pos="4807.8,178", width=0.86659]; "gene as a model of disease association" -> type [color=blue, label=type, - lp="5414.8,221.5", - pos="e,5397.3,196.13 3497.4,251.67 3521.1,249.78 3545.7,248.1 3568.8,247 3594.1,245.8 5374,246.99 5391.8,229 5397.7,223.04 5399.1,214.44 \ -5398.6,206.06", + lp="4914.8,221.5", + pos="e,4832.5,189.33 3785.4,251.72 3808.8,249.86 3833,248.17 3855.8,247 3884.6,245.52 4874.6,249.59 4894.8,229 4899.5,224.25 4898.5,219.51 \ +4894.8,214 4882.4,195.87 4869.2,204.2 4848.8,196 4846.6,195.1 4844.3,194.17 4841.9,193.22", style=solid]; category [height=0.5, - pos="5492.8,178", + pos="4908.8,178", width=1.4263]; "gene as a model of disease association" -> category [color=blue, label=category, - lp="5491.3,221.5", - pos="e,5479.5,195.46 3497.4,251.66 3521.1,249.78 3545.7,248.1 3568.8,247 3620.6,244.54 5386.3,247.29 5434.8,229 5449.1,223.62 5462.2,\ -213.01 5472.3,202.95", - style=solid]; - subject [height=0.5, - pos="5606.8,178", - width=1.2277]; - "gene as a model of disease association" -> subject [color=blue, - label=subject, - lp="5585.8,221.5", - pos="e,5588.5,194.56 3497.4,251.66 3521.1,249.77 3545.7,248.09 3568.8,247 3623.1,244.43 5474.6,244.23 5526.8,229 5546.2,223.32 5565.6,\ -211.46 5580.4,200.71", + lp="4971.3,221.5", + pos="e,4926.3,194.94 3785.2,251.73 3808.6,249.86 3832.9,248.17 3855.8,247 3885.7,245.47 4913.8,250.37 4934.8,229 4942,221.63 4938.9,211.83 \ +4932.7,202.85", + style=solid]; + "subject aspect qualifier" [height=0.5, + pos="5096.8,178", + width=3.3039]; + "gene as a model of disease association" -> "subject aspect qualifier" [color=blue, + label="subject aspect qualifier", + lp="5127.3,221.5", + pos="e,5074.1,195.76 3785.2,251.71 3808.6,249.84 3832.9,248.15 3855.8,247 3919.7,243.78 4945,245.53 5006.8,229 5027.6,223.43 5048.8,212 \ +5065.4,201.48", + style=solid]; + "object direction qualifier" [height=0.5, + pos="5358.8,178", + width=3.4664]; + "gene as a model of disease association" -> "object direction qualifier" [color=blue, + label="object direction qualifier", + lp="5359.8,221.5", + pos="e,5322.4,195.31 3784.9,251.69 3808.4,249.81 3832.8,248.13 3855.8,247 4006.6,239.57 5066,255.1 5214.8,229 5248.6,223.07 5285.1,210.31 \ +5312.9,199.17", + style=solid]; + predicate [height=0.5, + pos="5555.8,178", + width=1.5165]; + "gene as a model of disease association" -> predicate [color=blue, + label=predicate, + lp="5527.8,221.5", + pos="e,5531.7,194.34 3784.6,251.67 3808.3,249.79 3832.8,248.11 3855.8,247 3944.4,242.72 5365.4,249.19 5451.8,229 5476.9,223.13 5503,210.54 \ +5522.8,199.46", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="5753.8,178", + pos="5713.8,178", width=2.3651]; "gene as a model of disease association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="5738.8,221.5", - pos="e,5720.6,194.62 3497.4,251.65 3521.1,249.76 3545.7,248.09 3568.8,247 3682.4,241.66 5503.9,249.16 5615.8,229 5648.8,223.05 5684.4,\ -209.97 5711.2,198.68", + lp="5692.8,221.5", + pos="e,5678.4,194.48 3784.6,251.66 3808.3,249.78 3832.8,248.1 3855.8,247 4045.6,237.91 5378.5,260.8 5565.8,229 5601.5,222.94 5640.2,209.62 \ +5669,198.25", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="5932.8,178", + pos="5892.8,178", width=2.1123]; "gene as a model of disease association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="5920.8,221.5", - pos="e,5903.2,194.87 3497.3,251.63 3521.1,249.75 3545.7,248.08 3568.8,247 3693.2,241.19 5688.7,253.56 5810.8,229 5839.8,223.17 5870.6,\ -210.49 5894,199.36", + lp="5876.8,221.5", + pos="e,5862.2,194.61 3784.4,251.66 3808.1,249.77 3832.7,248.09 3855.8,247 3961.7,241.98 5660.7,249.13 5764.8,229 5795.4,223.09 5828.1,\ +210.18 5852.8,198.97", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="6069.8,178", + pos="6022.8,178", width=1.011]; "gene as a model of disease association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="6071.3,221.5", - pos="e,6051.4,193.86 3497.1,251.64 3520.9,249.75 3545.6,248.08 3568.8,247 3635.9,243.89 5921.1,247.05 5985.8,229 6006.6,223.19 6027.5,\ -210.78 6043.3,199.77", + lp="6027.3,221.5", + pos="e,6005.2,193.84 3784.4,251.64 3808.1,249.76 3832.7,248.09 3855.8,247 3913.7,244.28 5886.1,245.06 5941.8,229 5961.8,223.22 5981.8,\ +210.98 5996.9,200.06", + style=solid]; + "sex qualifier" [color=blue, + height=0.5, + label="biological sex", + pos="6150.8,178", + width=2.0401]; + "gene as a model of disease association" -> "sex qualifier" [color=blue, + label="sex qualifier", + lp="6155.8,221.5", + pos="e,6134.4,195.76 3784.3,251.63 3808.1,249.75 3832.7,248.08 3855.8,247 3917.6,244.12 6024.1,248.52 6082.8,229 6098.9,223.63 6114.4,\ +212.83 6126.6,202.64", + style=solid]; + "has count" [color=blue, + height=0.5, + label=integer, + pos="6286.8,178", + width=1.2277]; + "gene as a model of disease association" -> "has count" [color=blue, + label="has count", + lp="6272.8,221.5", + pos="e,6268.1,194.34 3784.1,251.65 3807.9,249.76 3832.6,248.08 3855.8,247 3920.9,243.97 6141,246.71 6203.8,229 6224,223.31 6244.1,211.32 \ +6259.6,200.51", + style=solid]; + "has total" [color=blue, + height=0.5, + label=integer, + pos="6392.8,178", + width=1.2277]; + "gene as a model of disease association" -> "has total" [color=blue, + label="has total", + lp="6377.3,221.5", + pos="e,6374.3,194.58 3784.1,251.64 3807.9,249.75 3832.6,248.07 3855.8,247 3923.9,243.84 6246.2,247.87 6311.8,229 6331.4,223.35 6351,211.48 \ +6366,200.73", + style=solid]; + "has quotient" [color=blue, + height=0.5, + label=double, + pos="6496.8,178", + width=1.1735]; + "gene as a model of disease association" -> "has quotient" [color=blue, + label="has quotient", + lp="6492.8,221.5", + pos="e,6477.8,194.34 3784.1,251.64 3807.9,249.75 3832.6,248.07 3855.8,247 3926.7,243.72 6344.4,248.08 6412.8,229 6433.3,223.27 6454,211.11 \ +6469.6,200.21", + style=solid]; + "has percentage" [color=blue, + height=0.5, + label=double, + pos="6598.8,178", + width=1.1735]; + "gene as a model of disease association" -> "has percentage" [color=blue, + label="has percentage", + lp="6621.8,221.5", + pos="e,6585.8,195.47 3784.1,251.63 3807.9,249.74 3832.6,248.07 3855.8,247 3930.3,243.57 6472,255.52 6541.8,229 6555.9,223.63 6568.8,213.03 \ +6578.8,202.96", + style=solid]; + object [height=0.5, + pos="6754.8,91", + width=1.0832]; + "gene as a model of disease association" -> object [color=blue, + label=object, + lp="6748.8,178", + pos="e,6748.2,108.8 3784.1,251.62 3807.9,249.73 3832.6,248.06 3855.8,247 3895,245.2 6647.2,249.21 6680.8,229 6701.5,216.53 6729.5,154.42 \ +6744.4,118.25", + style=solid]; + subject [height=0.5, + pos="6825.8,178", + width=1.2277]; + "gene as a model of disease association" -> subject [color=blue, + label=subject, + lp="6797.8,221.5", + pos="e,6805.1,194.12 3784.1,251.62 3807.9,249.73 3832.6,248.06 3855.8,247 3935.7,243.34 6656.4,248.94 6733.8,229 6756.3,223.21 6779.2,\ +210.75 6796.6,199.72", style=solid]; - relation [height=0.5, - pos="5557.8,18", - width=1.2999]; - object -> relation [pos="e,5546.3,35.705 5520.4,73.174 5526.4,64.509 5533.8,53.768 5540.4,44.141", - style=dotted]; association_type [color=blue, height=0.5, label=string, - pos="3615.8,265", + pos="3902.8,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3746.8,265", + pos="4033.8,265", width=2.0762]; + "gene to disease or phenotypic feature association_subject aspect qualifier" [color=blue, + height=0.5, + label=GeneOrGeneProductOrChemicalEntityAspectEnum, + pos="4375.8,265", + width=6.9147]; + "gene to disease or phenotypic feature association_object direction qualifier" [color=blue, + height=0.5, + label=DirectionQualifierEnum, + pos="4763.8,265", + width=3.358]; + "gene to disease or phenotypic feature association_predicate" [color=blue, + height=0.5, + label="predicate type", + pos="4980.8,265", + width=2.1665]; + relation [height=0.5, + pos="6789.8,18", + width=1.2999]; + object -> relation [pos="e,6781.3,36.198 6763.1,73.174 6767.2,64.896 6772.2,54.723 6776.8,45.438", + style=dotted]; + "gene to disease association_object" [color=blue, + height=0.5, + label=disease, + pos="5121.8,265", + width=1.2638]; subject -> object [label=relation, - lp="5564.8,134.5", - pos="e,5515.2,108.97 5574.3,165.59 5561.5,159.94 5547.4,152.13 5536.8,142 5529.8,135.31 5524.1,126.48 5519.6,118.1"]; - subject -> relation [pos="e,5569,35.828 5605.4,159.99 5603.3,139.02 5598.4,102.55 5587.8,73 5584.3,63.258 5579.2,53.189 5574.2,44.423", + lp="6783.8,134.5", + pos="e,6751,109.01 6789.4,167.42 6776.6,162.12 6763.4,154.06 6755.8,142 6751.5,135.26 6750.2,126.93 6750.2,119.01"]; + subject -> relation [pos="e,6794,36.005 6822.1,160.05 6817.7,139.44 6809.9,103.63 6802.8,73 6800.8,64.183 6798.5,54.574 6796.4,45.938", style=dotted]; "gene as a model of disease association_subject" [color=blue, height=0.5, label="gene or gene product", - pos="3949.8,265", + pos="5295.8,265", width=3.0692]; } diff --git a/graphviz/gene_as_a_model_of_disease_association.svg b/graphviz/gene_as_a_model_of_disease_association.svg index 960c221b66..a01889738c 100644 --- a/graphviz/gene_as_a_model_of_disease_association.svg +++ b/graphviz/gene_as_a_model_of_disease_association.svg @@ -4,16 +4,16 @@ - + %3 - + gene as a model of disease association - -gene as a model of disease association + +gene as a model of disease association @@ -24,7 +24,7 @@ gene as a model of disease association->gene to disease association - + is_a @@ -37,8 +37,8 @@ gene as a model of disease association->model to disease association mixin - - + + uses @@ -50,8 +50,8 @@ gene as a model of disease association->entity to disease association mixin - - + + uses @@ -63,7 +63,7 @@ gene as a model of disease association->id - + id @@ -76,9 +76,9 @@ gene as a model of disease association->iri - - -iri + + +iri @@ -89,9 +89,9 @@ gene as a model of disease association->name - - -name + + +name @@ -102,9 +102,9 @@ gene as a model of disease association->description - - -description + + +description @@ -115,442 +115,557 @@ gene as a model of disease association->has attribute - - -has attribute - - - -predicate - -predicate type - - - -gene as a model of disease association->predicate - - -predicate - - - -object - -named thing - - - -gene as a model of disease association->object - - -object + + +has attribute - + negated - -boolean + +boolean - + gene as a model of disease association->negated - - -negated + + +negated - + qualifiers - -ontology class + +ontology class - + gene as a model of disease association->qualifiers - - -qualifiers + + +qualifiers - + publications - -publication + +publication - + gene as a model of disease association->publications - - -publications + + +publications - + has evidence - -evidence type + +evidence type - + gene as a model of disease association->has evidence - - -has evidence + + +has evidence - + knowledge source - -information resource + +string - + gene as a model of disease association->knowledge source - - -knowledge source + + +knowledge source - + primary knowledge source - -information resource + +string - + gene as a model of disease association->primary knowledge source - - -primary knowledge source + + +primary knowledge source - + aggregator knowledge source - -information resource + +string - + gene as a model of disease association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source - + timepoint - -time type + +time type - + gene as a model of disease association->timepoint - - -timepoint + + +timepoint - + original subject - -string + +string - + gene as a model of disease association->original subject - - -original subject + + +original subject - + original predicate - -uriorcurie + +uriorcurie - + gene as a model of disease association->original predicate - - -original predicate + + +original predicate - + original object - -string + +string - + gene as a model of disease association->original object - - -original object + + +original object - + subject category - -ontology class + +ontology class - + gene as a model of disease association->subject category - - -subject category + + +subject category - + object category - -ontology class + +ontology class - + gene as a model of disease association->object category - - -object category + + +object category - + subject closure - -string + +string - + gene as a model of disease association->subject closure - - -subject closure + + +subject closure - + object closure - -string + +string - + gene as a model of disease association->object closure - - -object closure + + +object closure - + subject category closure - -ontology class + +ontology class - + gene as a model of disease association->subject category closure - - -subject category closure + + +subject category closure - + object category closure - -ontology class + +ontology class - + gene as a model of disease association->object category closure - - -object category closure + + +object category closure - + subject namespace - -string + +string - + gene as a model of disease association->subject namespace - - -subject namespace + + +subject namespace - + object namespace - -string + +string - + gene as a model of disease association->object namespace - - -object namespace + + +object namespace - + subject label closure - -string + +string - + gene as a model of disease association->subject label closure - - -subject label closure + + +subject label closure - + object label closure - -string + +string - + gene as a model of disease association->object label closure - - -object label closure + + +object label closure - + retrieval source ids - -retrieval source + +retrieval source - + gene as a model of disease association->retrieval source ids - - -retrieval source ids + + +retrieval source ids - + type - -type + +type - + gene as a model of disease association->type - - -type + + +type - + category - -category + +category - + gene as a model of disease association->category - - -category + + +category - + + +subject aspect qualifier + +subject aspect qualifier + + + +gene as a model of disease association->subject aspect qualifier + + +subject aspect qualifier + + -subject - -subject +object direction qualifier + +object direction qualifier - + + +gene as a model of disease association->object direction qualifier + + +object direction qualifier + + + +predicate + +predicate + + -gene as a model of disease association->subject - - -subject +gene as a model of disease association->predicate + + +predicate - + frequency qualifier - -frequency value + +frequency value gene as a model of disease association->frequency qualifier - - -frequency qualifier + + +frequency qualifier - + severity qualifier - -severity value + +severity value gene as a model of disease association->severity qualifier - - -severity qualifier + + +severity qualifier - + onset qualifier - -onset + +onset gene as a model of disease association->onset qualifier - - -onset qualifier + + +onset qualifier - - -relation - -relation + + +sex qualifier + +biological sex - + + +gene as a model of disease association->sex qualifier + + +sex qualifier + + + +has count + +integer + + + +gene as a model of disease association->has count + + +has count + + + +has total + +integer + + -object->relation - - +gene as a model of disease association->has total + + +has total + + + +has quotient + +double + + + +gene as a model of disease association->has quotient + + +has quotient + + + +has percentage + +double + + + +gene as a model of disease association->has percentage + + +has percentage + + + +object + +object + + + +gene as a model of disease association->object + + +object + + + +subject + +subject + + + +gene as a model of disease association->subject + + +subject - + association_type - -string + +string - + association_category - -category type + +category type + + + +gene to disease or phenotypic feature association_subject aspect qualifier + +GeneOrGeneProductOrChemicalEntityAspectEnum + + + +gene to disease or phenotypic feature association_object direction qualifier + +DirectionQualifierEnum + + + +gene to disease or phenotypic feature association_predicate + +predicate type + + + +relation + +relation + + + +object->relation + + + + + +gene to disease association_object + +disease - + subject->object - - -relation + + +relation - + subject->relation - - + + - + gene as a model of disease association_subject - -gene or gene product + +gene or gene product diff --git a/graphviz/gene_has_variant_that_contributes_to_disease_association.gv b/graphviz/gene_has_variant_that_contributes_to_disease_association.gv index 305b97ee26..16c7d77f09 100644 --- a/graphviz/gene_has_variant_that_contributes_to_disease_association.gv +++ b/graphviz/gene_has_variant_that_contributes_to_disease_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,5100.4,283"]; + graph [bb="0,0,6363.4,283"]; node [label="\N"]; "gene has variant that contributes to disease association" [height=0.5, label="gene has variant that contributes to disease association", - pos="2681.8,265", + pos="3189.8,265", width=7.5104]; "gene to disease association" [height=0.5, pos="137.79,178", width=3.8274]; "gene has variant that contributes to disease association" -> "gene to disease association" [label=is_a, lp="430.79,221.5", - pos="e,203.33,193.84 2414.5,262.3 1857.9,258.41 610.43,247.72 416.79,229 347.25,222.28 269.03,207.63 213.14,195.92"]; + pos="e,203.32,193.9 2920.6,263.13 2272.5,260.66 660.89,252.25 416.79,229 347.24,222.37 269.02,207.72 213.14,195.98"]; id [color=blue, height=0.5, label=string, @@ -19,7 +19,7 @@ digraph { "gene has variant that contributes to disease association" -> id [color=blue, label=id, lp="545.79,221.5", - pos="e,360.78,189.98 2413.9,262.45 1880.3,258.94 720.03,249.11 538.79,229 467.06,221.04 449.3,215.43 379.79,196 376.68,195.13 373.48,\ + pos="e,360.78,189.98 2920.3,263.37 2292.9,261.48 770.32,254.32 538.79,229 467.04,221.15 449.3,215.43 379.79,196 376.68,195.13 373.48,\ 194.17 370.28,193.15", style=solid]; iri [color=blue, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "gene has variant that contributes to disease association" -> iri [color=blue, label=iri, - lp="658.79,221.5", - pos="e,465.7,190.19 2414.5,262.08 1903,258.01 821.12,247.35 650.79,229 576.43,220.99 558.18,214.78 485.79,196 482.41,195.12 478.93,194.16 \ -475.45,193.14", + lp="651.79,221.5", + pos="e,465.71,190.15 2920.6,263.23 2311.8,261.06 864.86,253.38 643.79,229 572.48,221.14 555.15,214.31 485.79,196 482.42,195.11 478.94,\ +194.13 475.46,193.11", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "gene has variant that contributes to disease association" -> name [color=blue, label=name, - lp="765.79,221.5", - pos="e,589.54,191.54 2413.6,262.63 1920.7,259.61 906.14,250.81 745.79,229 695.01,222.09 638.42,206.58 599.53,194.65", + lp="754.79,221.5", + pos="e,588.02,191.82 2919.6,263.99 2326.4,263.42 945.88,258.85 734.79,229 687.24,222.28 634.5,206.99 597.9,195.08", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "gene has variant that contributes to disease association" -> description [color=blue, label=description, - lp="886.29,221.5", - pos="e,735.6,194.15 2412.1,263.54 1939,262.03 995.26,255.68 845.79,229 810.95,222.78 773.21,209.42 745.11,198.07", + lp="868.29,221.5", + pos="e,731.9,194.56 2921.6,262.62 2324.3,259.19 928.74,249.07 827.79,229 797.63,223 765.43,210.1 741.14,198.91", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "gene has variant that contributes to disease association" -> "has attribute" [color=blue, label="has attribute", - lp="1031.8,221.5", - pos="e,876.41,192.95 2412.4,263.26 1968.9,261.32 1120.7,254.31 984.79,229 950.32,222.58 913.03,208.62 885.92,197.07", + lp="1002.8,221.5", + pos="e,871.71,194.07 2921.4,262.74 2348.4,259.65 1049.9,250.33 955.79,229 929.26,222.99 901.41,210.09 880.51,198.9", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "gene has variant that contributes to disease association" -> negated [color=blue, label=negated, - lp="1186.8,221.5", - pos="e,997.63,190.46 2411.4,264.61 2040.1,264.27 1392,259.15 1157.8,229 1105.2,222.23 1046.5,205.81 1007.6,193.62", + lp="1140.8,221.5", + pos="e,993.41,192.04 2919.6,264.09 2397.2,263.59 1284.9,258.95 1111.8,229 1073.7,222.42 1032.2,207.69 1002.9,195.91", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "gene has variant that contributes to disease association" -> qualifiers [color=blue, label=qualifiers, - lp="1325.3,221.5", - pos="e,1146.5,193.2 2411.1,264.76 2069.1,264.39 1500,259.03 1291.8,229 1245.1,222.26 1193.3,207.87 1156.1,196.25", + lp="1251.3,221.5", + pos="e,1132.5,195.02 2922.6,262.06 2402.9,257.9 1299.4,247 1217.8,229 1191.1,223.12 1163.1,210.74 1141.6,199.77", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "gene has variant that contributes to disease association" -> publications [color=blue, label=publications, - lp="1470.8,221.5", - pos="e,1297.5,192.85 2411.2,264.86 2100.2,264.36 1609.1,258.62 1426.8,229 1385.4,222.28 1339.9,207.95 1307.2,196.35", + lp="1353.8,221.5", + pos="e,1272.6,195.84 2919.3,264.42 2416.5,264.43 1382,260.59 1309.8,229 1297.6,223.65 1286.9,213.55 1278.8,203.82", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,284 +100,396 @@ digraph { width=2.0943]; "gene has variant that contributes to disease association" -> "has evidence" [color=blue, label="has evidence", - lp="1629.3,221.5", - pos="e,1455.8,193.63 2412.2,263.49 2139.3,261.53 1736.2,254.23 1582.8,229 1542.4,222.35 1498,208.52 1465.5,197.09", + lp="1453.3,221.5", + pos="e,1407.2,195.97 2919.9,263.52 2427.9,261.98 1432.9,255.6 1406.8,229 1400.6,222.73 1400.9,213.85 1403.5,205.31", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1619.8,178", - width=3.015]; + label=string, + pos="1549.8,178", + width=1.0652]; "gene has variant that contributes to disease association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1784.3,221.5", - pos="e,1645.3,195.61 2421.1,260.2 2159.4,255.48 1785.9,245.89 1719.8,229 1696.7,223.1 1672.7,211.34 1654,200.71", + lp="1572.3,221.5", + pos="e,1526.5,192.43 2920.6,263.18 2451.6,261.09 1532.1,253.84 1507.8,229 1498.4,219.46 1506.6,208.11 1518.1,198.64", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1854.8,178", - width=3.015]; + label=string, + pos="1644.8,178", + width=1.0652]; "gene has variant that contributes to disease association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1955.8,221.5", - pos="e,1851.8,196.33 2418.5,260.89 2186.2,256.9 1881.4,248.05 1860.8,229 1854.7,223.32 1852.3,214.91 1851.7,206.59", + lp="1742.8,221.5", + pos="e,1640.5,196.25 2921.6,262.49 2486,259.42 1670.4,250.76 1647.8,229 1641.8,223.23 1639.9,214.79 1639.8,206.49", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2089.8,178", - width=3.015]; + label=string, + pos="1819.8,178", + width=1.0652]; "gene has variant that contributes to disease association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2164.3,221.5", - pos="e,2068,195.87 2433.5,257.84 2265.3,252.41 2071.1,243.13 2057.8,229 2050.6,221.43 2054.1,212.05 2060.9,203.46", + lp="1965.3,221.5", + pos="e,1827.8,195.73 2921.4,262.78 2546.2,260.24 1905.3,252.46 1858.8,229 1848.1,223.61 1839.5,213.78 1833.1,204.25", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2271.8,178", + pos="2045.8,178", width=1.5346]; "gene has variant that contributes to disease association" -> timepoint [color=blue, label=timepoint, - lp="2318.8,221.5", - pos="e,2271.2,196.43 2456.3,255.06 2374.4,249.74 2298.3,241.51 2283.8,229 2277.3,223.36 2273.9,214.85 2272.4,206.44", + lp="2133.8,221.5", + pos="e,2058.1,195.81 2928.7,260.26 2618.1,255.11 2136.5,244.68 2098.8,229 2085.7,223.56 2073.9,213.3 2064.8,203.49", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2383.8,178", + pos="2157.8,178", width=1.0652]; "gene has variant that contributes to disease association" -> "original subject" [color=blue, label="original subject", - lp="2416.8,221.5", - pos="e,2368,194.82 2483,252.75 2423,247.32 2370.3,239.62 2360.8,229 2354.1,221.56 2356.7,211.86 2362.2,202.98", + lp="2242.8,221.5", + pos="e,2162.8,196.05 2925.6,261.09 2639.1,256.98 2218.1,247.79 2186.8,229 2177.8,223.64 2171.4,214.39 2166.9,205.3", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2497.8,178", + pos="2283.8,178", width=1.5887]; "gene has variant that contributes to disease association" -> "original predicate" [color=blue, label="original predicate", - lp="2543.3,221.5", - pos="e,2484,195.8 2528.1,250.19 2505.7,245.17 2487.6,238.33 2479.8,229 2473.9,222.05 2475.2,213.06 2479.1,204.62", + lp="2382.3,221.5", + pos="e,2290.8,196.11 2933.5,259.23 2686.3,253.78 2345.6,243.67 2318.8,229 2309,223.66 2301.4,214.29 2295.8,205.1", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2611.8,178", + pos="2412.8,178", width=1.0652]; "gene has variant that contributes to disease association" -> "original object" [color=blue, label="original object", - lp="2667.3,221.5", - pos="e,2609.2,196.07 2635.5,247.23 2627.8,242.47 2620.7,236.48 2615.8,229 2611.4,222.32 2609.6,214 2609.2,206.08", + lp="2525.3,221.5", + pos="e,2427,195.27 2933.2,259.29 2745.4,254.51 2516.4,245.41 2473.8,229 2459,223.3 2445.1,212.51 2434.3,202.41", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2744.8,178", + pos="2545.8,178", width=2.1304]; "gene has variant that contributes to disease association" -> "subject category" [color=blue, label="subject category", - lp="2791.3,221.5", - pos="e,2739.4,196.22 2705.7,246.74 2711.8,241.53 2718,235.46 2722.8,229 2728,221.97 2732.3,213.49 2735.7,205.54", + lp="2662.3,221.5", + pos="e,2559.8,196.18 2947.8,256.94 2800.7,251.36 2635.1,242.28 2602.8,229 2589.2,223.42 2576.6,213.21 2566.8,203.46", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2915.8,178", + pos="2716.8,178", width=2.1304]; "gene has variant that contributes to disease association" -> "object category" [color=blue, label="object category", - lp="2934.3,221.5", - pos="e,2899.7,195.91 2797.9,248.66 2817.4,243.8 2837.1,237.41 2854.8,229 2868.4,222.54 2881.6,212.41 2892.2,202.94", + lp="2792.3,221.5", + pos="e,2719,196.21 2951.9,256.4 2852.4,251.22 2755.5,242.72 2736.8,229 2729.3,223.51 2724.6,214.77 2721.7,206.12", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3048.8,178", + pos="2849.8,178", width=1.0652]; "gene has variant that contributes to disease association" -> "subject closure" [color=blue, label="subject closure", - lp="3071.3,221.5", - pos="e,3035.7,195.42 2872.1,252.2 2923.2,246.92 2970.7,239.45 2993.8,229 3007,223.04 3019.1,212.72 3028.7,203", + lp="2914.3,221.5", + pos="e,2848.5,196.31 2993.8,252.59 2929.3,247.02 2871,239.27 2859.8,229 2853.5,223.23 2850.5,214.69 2849.2,206.29", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3148.8,178", + pos="2962.8,178", width=1.0652]; "gene has variant that contributes to disease association" -> "object closure" [color=blue, label="object closure", - lp="3191.8,221.5", - pos="e,3146.9,196.18 2866.2,251.81 2987.3,243.45 3124.3,233.15 3129.8,229 3137.2,223.48 3141.7,214.73 3144.4,206.08", + lp="3033.8,221.5", + pos="e,2965.7,196.41 3046.6,249.72 3018.9,244.65 2995,237.91 2983.8,229 2976.6,223.28 2971.8,214.64 2968.7,206.14", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3281.8,178", + pos="3095.8,178", width=2.1304]; "gene has variant that contributes to disease association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3350.3,221.5", - pos="e,3274.4,196.04 2873.8,252.32 3036.9,242.37 3244.7,229.58 3245.8,229 3255.6,223.57 3263.4,214.19 3269.3,205", + lp="3179.3,221.5", + pos="e,3089.2,196.21 3113.1,247.64 3104.7,242.91 3097.3,236.83 3091.8,229 3087.2,222.47 3086.4,214.19 3087.3,206.26", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3473.8,178", + pos="3288.8,178", width=2.1304]; "gene has variant that contributes to disease association" -> "object category closure" [color=blue, label="object category closure", - lp="3541.3,221.5", - pos="e,3467.7,196.08 2869.3,252.02 2900.2,250.21 2931.9,248.47 2961.8,247 2988.4,245.69 3418.6,242.25 3441.8,229 3451.2,223.63 3458.3,\ -214.25 3463.3,205.06", + lp="3361.3,221.5", + pos="e,3284.6,196.08 3240.8,247.2 3250.3,242.41 3259.5,236.42 3266.8,229 3273.2,222.5 3277.9,213.82 3281.3,205.51", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3663.8,178", + pos="3478.8,178", width=1.0652]; "gene has variant that contributes to disease association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3713.8,221.5", - pos="e,3656.8,196.17 2867,251.87 2898.6,250.06 2931.1,248.34 2961.8,247 2998.8,245.38 3596.1,246.56 3628.8,229 3638.6,223.73 3646.2,214.37 \ -3651.8,205.16", + lp="3531.8,221.5", + pos="e,3473,196.18 3366.6,251.37 3402.3,246.23 3433.5,239.04 3448.8,229 3457.4,223.3 3464,214.15 3468.7,205.24", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3822.8,178", + pos="3637.8,178", width=1.0652]; "gene has variant that contributes to disease association" -> "object namespace" [color=blue, label="object namespace", - lp="3866.8,221.5", - pos="e,3815.4,195.72 2865.9,251.8 2897.8,249.98 2930.8,248.28 2961.8,247 3007.5,245.11 3745.1,250.05 3785.8,229 3796.1,223.66 3804.3,\ -213.97 3810.3,204.54", + lp="3683.8,221.5", + pos="e,3631,195.93 3375.1,251.88 3480.4,244.4 3593.4,235.1 3603.8,229 3613.3,223.44 3620.7,214.03 3626.2,204.86", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3973.8,178", + pos="3732.8,178", width=1.0652]; "gene has variant that contributes to disease association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4026.8,221.5", - pos="e,3965.8,195.76 2865.1,251.76 2897.3,249.93 2930.5,248.24 2961.8,247 3015.8,244.86 3886.4,253.17 3934.8,229 3945.5,223.65 3954.1,\ -213.83 3960.5,204.29", + lp="3830.8,221.5", + pos="e,3746.8,195.12 3381.4,252.25 3544.1,242.25 3751.4,229.43 3751.8,229 3758.3,222.07 3756.6,212.68 3752.1,203.91", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4144.8,178", + pos="3827.8,178", width=1.0652]; "gene has variant that contributes to disease association" -> "object label closure" [color=blue, label="object label closure", - lp="4192.3,221.5", - pos="e,4136.5,195.78 2864.7,251.71 2897.1,249.87 2930.4,248.2 2961.8,247 2993.5,245.79 4076.3,242.98 4104.8,229 4115.6,223.68 4124.5,\ -213.86 4131.1,204.32", + lp="3982.3,221.5", + pos="e,3857.2,189.9 3378,252.06 3408.7,250.26 3440.1,248.51 3469.8,247 3494.2,245.76 3891.9,246.61 3908.8,229 3913.4,224.19 3912.4,219.57 \ +3908.8,214 3906.1,209.93 3886.1,201.26 3866.6,193.57", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4297.8,178", + pos="3968.8,178", width=2.347]; "gene has variant that contributes to disease association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4351.3,221.5", - pos="e,4291.8,196.17 2864,251.7 2896.5,249.85 2930.2,248.18 2961.8,247 2998,245.65 4234.1,246.61 4265.8,229 4275.2,223.74 4282.3,214.38 \ -4287.4,205.18", + lp="4131.3,221.5", + pos="e,4023.3,191.8 3375.8,251.93 3407.1,250.11 3439.4,248.39 3469.8,247 3502.3,245.51 4033.1,252.38 4055.8,229 4069.5,214.88 4054.2,\ +203.5 4032.8,195.17", style=solid]; type [height=0.5, - pos="4431.8,178", + pos="4102.8,178", width=0.86659]; "gene has variant that contributes to disease association" -> type [color=blue, label=type, - lp="4449.8,221.5", - pos="e,4434.5,195.98 2864,251.66 2896.5,249.82 2930.2,248.15 2961.8,247 2982.1,246.26 4409.5,242.43 4424.8,229 4431.2,223.32 4433.8,214.65 \ -4434.4,206.11", + lp="4224.8,221.5", + pos="e,4126.9,189.5 3374.6,251.83 3406.4,250.01 3439,248.31 3469.8,247 3490.2,246.13 4190.5,243.62 4204.8,229 4209.4,224.23 4208.8,219.34 \ +4204.8,214 4187.9,191.36 4170.4,205.43 4143.8,196 4141.4,195.15 4138.9,194.23 4136.4,193.27", style=solid]; category [height=0.5, - pos="4532.8,178", + pos="4203.8,178", width=1.4263]; "gene has variant that contributes to disease association" -> category [color=blue, label=category, - lp="4528.3,221.5", - pos="e,4518,195.47 2863.6,251.67 2896.3,249.82 2930,248.15 2961.8,247 3003.7,245.48 4430.3,243.03 4469.8,229 4485,223.58 4499.4,212.83 \ -4510.5,202.67", + lp="4281.3,221.5", + pos="e,4228.5,193.79 3374.2,251.82 3406.1,250 3438.9,248.3 3469.8,247 3491.3,246.1 4229.7,244.4 4244.8,229 4253.6,220.02 4246.8,209.34 \ +4236.5,200.16", + style=solid]; + "subject aspect qualifier" [height=0.5, + pos="4391.8,178", + width=3.3039]; + "gene has variant that contributes to disease association" -> "subject aspect qualifier" [color=blue, + label="subject aspect qualifier", + lp="4431.3,221.5", + pos="e,4373,195.95 3373.9,251.79 3405.8,249.96 3438.8,248.27 3469.8,247 3516.8,245.07 4271.9,243.12 4316.8,229 4334.3,223.48 4351.6,212.48 \ +4365.1,202.2", + style=solid]; + "object direction qualifier" [height=0.5, + pos="4653.8,178", + width=3.4664]; + "gene has variant that contributes to disease association" -> "object direction qualifier" [color=blue, + label="object direction qualifier", + lp="4660.8,221.5", + pos="e,4619.5,195.39 3372.7,251.74 3405.1,249.91 3438.4,248.22 3469.8,247 3586.3,242.47 4404.2,250.55 4518.8,229 4550.4,223.05 4584.3,\ +210.45 4610.3,199.39", + style=solid]; + "frequency qualifier" [color=blue, + height=0.5, + label="frequency value", + pos="4881.8,178", + width=2.3651]; + "gene has variant that contributes to disease association" -> "frequency qualifier" [color=blue, + label="frequency qualifier", + lp="4871.8,221.5", + pos="e,4850.4,194.81 3372.3,251.68 3404.8,249.85 3438.3,248.18 3469.8,247 3612.3,241.68 4612.8,256.19 4752.8,229 4783.5,223.03 4816.4,\ +210.18 4841.3,199", + style=solid]; + "severity qualifier" [color=blue, + height=0.5, + label="severity value", + pos="5060.8,178", + width=2.1123]; + "gene has variant that contributes to disease association" -> "severity qualifier" [color=blue, + label="severity qualifier", + lp="5051.8,221.5", + pos="e,5032.5,194.83 3372,251.66 3404.5,249.82 3438.2,248.15 3469.8,247 3551.6,244.02 4863.7,245.91 4943.8,229 4971.6,223.13 5001,210.54 \ +5023.4,199.46", + style=solid]; + "onset qualifier" [color=blue, + height=0.5, + label=onset, + pos="5190.8,178", + width=1.011]; + "gene has variant that contributes to disease association" -> "onset qualifier" [color=blue, + label="onset qualifier", + lp="5199.3,221.5", + pos="e,5174.4,194.3 3371.6,251.64 3404.3,249.8 3438,248.14 3469.8,247 3515.5,245.36 5073.1,242.63 5116.8,229 5135.1,223.3 5152.9,211.48 \ +5166.5,200.76", + style=solid]; + "sex qualifier" [color=blue, + height=0.5, + label="biological sex", + pos="5318.8,178", + width=2.0401]; + "gene has variant that contributes to disease association" -> "sex qualifier" [color=blue, + label="sex qualifier", + lp="5326.8,221.5", + pos="e,5303.5,195.73 3371.2,251.64 3404,249.79 3437.9,248.13 3469.8,247 3519.3,245.25 5208,245.38 5254.8,229 5270.3,223.59 5284.9,212.79 \ +5296.2,202.61", + style=solid]; + "has count" [color=blue, + height=0.5, + label=integer, + pos="5454.8,178", + width=1.2277]; + "gene has variant that contributes to disease association" -> "has count" [color=blue, + label="has count", + lp="5442.8,221.5", + pos="e,5436.5,194.56 3371.2,251.63 3404,249.78 3437.9,248.12 3469.8,247 3522.7,245.15 5324,243.83 5374.8,229 5394.2,223.32 5413.6,211.45 \ +5428.4,200.71", + style=solid]; + "has total" [color=blue, + height=0.5, + label=integer, + pos="5560.8,178", + width=1.2277]; + "gene has variant that contributes to disease association" -> "has total" [color=blue, + label="has total", + lp="5546.3,221.5", + pos="e,5542.8,194.56 3371.2,251.61 3404,249.76 3437.9,248.11 3469.8,247 3525.6,245.06 5428.2,244.8 5481.8,229 5501.1,223.32 5520.1,211.46 \ +5534.7,200.71", + style=solid]; + "has quotient" [color=blue, + height=0.5, + label=double, + pos="5664.8,178", + width=1.1735]; + "gene has variant that contributes to disease association" -> "has quotient" [color=blue, + label="has quotient", + lp="5660.8,221.5", + pos="e,5646.1,194.33 3370.8,251.62 3403.8,249.77 3437.8,248.11 3469.8,247 3528.4,244.97 5525.3,244.95 5581.8,229 5602,223.3 5622.1,211.31 \ +5637.6,200.5", + style=solid]; + "has percentage" [color=blue, + height=0.5, + label=double, + pos="5766.8,178", + width=1.1735]; + "gene has variant that contributes to disease association" -> "has percentage" [color=blue, + label="has percentage", + lp="5789.8,221.5", + pos="e,5753.8,195.46 3370.8,251.61 3403.8,249.76 3437.8,248.1 3469.8,247 3532,244.86 5651.6,251.16 5709.8,229 5723.9,223.62 5736.8,213.02 \ +5746.8,202.96", style=solid]; "subject form or variant qualifier" [color=blue, height=0.5, label=string, - pos="4640.8,178", + pos="5872.8,178", width=1.0652]; "gene has variant that contributes to disease association" -> "subject form or variant qualifier" [color=blue, label="subject form or variant qualifier", - lp="4710.3,221.5", - pos="e,4623.6,194.3 2863.6,251.65 2896.3,249.81 2930,248.14 2961.8,247 3050.7,243.8 4478.6,254.76 4563.8,229 4582.6,223.31 4601.2,211.49 \ -4615.4,200.77", + lp="5976.3,221.5", + pos="e,5869.5,196.05 3370.8,251.6 3403.8,249.74 3437.8,248.09 3469.8,247 3502.8,245.87 5820.9,246.7 5848.8,229 5857.1,223.7 5862.7,214.59 \ +5866.3,205.59", style=solid]; subject [height=0.5, - pos="4848.8,178", + pos="6111.8,178", width=1.2277]; "gene has variant that contributes to disease association" -> subject [color=blue, label=subject, - lp="4866.8,221.5", - pos="e,4846.7,196.43 2863.2,251.63 2896,249.78 2929.9,248.12 2961.8,247 2987.7,246.09 4807.4,243.64 4828.8,229 4836.5,223.71 4841.3,214.89 \ -4844.2,206.12", + lp="6131.8,221.5", + pos="e,6110.8,196.36 3370.5,251.6 3403.5,249.74 3437.7,248.08 3469.8,247 3506.2,245.77 6065.2,250.33 6094.8,229 6102.2,223.68 6106.4,\ +214.98 6108.8,206.31", style=solid]; object [height=0.5, - pos="4891.8,91", + pos="6154.8,91", width=1.0832]; "gene has variant that contributes to disease association" -> object [color=blue, label=object, - lp="4946.8,178", - pos="e,4905.2,108.09 2863.2,251.62 2896,249.77 2929.9,248.12 2961.8,247 2988.6,246.06 4876,246.07 4896.8,229 4932.3,199.77 4928,171.1 \ -4914.8,127 4913.8,123.55 4912.3,120.13 4910.5,116.85", + lp="6210.8,178", + pos="e,6168.2,108.09 3370.5,251.59 3403.5,249.74 3437.7,248.08 3469.8,247 3488.5,246.37 6147.5,241.01 6161.8,229 6196.9,199.52 6190.9,\ +170.96 6177.8,127 6176.8,123.55 6175.3,120.13 6173.5,116.85", style=solid]; predicate [height=0.5, - pos="5045.8,178", + pos="6308.8,178", width=1.5165]; "gene has variant that contributes to disease association" -> predicate [color=blue, label=predicate, - lp="5018.8,221.5", - pos="e,5022,194.36 2863.2,251.62 2896,249.77 2929.9,248.11 2961.8,247 3071.8,243.16 4835.6,254.15 4942.8,229 4967.7,223.16 4993.6,210.56 \ -5013.2,199.48", + lp="6281.8,221.5", + pos="e,6285,194.38 3370.5,251.59 3403.5,249.73 3437.7,248.08 3469.8,247 3545.7,244.45 6131.8,246.27 6205.8,229 6230.7,223.19 6256.6,210.59 \ +6276.2,199.5", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3008.8,265", + pos="3516.8,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3139.8,265", + pos="3647.8,265", width=2.0762]; + "gene to disease or phenotypic feature association_subject aspect qualifier" [color=blue, + height=0.5, + label=GeneOrGeneProductOrChemicalEntityAspectEnum, + pos="3989.8,265", + width=6.9147]; + "gene to disease or phenotypic feature association_object direction qualifier" [color=blue, + height=0.5, + label=DirectionQualifierEnum, + pos="4377.8,265", + width=3.358]; subject -> object [label=relation, - lp="4886.8,134.5", - pos="e,4873.9,107.23 4849.9,159.55 4851.1,149.57 4853.6,137.07 4858.8,127 4861,122.68 4863.9,118.52 4867.1,114.66"]; + lp="6149.8,134.5", + pos="e,6136.9,107.23 6112.9,159.55 6114.1,149.57 6116.6,137.07 6121.8,127 6124,122.68 6126.9,118.52 6130.1,114.66"]; relation [height=0.5, - pos="4836.8,18", + pos="6099.8,18", width=1.2999]; - subject -> relation [pos="e,4838.1,36.188 4847.5,159.79 4845.4,132.48 4841.3,78.994 4838.9,46.38", + subject -> relation [pos="e,6101.1,36.188 6110.5,159.79 6108.4,132.48 6104.3,78.994 6101.9,46.38", style=dotted]; "gene has variant that contributes to disease association_subject" [color=blue, height=0.5, label="gene or gene product", - pos="3342.8,265", + pos="4626.8,265", width=3.0692]; - object -> relation [pos="e,4849.6,35.54 4879.3,73.889 4872.4,64.939 4863.6,53.617 4855.8,43.584", + object -> relation [pos="e,6112.6,35.54 6142.3,73.889 6135.4,64.939 6126.6,53.617 6118.8,43.584", style=dotted]; "gene has variant that contributes to disease association_object" [color=blue, height=0.5, label=disease, - pos="3516.8,265", + pos="4800.8,265", width=1.2638]; "gene has variant that contributes to disease association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3657.8,265", + pos="4941.8,265", width=2.1665]; } diff --git a/graphviz/gene_has_variant_that_contributes_to_disease_association.svg b/graphviz/gene_has_variant_that_contributes_to_disease_association.svg index 579302beae..84515b0660 100644 --- a/graphviz/gene_has_variant_that_contributes_to_disease_association.svg +++ b/graphviz/gene_has_variant_that_contributes_to_disease_association.svg @@ -4,16 +4,16 @@ - + %3 - + gene has variant that contributes to disease association - -gene has variant that contributes to disease association + +gene has variant that contributes to disease association @@ -24,8 +24,8 @@ gene has variant that contributes to disease association->gene to disease association - - + + is_a @@ -37,7 +37,7 @@ gene has variant that contributes to disease association->id - + id @@ -50,9 +50,9 @@ gene has variant that contributes to disease association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ gene has variant that contributes to disease association->name - - -name + + +name @@ -76,9 +76,9 @@ gene has variant that contributes to disease association->description - - -description + + +description @@ -89,9 +89,9 @@ gene has variant that contributes to disease association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ gene has variant that contributes to disease association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ gene has variant that contributes to disease association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ gene has variant that contributes to disease association->publications - - -publications + + +publications @@ -141,376 +141,518 @@ gene has variant that contributes to disease association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string gene has variant that contributes to disease association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string gene has variant that contributes to disease association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string gene has variant that contributes to disease association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type gene has variant that contributes to disease association->timepoint - - -timepoint + + +timepoint original subject - -string + +string gene has variant that contributes to disease association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie gene has variant that contributes to disease association->original predicate - - -original predicate + + +original predicate original object - -string + +string gene has variant that contributes to disease association->original object - - -original object + + +original object subject category - -ontology class + +ontology class gene has variant that contributes to disease association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class gene has variant that contributes to disease association->object category - - -object category + + +object category subject closure - -string + +string gene has variant that contributes to disease association->subject closure - - -subject closure + + +subject closure object closure - -string + +string gene has variant that contributes to disease association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class gene has variant that contributes to disease association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class gene has variant that contributes to disease association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string gene has variant that contributes to disease association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string gene has variant that contributes to disease association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string gene has variant that contributes to disease association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string gene has variant that contributes to disease association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source gene has variant that contributes to disease association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type gene has variant that contributes to disease association->type - - -type + + +type category - -category + +category gene has variant that contributes to disease association->category - - -category + + +category - + +subject aspect qualifier + +subject aspect qualifier + + + +gene has variant that contributes to disease association->subject aspect qualifier + + +subject aspect qualifier + + + +object direction qualifier + +object direction qualifier + + + +gene has variant that contributes to disease association->object direction qualifier + + +object direction qualifier + + + +frequency qualifier + +frequency value + + + +gene has variant that contributes to disease association->frequency qualifier + + +frequency qualifier + + + +severity qualifier + +severity value + + + +gene has variant that contributes to disease association->severity qualifier + + +severity qualifier + + + +onset qualifier + +onset + + + +gene has variant that contributes to disease association->onset qualifier + + +onset qualifier + + + +sex qualifier + +biological sex + + + +gene has variant that contributes to disease association->sex qualifier + + +sex qualifier + + + +has count + +integer + + + +gene has variant that contributes to disease association->has count + + +has count + + + +has total + +integer + + + +gene has variant that contributes to disease association->has total + + +has total + + + +has quotient + +double + + + +gene has variant that contributes to disease association->has quotient + + +has quotient + + + +has percentage + +double + + + +gene has variant that contributes to disease association->has percentage + + +has percentage + + + subject form or variant qualifier - -string + +string - + gene has variant that contributes to disease association->subject form or variant qualifier - - -subject form or variant qualifier + + +subject form or variant qualifier - + subject - -subject + +subject - + gene has variant that contributes to disease association->subject - - -subject + + +subject - + object - -object + +object - + gene has variant that contributes to disease association->object - - -object + + +object - + predicate - -predicate + +predicate - + gene has variant that contributes to disease association->predicate - - -predicate + + +predicate association_type - -string + +string association_category - -category type + +category type + + + +gene to disease or phenotypic feature association_subject aspect qualifier + +GeneOrGeneProductOrChemicalEntityAspectEnum + + + +gene to disease or phenotypic feature association_object direction qualifier + +DirectionQualifierEnum - + subject->object - - -relation + + +relation - + relation - -relation + +relation - + subject->relation - - + + - + gene has variant that contributes to disease association_subject - -gene or gene product + +gene or gene product - + object->relation - - + + - + gene has variant that contributes to disease association_object - -disease + +disease - + gene has variant that contributes to disease association_predicate - -predicate type + +predicate type diff --git a/graphviz/gene_to_disease_association.gv b/graphviz/gene_to_disease_association.gv index 9ef876afa8..db00ac927e 100644 --- a/graphviz/gene_to_disease_association.gv +++ b/graphviz/gene_to_disease_association.gv @@ -1,367 +1,500 @@ digraph { - graph [bb="0,0,4878.7,283"]; + graph [bb="0,0,7020.1,283"]; node [label="\N"]; "gene to disease association" [height=0.5, label="gene to disease association", - pos="2498.4,265", + pos="3838.1,265", width=3.8274]; - association [height=0.5, - pos="62.394,178", - width=1.7332]; - "gene to disease association" -> association [label=is_a, - lp="280.39,221.5", - pos="e,102.91,191.79 2360.9,263.64 1906.9,262.21 473,255.59 266.39,229 213.1,222.14 153.57,206.61 112.64,194.67"]; + "gene to disease or phenotypic feature association" [height=0.5, + pos="241.13,178", + width=6.698]; + "gene to disease association" -> "gene to disease or phenotypic feature association" [label=is_a, + lp="969.13,221.5", + pos="e,391.77,192.09 3700.7,263.39 3203.7,261 1499.7,251.35 955.13,229 764.92,221.19 546.67,204.82 402.05,192.94"]; + "entity to disease association mixin" [height=0.5, + pos="671.13,178", + width=4.7482]; + "gene to disease association" -> "entity to disease association mixin" [label=uses, + lp="1179.6,221.5", + pos="e,775.53,192.31 3700.5,263.81 3226.7,262.88 1664.3,257.69 1163.1,229 1033.4,221.58 885.18,205.46 785.62,193.52"]; + "gene to entity association mixin" [height=0.5, + pos="1019.1,178", + width=4.4232]; + "gene to disease association" -> "gene to entity association mixin" [label=uses, + lp="1330.6,221.5", + pos="e,1090,194.16 3700.6,263.33 3208.4,260.77 1551.5,250.63 1314.1,229 1241.1,222.35 1159,207.84 1100,196.16"]; id [color=blue, height=0.5, label=string, - pos="181.39,178", + pos="1235.1,178", width=1.0652]; "gene to disease association" -> id [color=blue, label=id, - lp="396.39,221.5", - pos="e,210.38,189.98 2360.9,263.21 1923.9,260.49 583.9,250.48 389.39,229 317.23,221.03 299.34,215.5 229.39,196 226.29,195.13 223.09,194.17 \ -219.89,193.15", + lp="1448.1,221.5", + pos="e,1264.1,189.97 3700.5,263.53 3224.6,261.68 1665,253.79 1441.1,229 1369.8,221.11 1352.2,215.35 1283.1,196 1280,195.13 1276.8,194.16 \ +1273.6,193.14", style=solid]; iri [color=blue, height=0.5, label="iri type", - pos="282.39,178", + pos="1336.1,178", width=1.2277]; "gene to disease association" -> iri [color=blue, label=iri, - lp="503.39,221.5", - pos="e,315.31,190.16 2361.2,263.08 1939.4,260.05 679.14,249.38 495.39,229 423.23,221 405.62,214.45 335.39,196 332.02,195.11 328.55,194.14 \ -325.06,193.12", + lp="1553.1,221.5", + pos="e,1369.1,190.13 3700.5,263.45 3238.3,261.38 1758.3,252.95 1545.1,229 1474.7,221.09 1457.6,214.18 1389.1,196 1385.8,195.11 1382.3,\ +194.12 1378.8,193.1", style=solid]; name [color=blue, height=0.5, label="label type", - pos="401.39,178", + pos="1455.1,178", width=1.5707]; "gene to disease association" -> name [color=blue, label=name, - lp="607.39,221.5", - pos="e,438.25,191.77 2361,263.42 1952.2,261.43 761.12,253.56 587.39,229 538.92,222.15 485.05,206.78 447.81,194.87", + lp="1655.1,221.5", + pos="e,1491.1,191.92 3700.4,263.85 3250.1,263.09 1838.3,258.34 1635.1,229 1588.5,222.26 1536.8,207.06 1500.8,195.18", style=solid]; description [color=blue, height=0.5, label="narrative text", - pos="551.39,178", + pos="1605.1,178", width=2.0943]; "gene to disease association" -> description [color=blue, label=description, - lp="723.89,221.5", - pos="e,582.77,194.4 2360.4,264.05 1965.1,263.83 846,260.39 683.39,229 651.71,222.88 617.7,209.83 592.13,198.6", + lp="1767.6,221.5", + pos="e,1634.7,194.79 3700.9,263.12 3247.8,260.05 1823.6,248.84 1727.1,229 1698.2,223.04 1667.4,210.36 1644,199.27", style=solid]; "has attribute" [color=blue, height=0.5, label=attribute, - pos="696.39,178", + pos="1750.1,178", width=1.4443]; "gene to disease association" -> "has attribute" [color=blue, label="has attribute", - lp="862.39,221.5", - pos="e,722.86,193.55 2360.4,264.1 1985.2,263.96 964.27,260.62 815.39,229 786.11,222.78 754.98,209.44 731.91,198.1", - style=solid]; - subject [color=blue, - height=0.5, - label="named thing", - pos="836.39,178", - width=1.9318]; - "gene to disease association" -> subject [color=blue, - label=subject, - lp="989.39,221.5", - pos="e,866.52,194.37 2361,263.62 2009.9,262.26 1098,256.13 963.39,229 932.94,222.86 900.37,209.9 875.84,198.71", - style=solid]; - predicate [color=blue, - height=0.5, - label="predicate type", - pos="1002.4,178", - width=2.1665]; - "gene to disease association" -> predicate [color=blue, - label=predicate, - lp="1068.4,221.5", - pos="e,1008.4,196.14 2360.5,264.19 2006.9,264.21 1091.5,261.15 1034.4,229 1025,223.69 1017.9,214.33 1012.8,205.13", - style=solid]; - object [color=blue, - height=0.5, - label="named thing", - pos="934.39,91", - width=1.9318]; - "gene to disease association" -> object [color=blue, - label=object, - lp="1147.4,178", - pos="e,976.03,105.47 2362.5,261.94 2100.9,257.65 1536.5,246.63 1342.4,229 1245.2,220.17 1212.5,240.02 1125.4,196 1105.2,185.79 1108.1,\ -172.77 1089.4,160 1057.3,138.07 1017,120.64 985.5,108.92", + lp="1900.1,221.5", + pos="e,1774,194.29 3700.7,263.2 3265.8,260.47 1942.7,250.42 1853.1,229 1828.3,223.05 1802.4,210.46 1782.8,199.4", style=solid]; negated [color=blue, height=0.5, label=boolean, - pos="1225.4,178", + pos="1867.1,178", width=1.2999]; "gene to disease association" -> negated [color=blue, label=negated, - lp="1452.4,221.5", - pos="e,1260,190.37 2361.3,262.85 2113.6,260.22 1600.6,252.1 1423.4,229 1369.6,221.98 1309.4,205.49 1269.6,193.36", + lp="2033.1,221.5", + pos="e,1895.5,192.49 3700.5,263.99 3302.7,263.59 2168.9,259.75 2004.1,229 1969.4,222.53 1931.9,208.28 1904.9,196.64", style=solid]; qualifiers [color=blue, height=0.5, label="ontology class", - pos="1366.4,178", + pos="2008.1,178", width=2.1304]; "gene to disease association" -> qualifiers [color=blue, label=qualifiers, - lp="1585.9,221.5", - pos="e,1408.3,193.18 2361.5,262.73 2137.9,260.02 1704.1,251.9 1552.4,229 1506.1,222.01 1454.8,207.72 1417.8,196.19", + lp="2137.6,221.5", + pos="e,2031.7,195.24 3700.9,262.94 3304.5,259.64 2180.9,248.62 2104.1,229 2081.6,223.26 2058.5,211.42 2040.6,200.71", style=solid]; publications [color=blue, height=0.5, label=publication, - pos="1523.4,178", + pos="2165.1,178", width=1.7332]; "gene to disease association" -> publications [color=blue, label=publications, - lp="1723.4,221.5", - pos="e,1558,193.06 2361.8,262.57 2163.6,259.75 1806.3,251.62 1679.4,229 1640.7,222.11 1598.4,208.11 1567.6,196.67", + lp="2231.1,221.5", + pos="e,2167.9,196.44 3701.1,263.05 3310.7,260.07 2218.4,249.91 2187.1,229 2179.2,223.72 2174.1,214.91 2170.9,206.14", style=solid]; "has evidence" [color=blue, height=0.5, label="evidence type", - pos="1679.4,178", + pos="2321.1,178", width=2.0943]; "gene to disease association" -> "has evidence" [color=blue, label="has evidence", - lp="1869.9,221.5", - pos="e,1713.8,194.06 2363,261.49 2196.3,257.61 1923,248.47 1823.4,229 1788.9,222.26 1751.4,209.05 1723.4,197.9", + lp="2329.6,221.5", + pos="e,2296.5,195.13 3700.6,263.43 3325,261.56 2307.7,254.18 2283.1,229 2275.1,220.76 2280.1,210.79 2288.9,201.94", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1881.4,178", - width=3.015]; + label=string, + pos="2453.1,178", + width=1.0652]; "gene to disease association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2009.9,221.5", - pos="e,1897.3,195.93 2360.5,264.52 2221.9,263.4 2018.5,256.79 1945.4,229 1930.4,223.32 1916.2,212.85 1904.9,202.96", + lp="2447.6,221.5", + pos="e,2424.2,189.84 3700.8,263.21 3342.6,260.83 2406,252.38 2383.1,229 2378.5,224.23 2379.6,219.67 2383.1,214 2387.1,207.6 2400.7,200.19 \ +2414.9,193.84", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2116.4,178", - width=3.015]; + label=string, + pos="2548.1,178", + width=1.0652]; "gene to disease association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2176.4,221.5", - pos="e,2093.1,195.58 2363,261.61 2248.6,258.14 2100.4,249.67 2081.4,229 2074.1,221.04 2078.2,211.47 2085.7,202.85", + lp="2615.1,221.5", + pos="e,2530.1,194.35 3701.1,262.86 3367.9,259.75 2540.5,249.94 2520.1,229 2512.6,221.28 2516.5,211.15 2523.4,202.02", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2351.4,178", - width=3.015]; + label=string, + pos="2690.1,178", + width=1.0652]; "gene to disease association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2385.9,221.5", - pos="e,2303,194.15 2372.2,257.75 2331,252.87 2292.4,244.23 2279.4,229 2269.3,217.19 2278.7,206.86 2293.6,198.69", + lp="2837.6,221.5", + pos="e,2698.8,195.72 3701.3,262.68 3414.7,259.5 2773.9,250.07 2731.1,229 2720.2,223.61 2711.1,213.78 2704.4,204.25", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2533.4,178", + pos="2917.1,178", width=1.5346]; "gene to disease association" -> timepoint [color=blue, label=timepoint, - lp="2534.4,221.5", - pos="e,2513.1,194.83 2495.7,246.69 2494.9,236.76 2495.1,224.26 2499.4,214 2501.1,209.95 2503.5,206.11 2506.2,202.56", + lp="3004.1,221.5", + pos="e,2929.1,195.77 3700.6,263.79 3472.5,262.66 3034.4,256.83 2969.1,229 2956.2,223.5 2944.6,213.23 2935.7,203.43", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2645.4,178", + pos="3029.1,178", width=1.0652]; "gene to disease association" -> "original subject" [color=blue, label="original subject", - lp="2647.4,221.5", - pos="e,2623.9,193.16 2533.9,247.58 2545.4,241.98 2558.1,235.49 2569.4,229 2570.6,228.29 2594.6,212.48 2615.4,198.82", + lp="3112.1,221.5", + pos="e,3033.5,195.97 3702.9,261.39 3486.3,256.73 3083,245.85 3056.1,229 3047.5,223.61 3041.5,214.49 3037.3,205.49", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2759.4,178", + pos="3154.1,178", width=1.5887]; "gene to disease association" -> "original predicate" [color=blue, label="original predicate", - lp="2789.9,221.5", - pos="e,2745.8,195.62 2597.8,252.47 2640.6,246.4 2685.3,238.29 2704.4,229 2717.2,222.76 2729.2,212.6 2738.7,203.05", + lp="3250.6,221.5", + pos="e,3160.5,196.03 3700.9,263.15 3523.1,261.05 3230.4,253.82 3187.1,229 3177.7,223.57 3170.4,214.18 3165.1,205", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2873.4,178", + pos="3283.1,178", width=1.0652]; "gene to disease association" -> "original object" [color=blue, label="original object", - lp="2917.9,221.5", - pos="e,2871.5,196.15 2596.4,252.26 2612.8,250.42 2629.5,248.6 2645.4,247 2691.8,242.32 2817.2,257.09 2854.4,229 2861.7,223.45 2866.3,\ -214.69 2869,206.05", + lp="3392.6,221.5", + pos="e,3296.6,195.15 3700.5,263.95 3576.3,262.16 3403.9,254.85 3341.1,229 3327,223.19 3313.9,212.54 3303.7,202.56", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3006.4,178", + pos="3416.1,178", width=2.1304]; "gene to disease association" -> "subject category" [color=blue, label="subject category", - lp="3048.9,221.5", - pos="e,3000,196.03 2594.4,252.05 2611.4,250.18 2628.9,248.41 2645.4,247 2681.8,243.9 2941.7,247.17 2973.4,229 2982.9,223.56 2990.1,214.17 \ -2995.4,204.99", + lp="3528.6,221.5", + pos="e,3429,195.99 3704.8,260.4 3616.7,256.32 3510.2,247.59 3469.1,229 3456.4,223.23 3444.8,213.13 3435.7,203.51", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3177.4,178", + pos="3587.1,178", width=2.1304]; "gene to disease association" -> "object category" [color=blue, label="object category", - lp="3195.9,221.5", - pos="e,3161.5,195.82 2593.6,251.91 2610.8,250.04 2628.6,248.29 2645.4,247 2697.2,243.01 3063.6,246.66 3112.4,229 3127.8,223.41 3142.6,\ -212.71 3154.1,202.63", + lp="3657.6,221.5", + pos="e,3587.8,196.34 3712.9,257.44 3665.8,252.54 3619.4,243.97 3602.1,229 3595.5,223.27 3591.7,214.73 3589.6,206.33", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3310.4,178", + pos="3720.1,178", width=1.0652]; "gene to disease association" -> "subject closure" [color=blue, label="subject closure", - lp="3333.9,221.5", - pos="e,3297.9,195.34 2592.8,251.87 2610.2,249.97 2628.4,248.23 2645.4,247 2713,242.1 3192.5,254.38 3255.4,229 3269.1,223.46 3281.6,212.84 \ -3291.2,202.81", + lp="3777.6,221.5", + pos="e,3716.6,196.01 3752.2,250.9 3741,245.74 3730.8,238.67 3723.1,229 3718.1,222.64 3716.3,214.28 3716.1,206.23", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3408.4,178", + pos="3833.1,178", width=1.0652]; "gene to disease association" -> "object closure" [color=blue, label="object closure", - lp="3450.4,221.5", - pos="e,3406.3,196.38 2592.8,251.8 2610.2,249.91 2628.4,248.19 2645.4,247 2686.6,244.13 3354.5,252.56 3388.4,229 3396.1,223.65 3400.8,\ -214.82 3403.7,206.06", + lp="3886.1,221.5", + pos="e,3834.1,196.18 3837.1,246.8 3836.4,235.16 3835.5,219.55 3834.7,206.24", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3541.4,178", + pos="3966.1,178", width=2.1304]; "gene to disease association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3608.9,221.5", - pos="e,3533.8,196.22 2592.4,251.8 2610,249.89 2628.2,248.17 2645.4,247 2693,243.75 3462,250.93 3504.4,229 3514.6,223.74 3522.7,214.25 \ -3528.7,204.94", + lp="4038.6,221.5", + pos="e,3960.4,196.41 3903.9,249.16 3916.5,244.21 3928.9,237.65 3939.1,229 3946.4,222.78 3952.1,214.06 3956.3,205.64", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3731.4,178", + pos="4159.1,178", width=2.1304]; "gene to disease association" -> "object category closure" [color=blue, label="object category closure", - lp="3798.9,221.5", - pos="e,3725.7,196.15 2592,251.79 2609.7,249.87 2628.1,248.15 2645.4,247 2674.6,245.06 3674.9,243.47 3700.4,229 3709.6,223.76 3716.5,214.54 \ -3721.3,205.43", + lp="4228.6,221.5", + pos="e,4153.7,196.22 3936.9,252.42 4021.2,242.49 4129.1,229.68 4130.1,229 4138.6,223.41 4144.9,214.41 4149.5,205.57", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3921.4,178", + pos="4349.1,178", width=1.0652]; "gene to disease association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3971.4,221.5", - pos="e,3914.7,195.72 2592,251.75 2609.7,249.84 2628.1,248.12 2645.4,247 2679.8,244.77 3855.9,245.14 3886.4,229 3896.5,223.66 3904.3,213.98 \ -3909.9,204.54", + lp="4400.1,221.5", + pos="e,4342.7,196.03 3934.1,252.05 3951.1,250.18 3968.6,248.4 3985.1,247 4021.8,243.88 4284.2,247.33 4316.1,229 4325.6,223.57 4332.9,\ +214.18 4338.1,204.99", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4080.4,178", + pos="4508.1,178", width=1.0652]; "gene to disease association" -> "object namespace" [color=blue, label="object namespace", - lp="4124.4,221.5", - pos="e,4073,195.76 2592,251.73 2609.7,249.82 2628.1,248.11 2645.4,247 2684.2,244.52 4008.8,246.7 4043.4,229 4053.7,223.7 4061.9,214.02 \ -4067.9,204.58", + lp="4553.1,221.5", + pos="e,4500.8,196.14 3932.9,251.94 3950.3,250.04 3968.2,248.29 3985.1,247 4039.1,242.89 4424.4,254.57 4472.1,229 4482.1,223.64 4490,214.14 \ +4495.8,204.84", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4231.4,178", + pos="4619.1,178", width=1.0652]; "gene to disease association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4284.4,221.5", - pos="e,4223.4,195.79 2592,251.71 2609.7,249.8 2628.1,248.1 2645.4,247 2688.3,244.28 4153.9,248.08 4192.4,229 4203.1,223.69 4211.8,213.87 \ -4218.2,204.33", + lp="4702.1,221.5", + pos="e,4625.5,196.07 3932.5,251.86 3950,249.96 3968.1,248.22 3985.1,247 4020.4,244.47 4596.5,254.35 4621.1,229 4627,222.98 4628.1,214.37 \ +4627.3,205.99", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4402.4,178", + pos="4714.1,178", width=1.0652]; "gene to disease association" -> "object label closure" [color=blue, label="object label closure", - lp="4450.9,221.5", - pos="e,4394.1,195.8 2591.6,251.74 2609.4,249.81 2628,248.1 2645.4,247 2693,244.01 4319.5,249.89 4362.4,229 4373.3,223.71 4382.1,213.89 \ -4388.7,204.35", + lp="4854.6,221.5", + pos="e,4744.6,188.95 3932.1,251.82 3949.7,249.91 3968,248.18 3985.1,247 4007.2,245.48 4764.7,244.8 4780.1,229 4793.6,215.21 4774.8,202.14 \ +4753.9,192.83", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4564.4,178", + pos="4855.1,178", width=2.347]; "gene to disease association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4612.9,221.5", - pos="e,4555.8,196.3 2591.6,251.72 2609.4,249.8 2628,248.09 2645.4,247 2697.5,243.75 4477.5,251.84 4524.4,229 4535.1,223.79 4543.9,214.17 \ -4550.4,204.76", + lp="5002.6,221.5", + pos="e,4901.2,193.16 3932.1,251.77 3949.7,249.87 3968,248.15 3985.1,247 4011.3,245.24 4909.8,247.7 4928.1,229 4940,216.91 4928.1,205.96 \ +4910.7,197.4", style=solid]; type [height=0.5, - pos="4726.4,178", + pos="4989.1,178", width=0.86659]; "gene to disease association" -> type [color=blue, label=type, - lp="4721.4,221.5", - pos="e,4718.1,195.81 2591.6,251.71 2609.4,249.79 2628,248.08 2645.4,247 2702,243.49 4635.4,253.79 4686.4,229 4697.3,223.72 4706.1,213.9 \ -4712.7,204.36", + lp="5096.1,221.5", + pos="e,5013.8,189.33 3931.7,251.78 3949.4,249.86 3967.8,248.14 3985.1,247 4015.4,245.01 5054.9,250.61 5076.1,229 5080.8,224.25 5079.9,\ +219.51 5076.1,214 5063.8,195.87 5050.5,204.2 5030.1,196 5027.9,195.1 5025.6,194.17 5023.3,193.22", style=solid]; category [height=0.5, - pos="4827.4,178", + pos="5090.1,178", width=1.4263]; "gene to disease association" -> category [color=blue, label=category, - lp="4807.9,221.5", - pos="e,4807.2,194.82 2591.6,251.71 2609.4,249.79 2628,248.08 2645.4,247 2761.6,239.8 4629.1,259.79 4741.4,229 4762.1,223.34 4782.9,211.42 \ -4798.9,200.65", + lp="5152.6,221.5", + pos="e,5107.6,194.94 3931.7,251.77 3949.4,249.85 3967.8,248.14 3985.1,247 4016.5,244.94 5094.1,251.39 5116.1,229 5123.4,221.63 5120.2,\ +211.83 5114,202.86", + style=solid]; + "subject aspect qualifier" [height=0.5, + pos="5278.1,178", + width=3.3039]; + "gene to disease association" -> "subject aspect qualifier" [color=blue, + label="subject aspect qualifier", + lp="5308.6,221.5", + pos="e,5255.4,195.77 3931.7,251.76 3949.4,249.84 3967.8,248.13 3985.1,247 4051.8,242.66 5123.6,246.25 5188.1,229 5209,223.43 5230.2,212.01 \ +5246.7,201.48", + style=solid]; + "object direction qualifier" [height=0.5, + pos="5540.1,178", + width=3.4664]; + "gene to disease association" -> "object direction qualifier" [color=blue, + label="object direction qualifier", + lp="5541.1,221.5", + pos="e,5503.7,195.31 3931.7,251.72 3949.4,249.81 3967.8,248.11 3985.1,247 4141.6,236.98 5241.7,256.06 5396.1,229 5429.9,223.08 5466.5,\ +210.32 5494.3,199.17", + style=solid]; + predicate [height=0.5, + pos="5737.1,178", + width=1.5165]; + "gene to disease association" -> predicate [color=blue, + label=predicate, + lp="5709.1,221.5", + pos="e,5713,194.34 3931.7,251.7 3949.4,249.79 3967.8,248.09 3985.1,247 4076.5,241.23 5544,249.83 5633.1,229 5658.2,223.14 5684.4,210.54 \ +5704.1,199.46", + style=solid]; + "frequency qualifier" [color=blue, + height=0.5, + label="frequency value", + pos="5895.1,178", + width=2.3651]; + "gene to disease association" -> "frequency qualifier" [color=blue, + label="frequency qualifier", + lp="5874.1,221.5", + pos="e,5859.8,194.48 3931.3,251.73 3949.1,249.81 3967.7,248.09 3985.1,247 4180.5,234.74 5554.1,261.74 5747.1,229 5782.8,222.95 5821.5,\ +209.62 5850.4,198.25", + style=solid]; + "severity qualifier" [color=blue, + height=0.5, + label="severity value", + pos="6074.1,178", + width=2.1123]; + "gene to disease association" -> "severity qualifier" [color=blue, + label="severity qualifier", + lp="6058.1,221.5", + pos="e,6043.5,194.61 3931.3,251.72 3949.1,249.79 3967.7,248.09 3985.1,247 4093.9,240.23 5839.2,249.66 5946.1,229 5976.7,223.09 6009.4,\ +210.19 6034.1,198.97", + style=solid]; + "onset qualifier" [color=blue, + height=0.5, + label=onset, + pos="6204.1,178", + width=1.011]; + "gene to disease association" -> "onset qualifier" [color=blue, + label="onset qualifier", + lp="6208.6,221.5", + pos="e,6186.5,193.85 3931.3,251.71 3949.1,249.78 3967.7,248.08 3985.1,247 4044.4,243.33 6066.1,245.45 6123.1,229 6143.2,223.22 6163.1,\ +210.98 6178.2,200.06", + style=solid]; + "sex qualifier" [color=blue, + height=0.5, + label="biological sex", + pos="6332.1,178", + width=2.0401]; + "gene to disease association" -> "sex qualifier" [color=blue, + label="sex qualifier", + lp="6337.1,221.5", + pos="e,6315.7,195.76 3931.3,251.7 3949.1,249.78 3967.7,248.07 3985.1,247 4048.3,243.11 6204.1,248.97 6264.1,229 6280.3,223.63 6295.8,\ +212.83 6307.9,202.64", + style=solid]; + "has count" [color=blue, + height=0.5, + label=integer, + pos="6468.1,178", + width=1.2277]; + "gene to disease association" -> "has count" [color=blue, + label="has count", + lp="6454.1,221.5", + pos="e,6449.4,194.34 3931.3,251.69 3949.1,249.77 3967.7,248.07 3985.1,247 4051.7,242.91 6321,247.09 6385.1,229 6405.3,223.31 6425.5,211.32 \ +6440.9,200.51", + style=solid]; + "has total" [color=blue, + height=0.5, + label=integer, + pos="6574.1,178", + width=1.2277]; + "gene to disease association" -> "has total" [color=blue, + label="has total", + lp="6558.6,221.5", + pos="e,6555.6,194.58 3931.3,251.69 3949.1,249.77 3967.7,248.07 3985.1,247 4054.7,242.74 6426.2,248.26 6493.1,229 6512.8,223.35 6532.4,\ +211.48 6547.3,200.73", + style=solid]; + "has quotient" [color=blue, + height=0.5, + label=double, + pos="6678.1,178", + width=1.1735]; + "gene to disease association" -> "has quotient" [color=blue, + label="has quotient", + lp="6674.1,221.5", + pos="e,6659.1,194.34 3931.3,251.68 3949.1,249.76 3967.7,248.07 3985.1,247 4057.5,242.58 6524.3,248.46 6594.1,229 6614.7,223.27 6635.3,\ +211.11 6651,200.22", + style=solid]; + "has percentage" [color=blue, + height=0.5, + label=double, + pos="6780.1,178", + width=1.1735]; + "gene to disease association" -> "has percentage" [color=blue, + label="has percentage", + lp="6803.1,221.5", + pos="e,6767.1,195.47 3931.3,251.68 3949.1,249.76 3967.7,248.06 3985.1,247 4061,242.37 6652,256.03 6723.1,229 6737.2,223.63 6750.2,213.03 \ +6760.1,202.97", + style=solid]; + subject [height=0.5, + pos="6902.1,178", + width=1.2277]; + "gene to disease association" -> subject [color=blue, + label=subject, + lp="6907.1,221.5", + pos="e,6893.8,195.82 3931.3,251.68 3949.1,249.76 3967.7,248.06 3985.1,247 4025,244.58 6826.2,246.42 6862.1,229 6873,223.73 6881.9,213.92 \ +6888.4,204.37", + style=solid]; + object [height=0.5, + pos="6945.1,91", + width=1.0832]; + "gene to disease association" -> object [color=blue, + label=object, + lp="6998.1,178", + pos="e,6958.5,108.09 3931.3,251.67 3949.1,249.75 3967.7,248.06 3985.1,247 4026.1,244.52 6901.9,250.04 6937.1,229 6977.8,204.69 6981.7,\ +172.39 6968.1,127 6967.1,123.55 6965.6,120.13 6963.9,116.85", style=solid]; - subject -> object [label=relation, - lp="919.39,134.5", - pos="e,915.56,108.34 855.29,160.61 870.2,147.68 891.19,129.47 907.8,115.07"]; - relation [height=0.5, - pos="848.39,18", - width=1.2999]; - subject -> relation [pos="e,847.09,36.188 837.7,159.79 839.78,132.48 843.84,78.994 846.31,46.38", - style=dotted]; - object -> relation [pos="e,867.35,34.647 914.45,73.533 902.81,63.922 887.97,51.669 875.3,41.213", - style=dotted]; association_type [color=blue, height=0.5, label=string, - pos="2692.4,265", + pos="4032.1,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2823.4,265", + pos="4163.1,265", width=2.0762]; + "gene to disease or phenotypic feature association_subject aspect qualifier" [color=blue, + height=0.5, + label=GeneOrGeneProductOrChemicalEntityAspectEnum, + pos="4505.1,265", + width=6.9147]; + "gene to disease or phenotypic feature association_object direction qualifier" [color=blue, + height=0.5, + label=DirectionQualifierEnum, + pos="4893.1,265", + width=3.358]; + "gene to disease or phenotypic feature association_predicate" [color=blue, + height=0.5, + label="predicate type", + pos="5110.1,265", + width=2.1665]; + subject -> object [label=relation, + lp="6940.1,134.5", + pos="e,6927.2,107.23 6903.2,159.55 6904.4,149.57 6906.9,137.07 6912.1,127 6914.4,122.68 6917.3,118.52 6920.5,114.66"]; + relation [height=0.5, + pos="6890.1,18", + width=1.2999]; + subject -> relation [pos="e,6891.4,36.188 6900.8,159.79 6898.7,132.48 6894.7,78.994 6892.2,46.38", + style=dotted]; + "gene to disease association_subject" [color=blue, + height=0.5, + label="gene or gene product", + pos="5316.1,265", + width=3.0692]; + object -> relation [pos="e,6902.9,35.54 6932.6,73.889 6925.7,64.939 6916.9,53.617 6909.2,43.584", + style=dotted]; + "gene to disease association_object" [color=blue, + height=0.5, + label=disease, + pos="5490.1,265", + width=1.2638]; } diff --git a/graphviz/gene_to_disease_association.svg b/graphviz/gene_to_disease_association.svg index 524fecdea6..ef5f782eef 100644 --- a/graphviz/gene_to_disease_association.svg +++ b/graphviz/gene_to_disease_association.svg @@ -4,482 +4,668 @@ - + %3 - + gene to disease association - -gene to disease association + +gene to disease association - + -association - -association +gene to disease or phenotypic feature association + +gene to disease or phenotypic feature association - + -gene to disease association->association - - -is_a +gene to disease association->gene to disease or phenotypic feature association + + +is_a - + +entity to disease association mixin + +entity to disease association mixin + + + +gene to disease association->entity to disease association mixin + + +uses + + + +gene to entity association mixin + +gene to entity association mixin + + + +gene to disease association->gene to entity association mixin + + +uses + + + id - -string + +string - + gene to disease association->id - - -id + + +id - + iri - -iri type + +iri type - + gene to disease association->iri - - -iri + + +iri - + name - -label type + +label type - + gene to disease association->name - - -name + + +name - + description - -narrative text + +narrative text - + gene to disease association->description - - -description + + +description - + has attribute - -attribute + +attribute - -gene to disease association->has attribute - - -has attribute - - - -subject - -named thing - - - -gene to disease association->subject - - -subject - - - -predicate - -predicate type - - -gene to disease association->predicate - - -predicate - - - -object - -named thing - - - -gene to disease association->object - - -object +gene to disease association->has attribute + + +has attribute - + negated - -boolean + +boolean - + gene to disease association->negated - - -negated + + +negated - + qualifiers - -ontology class + +ontology class - + gene to disease association->qualifiers - - -qualifiers + + +qualifiers - + publications - -publication + +publication - + gene to disease association->publications - - -publications + + +publications - + has evidence - -evidence type + +evidence type - + gene to disease association->has evidence - - -has evidence + + +has evidence - + knowledge source - -information resource + +string - + gene to disease association->knowledge source - - -knowledge source + + +knowledge source - + primary knowledge source - -information resource + +string - + gene to disease association->primary knowledge source - - -primary knowledge source + + +primary knowledge source - + aggregator knowledge source - -information resource + +string - + gene to disease association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source - + timepoint - -time type + +time type - + gene to disease association->timepoint - - -timepoint + + +timepoint - + original subject - -string + +string - + gene to disease association->original subject - - -original subject + + +original subject - + original predicate - -uriorcurie + +uriorcurie - + gene to disease association->original predicate - - -original predicate + + +original predicate - + original object - -string + +string - + gene to disease association->original object - - -original object + + +original object - + subject category - -ontology class + +ontology class - + gene to disease association->subject category - - -subject category + + +subject category - + object category - -ontology class + +ontology class - + gene to disease association->object category - - -object category + + +object category - + subject closure - -string + +string - + gene to disease association->subject closure - - -subject closure + + +subject closure - + object closure - -string + +string - + gene to disease association->object closure - - -object closure + + +object closure - + subject category closure - -ontology class + +ontology class - + gene to disease association->subject category closure - - -subject category closure + + +subject category closure - + object category closure - -ontology class + +ontology class - + gene to disease association->object category closure - - -object category closure + + +object category closure - + subject namespace - -string + +string - + gene to disease association->subject namespace - - -subject namespace + + +subject namespace - + object namespace - -string + +string - + gene to disease association->object namespace - - -object namespace + + +object namespace - + subject label closure - -string + +string - + gene to disease association->subject label closure - - -subject label closure + + +subject label closure - + object label closure - -string + +string - + gene to disease association->object label closure - - -object label closure + + +object label closure - + retrieval source ids - -retrieval source + +retrieval source - + gene to disease association->retrieval source ids - - -retrieval source ids + + +retrieval source ids - + type - -type + +type - + gene to disease association->type - - -type + + +type - + category - -category + +category - + gene to disease association->category - - -category + + +category - + + +subject aspect qualifier + +subject aspect qualifier + + + +gene to disease association->subject aspect qualifier + + +subject aspect qualifier + + + +object direction qualifier + +object direction qualifier + + -subject->object - - -relation +gene to disease association->object direction qualifier + + +object direction qualifier - - -relation - -relation + + +predicate + +predicate - + -subject->relation - - +gene to disease association->predicate + + +predicate - + + +frequency qualifier + +frequency value + + -object->relation - - +gene to disease association->frequency qualifier + + +frequency qualifier + + + +severity qualifier + +severity value + + + +gene to disease association->severity qualifier + + +severity qualifier + + + +onset qualifier + +onset + + + +gene to disease association->onset qualifier + + +onset qualifier + + + +sex qualifier + +biological sex + + + +gene to disease association->sex qualifier + + +sex qualifier + + + +has count + +integer + + + +gene to disease association->has count + + +has count + + + +has total + +integer + + + +gene to disease association->has total + + +has total + + + +has quotient + +double + + + +gene to disease association->has quotient + + +has quotient + + + +has percentage + +double + + + +gene to disease association->has percentage + + +has percentage + + + +subject + +subject + + + +gene to disease association->subject + + +subject + + + +object + +object + + + +gene to disease association->object + + +object - + association_type - -string + +string - + association_category - -category type + +category type + + + +gene to disease or phenotypic feature association_subject aspect qualifier + +GeneOrGeneProductOrChemicalEntityAspectEnum + + + +gene to disease or phenotypic feature association_object direction qualifier + +DirectionQualifierEnum + + + +gene to disease or phenotypic feature association_predicate + +predicate type + + + +subject->object + + +relation + + + +relation + +relation + + + +subject->relation + + + + + +gene to disease association_subject + +gene or gene product + + + +object->relation + + + + + +gene to disease association_object + +disease diff --git a/graphviz/gene_to_disease_or_phenotypic_feature_association.gv b/graphviz/gene_to_disease_or_phenotypic_feature_association.gv index 44e4760876..801ca5af09 100644 --- a/graphviz/gene_to_disease_or_phenotypic_feature_association.gv +++ b/graphviz/gene_to_disease_or_phenotypic_feature_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,7013.4,283"]; + graph [bb="0,0,6795.4,283"]; node [label="\N"]; "gene to disease or phenotypic feature association" [height=0.5, label="gene to disease or phenotypic feature association", - pos="3805.4,265", + pos="3587.4,265", width=6.698]; association [height=0.5, pos="62.394,178", width=1.7332]; "gene to disease or phenotypic feature association" -> association [label=is_a, - lp="700.39,221.5", - pos="e,106.72,190.73 3565.9,262.82 2936.5,259.47 1245.9,248.85 686.39,229 440.78,220.29 377.56,231.7 134.39,196 128.61,195.15 122.62,\ + lp="699.39,221.5", + pos="e,106.72,190.73 3348.4,262.59 2750.5,258.83 1201.3,247.55 685.39,229 440.23,220.18 377.12,231.65 134.39,196 128.61,195.15 122.62,\ 194.07 116.66,192.86"]; "entity to phenotypic feature association mixin" [height=0.5, pos="367.39,178", width=6.2286]; "gene to disease or phenotypic feature association" -> "entity to phenotypic feature association mixin" [label=uses, - lp="929.89,221.5", - pos="e,490.53,193.08 3565,263.55 2967.5,262.02 1426.5,255.56 913.39,229 772.24,221.69 611.14,206.04 500.72,194.18"]; + lp="928.89,221.5", + pos="e,490.57,193.08 3347.3,263.27 2782.4,261.17 1382,253.58 912.39,229 771.61,221.63 610.95,206.01 500.74,194.18"]; "gene to entity association mixin" [height=0.5, pos="768.39,178", width=4.4232]; "gene to disease or phenotypic feature association" -> "gene to entity association mixin" [label=uses, - lp="1080.9,221.5", - pos="e,839.47,194.18 3565.6,263.06 2943.5,260.32 1309.2,251.1 1064.4,229 991.16,222.39 908.74,207.88 849.51,196.18"]; + lp="1079.9,221.5", + pos="e,839.23,194.16 3348.1,262.78 2762,259.5 1286.4,249.32 1063.4,229 990.41,222.35 908.27,207.84 849.23,196.16"]; id [color=blue, height=0.5, label=string, @@ -31,9 +31,9 @@ digraph { width=1.0652]; "gene to disease or phenotypic feature association" -> id [color=blue, label=id, - lp="1199.4,221.5", - pos="e,1013.4,189.98 3565,263.39 2963.4,261.48 1423.8,254.18 1192.4,229 1120.2,221.15 1102.3,215.5 1032.4,196 1029.3,195.13 1026.1,194.17 \ -1022.9,193.15", + lp="1197.4,221.5", + pos="e,1013.4,189.97 3347.4,263.1 2782.4,260.62 1400.2,252.22 1190.4,229 1119.1,221.11 1101.5,215.35 1032.4,196 1029.3,195.13 1026.1,\ +194.16 1022.9,193.14", style=solid]; iri [color=blue, height=0.5, @@ -42,9 +42,9 @@ digraph { width=1.2277]; "gene to disease or phenotypic feature association" -> iri [color=blue, label=iri, - lp="1312.4,221.5", - pos="e,1118.3,190.2 3565.5,263.13 2982.9,260.67 1524.7,252.24 1304.4,229 1229.6,221.11 1211.2,214.85 1138.4,196 1135,195.13 1131.5,194.16 \ -1128.1,193.15", + lp="1302.4,221.5", + pos="e,1118.3,190.13 3347.7,262.96 2801.1,260.22 1493.8,251.4 1294.4,229 1224,221.09 1206.9,214.18 1138.4,196 1135,195.11 1131.5,194.12 \ +1128.1,193.1", style=solid]; name [color=blue, height=0.5, @@ -53,8 +53,8 @@ digraph { width=1.5707]; "gene to disease or phenotypic feature association" -> name [color=blue, label=name, - lp="1419.4,221.5", - pos="e,1242,191.48 3564.7,263.72 2997.6,262.6 1609.4,256.99 1399.4,229 1348.1,222.16 1290.9,206.5 1251.8,194.51", + lp="1404.4,221.5", + pos="e,1240.4,191.92 3346.9,263.64 2815.7,262.34 1574,256.38 1384.4,229 1337.7,222.26 1286,207.06 1250.1,195.18", style=solid]; description [color=blue, height=0.5, @@ -63,8 +63,8 @@ digraph { width=2.0943]; "gene to disease or phenotypic feature association" -> description [color=blue, label=description, - lp="1539.9,221.5", - pos="e,1388.4,194.19 3564.1,264.65 3013.9,265.52 1698.2,263.86 1499.4,229 1464.3,222.85 1426.3,209.48 1398,198.11", + lp="1516.9,221.5", + pos="e,1384,194.79 3348.4,262.41 2815,258.53 1566.5,247.53 1476.4,229 1447.4,223.04 1416.6,210.36 1393.2,199.27", style=solid]; "has attribute" [color=blue, height=0.5, @@ -73,8 +73,8 @@ digraph { width=1.4443]; "gene to disease or phenotypic feature association" -> "has attribute" [color=blue, label="has attribute", - lp="1685.4,221.5", - pos="e,1529,192.87 3564.3,264.56 3038.9,265.15 1823.2,262.77 1638.4,229 1603.4,222.61 1565.6,208.47 1538.2,196.86", + lp="1649.4,221.5", + pos="e,1523.2,194.29 3348.4,262.53 2839,259.03 1685.8,248.94 1602.4,229 1577.5,223.05 1551.6,210.46 1532,199.4", style=solid]; negated [color=blue, height=0.5, @@ -83,8 +83,8 @@ digraph { width=1.2999]; "gene to disease or phenotypic feature association" -> negated [color=blue, label=negated, - lp="1840.4,221.5", - pos="e,1650.4,190.52 3566.2,262.67 3074.3,259.52 1980.9,250.22 1811.4,229 1758.4,222.37 1699.3,205.86 1660.2,193.61", + lp="1782.4,221.5", + pos="e,1644.7,192.49 3346.6,263.83 2884.6,262.85 1905.6,257.4 1753.4,229 1718.7,222.53 1681.2,208.28 1654.2,196.64", style=solid]; qualifiers [color=blue, height=0.5, @@ -93,8 +93,8 @@ digraph { width=2.1304]; "gene to disease or phenotypic feature association" -> qualifiers [color=blue, label=qualifiers, - lp="1979.9,221.5", - pos="e,1799.2,193.16 3566,262.69 3099.9,259.68 2102.3,250.77 1946.4,229 1899,222.39 1846.5,207.91 1808.9,196.22", + lp="1886.9,221.5", + pos="e,1781,195.24 3349.3,262.06 2890.9,257.94 1924.4,247.15 1853.4,229 1830.9,223.26 1807.8,211.42 1789.9,200.71", style=solid]; publications [color=blue, height=0.5, @@ -103,8 +103,8 @@ digraph { width=1.7332]; "gene to disease or phenotypic feature association" -> publications [color=blue, label=publications, - lp="2127.4,221.5", - pos="e,1950.7,192.81 3565.9,262.68 3127,259.73 2225.5,251.06 2083.4,229 2040.7,222.38 1993.8,207.87 1960.2,196.18", + lp="1980.4,221.5", + pos="e,1917.2,196.44 3348.9,262.23 2898.5,258.45 1965.3,248.3 1936.4,229 1928.5,223.72 1923.4,214.91 1920.1,206.14", style=solid]; "has evidence" [color=blue, height=0.5, @@ -113,387 +113,388 @@ digraph { width=2.0943]; "gene to disease or phenotypic feature association" -> "has evidence" [color=blue, label="has evidence", - lp="2288.9,221.5", - pos="e,2109.4,193.49 3567.1,262.08 3161.7,258.3 2369.2,248.51 2242.4,229 2199.9,222.46 2153.1,208.39 2119,196.83", + lp="2078.9,221.5", + pos="e,2045.8,195.13 3347.8,262.87 2917.3,260.26 2055,252.15 2032.4,229 2024.3,220.76 2029.4,210.79 2038.2,201.94", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2272.4,178", - width=3.015]; + label=string, + pos="2202.4,178", + width=1.0652]; "gene to disease or phenotypic feature association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2447.9,221.5", - pos="e,2300.5,195.46 3565.1,263.28 3189.7,261.36 2494.9,254.4 2383.4,229 2357.5,223.11 2330.4,210.99 2309.4,200.16", + lp="2196.9,221.5", + pos="e,2173.5,189.84 3348.5,262.48 2941,259.31 2153.3,250.42 2132.4,229 2127.7,224.23 2128.9,219.67 2132.4,214 2136.3,207.6 2150,200.19 \ +2164.2,193.84", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2507.4,178", - width=3.015]; + label=string, + pos="2297.4,178", + width=1.0652]; "gene to disease or phenotypic feature association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2623.4,221.5", - pos="e,2509.8,196.4 3564.4,264.08 3206.1,263.24 2570.3,257.69 2528.4,229 2520.6,223.67 2515.7,214.84 2512.6,206.08", + lp="2364.4,221.5", + pos="e,2279.4,194.35 3349.8,261.86 2975.3,257.9 2288,248.06 2269.4,229 2261.9,221.28 2265.7,211.15 2272.7,202.02", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2742.4,178", - width=3.015]; + label=string, + pos="2439.4,178", + width=1.0652]; "gene to disease or phenotypic feature association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2832.9,221.5", - pos="e,2729.2,196.26 3564.2,264.56 3255,264.07 2755.1,258.65 2726.4,229 2720.2,222.56 2721.1,213.68 2724.6,205.19", + lp="2586.9,221.5", + pos="e,2448,195.72 3350.8,261.48 3037.1,257.41 2518.7,247.88 2480.4,229 2469.4,223.61 2460.4,213.78 2453.6,204.25", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2924.4,178", + pos="2666.4,178", width=1.5346]; "gene to disease or phenotypic feature association" -> timepoint [color=blue, label=timepoint, - lp="2993.4,221.5", - pos="e,2931.1,196.1 3575.4,259.58 3333.8,254.17 2985.1,243.85 2958.4,229 2948.8,223.64 2941.3,214.27 2935.9,205.08", + lp="2753.4,221.5", + pos="e,2678.4,195.77 3347.4,263.04 3110.3,260.69 2774.9,253.08 2718.4,229 2705.5,223.5 2693.9,213.23 2685,203.43", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="3036.4,178", + pos="2778.4,178", width=1.0652]; "gene to disease or phenotypic feature association" -> "original subject" [color=blue, label="original subject", - lp="3095.4,221.5", - pos="e,3032.2,196.19 3570.8,260.81 3352.6,256.68 3058.3,247.68 3039.4,229 3033.5,223.16 3031.6,214.71 3031.5,206.41", + lp="2861.4,221.5", + pos="e,2782.8,195.97 3358.7,259.24 3136.4,253.78 2828.7,243.64 2805.4,229 2796.8,223.61 2790.8,214.49 2786.6,205.49", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3150.4,178", + pos="2903.4,178", width=1.5887]; "gene to disease or phenotypic feature association" -> "original predicate" [color=blue, label="original predicate", - lp="3228.9,221.5", - pos="e,3150.8,196.14 3564.5,264.01 3396.5,261.8 3197,253.85 3165.4,229 3158.3,223.44 3154.5,214.68 3152.4,206.04", + lp="2999.9,221.5", + pos="e,2909.8,196.03 3350.4,261.56 3179.3,258.06 2972.3,249.57 2936.4,229 2926.9,223.57 2919.7,214.18 2914.4,205", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3264.4,178", + pos="3032.4,178", width=1.0652]; "gene to disease or phenotypic feature association" -> "original object" [color=blue, label="original object", - lp="3368.9,221.5", - pos="e,3276.4,195.13 3568,261.84 3467.1,257.88 3362.5,248.84 3317.4,229 3304.2,223.22 3292.3,212.72 3283.1,202.83", + lp="3141.9,221.5", + pos="e,3045.8,195.15 3351,261.4 3246.9,257.4 3137.6,248.44 3090.4,229 3076.3,223.19 3063.2,212.54 3053,202.56", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3397.4,178", + pos="3165.4,178", width=2.1304]; "gene to disease or phenotypic feature association" -> "subject category" [color=blue, label="subject category", - lp="3501.9,221.5", - pos="e,3407.7,195.96 3592.9,256.42 3529.8,251.37 3470.1,242.97 3442.4,229 3431.1,223.31 3421.3,213.48 3413.8,204.04", + lp="3277.9,221.5", + pos="e,3178.2,195.99 3378.9,255.87 3312.3,250.77 3248.1,242.48 3218.4,229 3205.7,223.23 3194.1,213.13 3185,203.51", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3568.4,178", + pos="3336.4,178", width=2.1304]; "gene to disease or phenotypic feature association" -> "object category" [color=blue, label="object category", - lp="3626.9,221.5", - pos="e,3564.4,196.39 3631.1,252.49 3603.8,247.29 3581.3,239.8 3571.4,229 3565.9,222.96 3564,214.59 3563.8,206.43", + lp="3406.9,221.5", + pos="e,3337,196.34 3420.6,251.95 3389.8,246.81 3363.5,239.47 3351.4,229 3344.8,223.27 3341,214.73 3338.9,206.33", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3701.4,178", + pos="3469.4,178", width=1.0652]; "gene to disease or phenotypic feature association" -> "subject closure" [color=blue, label="subject closure", - lp="3744.9,221.5", - pos="e,3691.4,195.72 3713.1,248.32 3704.3,243.44 3696.4,237.13 3690.4,229 3685.4,222.2 3685.6,213.53 3687.9,205.34", + lp="3526.9,221.5", + pos="e,3465.9,196.01 3496.1,248.25 3487,243.4 3478.8,237.11 3472.4,229 3467.4,222.64 3465.6,214.28 3465.4,206.23", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3801.4,178", + pos="3582.4,178", width=1.0652]; "gene to disease or phenotypic feature association" -> "object closure" [color=blue, label="object closure", - lp="3854.4,221.5", - pos="e,3802.2,196.18 3804.6,246.8 3804,235.16 3803.3,219.55 3802.7,206.24", + lp="3635.4,221.5", + pos="e,3583.4,196.18 3586.4,246.8 3585.7,235.16 3584.8,219.55 3584,206.24", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3934.4,178", + pos="3715.4,178", width=2.1304]; "gene to disease or phenotypic feature association" -> "subject category closure" [color=blue, label="subject category closure", - lp="4006.9,221.5", - pos="e,3928.3,196.41 3874.5,247.66 3885.9,242.9 3897.1,236.8 3906.4,229 3913.8,222.78 3919.6,214.06 3924,205.64", + lp="3787.9,221.5", + pos="e,3709.7,196.41 3656.8,247.67 3668.2,242.92 3679.2,236.81 3688.4,229 3695.7,222.78 3701.4,214.06 3705.6,205.64", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="4126.4,178", + pos="3908.4,178", width=2.1304]; "gene to disease or phenotypic feature association" -> "object category closure" [color=blue, label="object category closure", - lp="4195.9,221.5", - pos="e,4121.3,196.21 3998.7,254.22 4041.9,249.03 4080.3,241.11 4098.4,229 4106.8,223.39 4112.9,214.39 4117.3,205.56", + lp="3977.9,221.5", + pos="e,3903,196.22 3779.2,254.08 3822.5,248.89 3861.2,241 3879.4,229 3887.9,223.41 3894.2,214.41 3898.7,205.57", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4316.4,178", + pos="4098.4,178", width=1.0652]; "gene to disease or phenotypic feature association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4367.4,221.5", - pos="e,4309.9,195.96 3976.9,252.31 4112.7,242.92 4280,231 4283.4,229 4292.8,223.48 4300.1,214.07 4305.3,204.9", + lp="4149.4,221.5", + pos="e,4091.9,195.96 3758.9,252.31 3894.7,242.92 4062,231 4065.4,229 4074.8,223.48 4082.1,214.07 4087.3,204.9", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4475.4,178", + pos="4257.4,178", width=1.0652]; "gene to disease or phenotypic feature association" -> "object namespace" [color=blue, label="object namespace", - lp="4520.4,221.5", - pos="e,4468,196.1 3973.5,252.08 4000.8,250.28 4028.9,248.52 4055.4,247 4098,244.55 4401.8,249.36 4439.4,229 4449.4,223.59 4457.3,214.08 \ -4463.1,204.79", + lp="4302.4,221.5", + pos="e,4250,196.1 3755.5,252.08 3782.8,250.28 3810.9,248.52 3837.4,247 3880,244.55 4183.8,249.36 4221.4,229 4231.4,223.59 4239.3,214.08 \ +4245.1,204.79", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4586.4,178", + pos="4368.4,178", width=1.0652]; "gene to disease or phenotypic feature association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4669.4,221.5", - pos="e,4592.7,196.06 3971.4,251.91 3999.4,250.1 4028.2,248.38 4055.4,247 4085,245.49 4567.8,250.3 4588.4,229 4594.2,222.96 4595.4,214.35 \ -4594.5,205.97", + lp="4451.4,221.5", + pos="e,4374.7,196.06 3753.4,251.91 3781.4,250.1 3810.2,248.38 3837.4,247 3867,245.49 4349.8,250.3 4370.4,229 4376.2,222.96 4377.4,214.35 \ +4376.5,205.97", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4681.4,178", + pos="4463.4,178", width=1.0652]; "gene to disease or phenotypic feature association" -> "object label closure" [color=blue, label="object label closure", - lp="4821.9,221.5", - pos="e,4712.3,189.12 3970.1,251.82 3998.5,250 4027.8,248.3 4055.4,247 4074.6,246.1 4734,242.77 4747.4,229 4760.8,215.28 4742.3,202.29 \ -4721.6,192.99", + lp="4603.9,221.5", + pos="e,4494.3,189.12 3752.1,251.82 3780.5,250 3809.8,248.3 3837.4,247 3856.6,246.1 4516,242.77 4529.4,229 4542.8,215.28 4524.3,202.29 \ +4503.6,192.99", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4822.4,178", + pos="4604.4,178", width=2.347]; "gene to disease or phenotypic feature association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4969.9,221.5", - pos="e,4868.4,193.15 3969.1,251.78 3997.8,249.94 4027.5,248.25 4055.4,247 4078.7,245.96 4879.1,245.68 4895.4,229 4907.2,216.89 4895.3,\ -205.94 4877.9,197.39", + lp="4751.9,221.5", + pos="e,4650.4,193.15 3751.1,251.78 3779.8,249.94 3809.5,248.25 3837.4,247 3860.7,245.96 4661.1,245.68 4677.4,229 4689.2,216.89 4677.3,\ +205.94 4659.9,197.39", style=solid]; type [height=0.5, - pos="4956.4,178", + pos="4738.4,178", width=0.86659]; "gene to disease or phenotypic feature association" -> type [color=blue, label=type, - lp="5063.4,221.5", - pos="e,4981.1,189.33 3968.7,251.72 3997.6,249.89 4027.4,248.21 4055.4,247 4082.8,245.82 5024.2,248.59 5043.4,229 5048.1,224.24 5047.2,\ -219.51 5043.4,214 5031,195.87 5017.8,204.2 4997.4,196 4995.2,195.1 4992.9,194.17 4990.6,193.22", + lp="4845.4,221.5", + pos="e,4763.1,189.33 3750.7,251.72 3779.6,249.89 3809.4,248.21 3837.4,247 3864.8,245.82 4806.2,248.59 4825.4,229 4830.1,224.24 4829.2,\ +219.51 4825.4,214 4813,195.87 4799.8,204.2 4779.4,196 4777.2,195.1 4774.9,194.17 4772.6,193.22", style=solid]; category [height=0.5, - pos="5057.4,178", + pos="4839.4,178", width=1.4263]; "gene to disease or phenotypic feature association" -> category [color=blue, label=category, - lp="5119.9,221.5", - pos="e,5074.9,194.94 3968.4,251.73 3997.4,249.88 4027.3,248.2 4055.4,247 4083.9,245.78 5063.4,249.37 5083.4,229 5090.6,221.63 5087.5,\ -211.82 5081.3,202.85", + lp="4901.9,221.5", + pos="e,4856.9,194.94 3750.4,251.73 3779.4,249.88 3809.3,248.2 3837.4,247 3865.9,245.78 4845.4,249.37 4865.4,229 4872.6,221.63 4869.5,\ +211.82 4863.3,202.85", style=solid]; "subject aspect qualifier" [height=0.5, - pos="5245.4,178", + pos="5027.4,178", width=3.3039]; "gene to disease or phenotypic feature association" -> "subject aspect qualifier" [color=blue, label="subject aspect qualifier", - lp="5275.9,221.5", - pos="e,5222.7,195.76 3968.4,251.7 3997.4,249.86 4027.3,248.19 4055.4,247 4116.5,244.43 5096.4,244.81 5155.4,229 5176.2,223.42 5197.4,\ -211.99 5214,201.47", + lp="5057.9,221.5", + pos="e,5004.7,195.76 3750.4,251.7 3779.4,249.86 3809.3,248.19 3837.4,247 3898.5,244.43 4878.4,244.81 4937.4,229 4958.2,223.42 4979.4,\ +211.99 4996,201.47", style=solid]; "object direction qualifier" [height=0.5, - pos="5507.4,178", + pos="5289.4,178", width=3.4664]; "gene to disease or phenotypic feature association" -> "object direction qualifier" [color=blue, label="object direction qualifier", - lp="5508.4,221.5", - pos="e,5471,195.3 3967.7,251.68 3996.9,249.83 4027,248.16 4055.4,247 4200.6,241.07 5220.2,254.16 5363.4,229 5397.2,223.06 5433.7,210.3 \ -5461.5,199.16", + lp="5290.4,221.5", + pos="e,5253,195.3 3749.7,251.68 3778.9,249.83 3809,248.16 3837.4,247 3982.6,241.07 5002.2,254.16 5145.4,229 5179.2,223.06 5215.7,210.3 \ +5243.5,199.16", style=solid]; subject [height=0.5, - pos="5694.4,178", + pos="5476.4,178", width=1.2277]; "gene to disease or phenotypic feature association" -> subject [color=blue, label=subject, - lp="5664.4,221.5", - pos="e,5673.2,194.09 3967.4,251.65 3996.7,249.8 4026.9,248.13 4055.4,247 4141.2,243.59 5517.2,250.26 5600.4,229 5623.3,223.15 5646.7,\ -210.69 5664.5,199.67", + lp="5446.4,221.5", + pos="e,5455.2,194.09 3749.4,251.65 3778.7,249.8 3808.9,248.13 3837.4,247 3923.2,243.59 5299.2,250.26 5382.4,229 5405.3,223.15 5428.7,\ +210.69 5446.5,199.67", style=solid]; object [height=0.5, - pos="5737.4,91", + pos="5519.4,91", width=1.0832]; "gene to disease or phenotypic feature association" -> object [color=blue, label=object, - lp="5787.4,178", - pos="e,5750.8,108.09 3967.4,251.64 3996.7,249.78 4026.9,248.12 4055.4,247 4146.4,243.41 5607,254.51 5694.4,229 5721,221.23 5731.2,218.5 \ -5747.4,196 5765.7,170.69 5769.3,156.9 5760.4,127 5759.4,123.55 5757.9,120.13 5756.1,116.85", + lp="5569.4,178", + pos="e,5532.8,108.09 3749.4,251.64 3778.7,249.78 3808.9,248.12 3837.4,247 3928.4,243.41 5389,254.51 5476.4,229 5503,221.23 5513.2,218.5 \ +5529.4,196 5547.7,170.69 5551.3,156.9 5542.4,127 5541.4,123.55 5539.9,120.13 5538.1,116.85", style=solid]; predicate [height=0.5, - pos="5891.4,178", + pos="5673.4,178", width=1.5165]; "gene to disease or phenotypic feature association" -> predicate [color=blue, label=predicate, - lp="5864.4,221.5", - pos="e,5867.6,194.35 3967,251.64 3996.4,249.79 4026.8,248.12 4055.4,247 4151.6,243.23 5694.7,251.06 5788.4,229 5813.3,223.14 5839.2,210.55 \ -5858.8,199.47", + lp="5646.4,221.5", + pos="e,5649.6,194.35 3749,251.64 3778.4,249.79 3808.8,248.12 3837.4,247 3933.6,243.23 5476.7,251.06 5570.4,229 5595.3,223.14 5621.2,210.55 \ +5640.8,199.47", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="6049.4,178", + pos="5831.4,178", width=2.3651]; "gene to disease or phenotypic feature association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="6028.4,221.5", - pos="e,6014.3,194.49 3967,251.63 3996.4,249.77 4026.8,248.11 4055.4,247 4157.9,243.02 5801.2,246.24 5902.4,229 5937.8,222.96 5976.3,209.63 \ -6004.9,198.26", + lp="5810.4,221.5", + pos="e,5796.3,194.49 3749,251.63 3778.4,249.77 3808.8,248.11 3837.4,247 3939.9,243.02 5583.2,246.24 5684.4,229 5719.8,222.96 5758.3,209.63 \ +5786.9,198.26", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="6228.4,178", + pos="6010.4,178", width=2.1123]; "gene to disease or phenotypic feature association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="6212.4,221.5", - pos="e,6197.8,194.62 3967,251.61 3996.4,249.75 4026.8,248.1 4055.4,247 4168.9,242.64 5988.8,250.52 6100.4,229 6131,223.09 6163.7,210.19 \ -6188.4,198.97", + lp="5994.4,221.5", + pos="e,5979.8,194.62 3749,251.61 3778.4,249.75 3808.8,248.1 3837.4,247 3950.9,242.64 5770.8,250.52 5882.4,229 5913,223.09 5945.7,210.19 \ +5970.4,198.97", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="6358.4,178", + pos="6140.4,178", width=1.011]; "gene to disease or phenotypic feature association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="6362.9,221.5", - pos="e,6340.8,193.85 3966.7,251.61 3996.2,249.75 4026.7,248.09 4055.4,247 4117.1,244.66 6218.1,246.09 6277.4,229 6297.4,223.22 6317.4,\ -210.99 6332.5,200.07", + lp="6144.9,221.5", + pos="e,6122.8,193.85 3748.7,251.61 3778.2,249.75 3808.7,248.09 3837.4,247 3899.1,244.66 6000.1,246.09 6059.4,229 6079.4,223.22 6099.4,\ +210.99 6114.5,200.07", style=solid]; "sex qualifier" [color=blue, height=0.5, label="biological sex", - pos="6486.4,178", + pos="6268.4,178", width=2.0401]; "gene to disease or phenotypic feature association" -> "sex qualifier" [color=blue, label="sex qualifier", - lp="6491.4,221.5", - pos="e,6470,195.76 3966.7,251.6 3996.2,249.74 4026.7,248.08 4055.4,247 4121,244.52 6356.1,249.7 6418.4,229 6434.6,223.63 6450,212.84 \ -6462.2,202.65", + lp="6273.4,221.5", + pos="e,6252,195.76 3748.7,251.6 3778.2,249.74 3808.7,248.08 3837.4,247 3903,244.52 6138.1,249.7 6200.4,229 6216.6,223.63 6232,212.84 \ +6244.2,202.65", style=solid]; "has count" [color=blue, height=0.5, label=integer, - pos="6622.4,178", + pos="6404.4,178", width=1.2277]; "gene to disease or phenotypic feature association" -> "has count" [color=blue, label="has count", - lp="6608.4,221.5", - pos="e,6603.7,194.34 3966.7,251.59 3996.2,249.73 4026.7,248.08 4055.4,247 4124.3,244.41 6473,247.72 6539.4,229 6559.6,223.32 6579.8,211.33 \ -6595.2,200.51", + lp="6390.4,221.5", + pos="e,6385.7,194.34 3748.7,251.59 3778.2,249.73 3808.7,248.08 3837.4,247 3906.3,244.41 6255,247.72 6321.4,229 6341.6,223.32 6361.8,211.33 \ +6377.2,200.51", style=solid]; "has total" [color=blue, height=0.5, label=integer, - pos="6728.4,178", + pos="6510.4,178", width=1.2277]; "gene to disease or phenotypic feature association" -> "has total" [color=blue, label="has total", - lp="6712.9,221.5", - pos="e,6709.9,194.58 3966.7,251.58 3996.2,249.72 4026.7,248.07 4055.4,247 4127.3,244.31 6578.2,248.9 6647.4,229 6667,223.35 6686.6,211.48 \ -6701.6,200.73", + lp="6494.9,221.5", + pos="e,6491.9,194.58 3748.7,251.58 3778.2,249.72 3808.7,248.07 3837.4,247 3909.3,244.31 6360.2,248.9 6429.4,229 6449,223.35 6468.6,211.48 \ +6483.6,200.73", style=solid]; "has quotient" [color=blue, height=0.5, label=double, - pos="6832.4,178", + pos="6614.4,178", width=1.1735]; "gene to disease or phenotypic feature association" -> "has quotient" [color=blue, label="has quotient", - lp="6828.4,221.5", - pos="e,6813.4,194.34 3966.4,251.6 3996,249.73 4026.6,248.07 4055.4,247 4130.1,244.21 6676.3,249.08 6748.4,229 6768.9,223.27 6789.6,211.11 \ -6805.2,200.22", + lp="6610.4,221.5", + pos="e,6595.4,194.34 3748.4,251.6 3778,249.73 3808.6,248.07 3837.4,247 3912.1,244.21 6458.3,249.08 6530.4,229 6550.9,223.27 6571.6,211.11 \ +6587.2,200.22", style=solid]; "has percentage" [color=blue, height=0.5, label=double, - pos="6939.4,178", + pos="6721.4,178", width=1.1735]; "gene to disease or phenotypic feature association" -> "has percentage" [color=blue, label="has percentage", - lp="6958.4,221.5", - pos="e,6925.4,195.01 3966.4,251.59 3996,249.72 4026.6,248.07 4055.4,247 4133.7,244.09 6803.6,255.33 6877.4,229 6892.7,223.54 6907,212.56 \ -6918,202.28", + lp="6740.4,221.5", + pos="e,6707.4,195.01 3748.4,251.59 3778,249.72 3808.6,248.07 3837.4,247 3915.7,244.09 6585.6,255.33 6659.4,229 6674.7,223.54 6689,212.56 \ +6700,202.28", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="4102.4,265", + pos="3884.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="4233.4,265", + pos="4015.4,265", width=2.0762]; "gene to disease or phenotypic feature association_subject aspect qualifier" [color=blue, height=0.5, label=GeneOrGeneProductOrChemicalEntityAspectEnum, - pos="4575.4,265", + pos="4357.4,265", width=6.9147]; "gene to disease or phenotypic feature association_object direction qualifier" [color=blue, height=0.5, label=DirectionQualifierEnum, - pos="4963.4,265", + pos="4745.4,265", width=3.358]; subject -> object [label=relation, - lp="5732.4,134.5", - pos="e,5719.5,107.23 5695.5,159.55 5696.7,149.57 5699.2,137.07 5704.4,127 5706.6,122.68 5709.5,118.52 5712.7,114.66"]; + lp="5514.4,134.5", + pos="e,5501.5,107.23 5477.5,159.55 5478.7,149.57 5481.2,137.07 5486.4,127 5488.6,122.68 5491.5,118.52 5494.7,114.66"]; relation [height=0.5, - pos="5682.4,18", + pos="5464.4,18", width=1.2999]; - subject -> relation [pos="e,5683.7,36.188 5693.1,159.79 5691,132.48 5687,78.994 5684.5,46.38", + subject -> relation [pos="e,5465.7,36.188 5475.1,159.79 5473,132.48 5469,78.994 5466.5,46.38", style=dotted]; "gene to disease or phenotypic feature association_subject" [color=blue, height=0.5, label="gene or gene product", - pos="5212.4,265", + pos="4994.4,265", width=3.0692]; - object -> relation [pos="e,5695.2,35.54 5724.9,73.889 5718,64.939 5709.2,53.617 5701.4,43.584", + object -> relation [pos="e,5477.2,35.54 5506.9,73.889 5500,64.939 5491.2,53.617 5483.4,43.584", style=dotted]; "gene to disease or phenotypic feature association_object" [color=blue, height=0.5, label="disease or phenotypic feature", - pos="5489.4,265", + pos="5271.4,265", width=4.1344]; "gene to disease or phenotypic feature association_predicate" [color=blue, height=0.5, label="predicate type", - pos="5734.4,265", + pos="5516.4,265", width=2.1665]; } diff --git a/graphviz/gene_to_disease_or_phenotypic_feature_association.svg b/graphviz/gene_to_disease_or_phenotypic_feature_association.svg index 5d80d95127..dc71ac5ca3 100644 --- a/graphviz/gene_to_disease_or_phenotypic_feature_association.svg +++ b/graphviz/gene_to_disease_or_phenotypic_feature_association.svg @@ -4,16 +4,16 @@ - + %3 - + gene to disease or phenotypic feature association - -gene to disease or phenotypic feature association + +gene to disease or phenotypic feature association @@ -24,9 +24,9 @@ gene to disease or phenotypic feature association->association - + -is_a +is_a @@ -37,9 +37,9 @@ gene to disease or phenotypic feature association->entity to phenotypic feature association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ gene to disease or phenotypic feature association->gene to entity association mixin - - -uses + + +uses @@ -63,9 +63,9 @@ gene to disease or phenotypic feature association->id - - -id + + +id @@ -76,9 +76,9 @@ gene to disease or phenotypic feature association->iri - - -iri + + +iri @@ -89,9 +89,9 @@ gene to disease or phenotypic feature association->name - - -name + + +name @@ -102,9 +102,9 @@ gene to disease or phenotypic feature association->description - - -description + + +description @@ -115,9 +115,9 @@ gene to disease or phenotypic feature association->has attribute - - -has attribute + + +has attribute @@ -128,9 +128,9 @@ gene to disease or phenotypic feature association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ gene to disease or phenotypic feature association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ gene to disease or phenotypic feature association->publications - - -publications + + +publications @@ -167,505 +167,505 @@ gene to disease or phenotypic feature association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string gene to disease or phenotypic feature association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string gene to disease or phenotypic feature association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string gene to disease or phenotypic feature association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type gene to disease or phenotypic feature association->timepoint - - -timepoint + + +timepoint original subject - -string + +string gene to disease or phenotypic feature association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie gene to disease or phenotypic feature association->original predicate - - -original predicate + + +original predicate original object - -string + +string gene to disease or phenotypic feature association->original object - - -original object + + +original object subject category - -ontology class + +ontology class gene to disease or phenotypic feature association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class gene to disease or phenotypic feature association->object category - - -object category + + +object category subject closure - -string + +string gene to disease or phenotypic feature association->subject closure - - -subject closure + + +subject closure object closure - -string + +string gene to disease or phenotypic feature association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class gene to disease or phenotypic feature association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class gene to disease or phenotypic feature association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string gene to disease or phenotypic feature association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string gene to disease or phenotypic feature association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string gene to disease or phenotypic feature association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string gene to disease or phenotypic feature association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source gene to disease or phenotypic feature association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type gene to disease or phenotypic feature association->type - - -type + + +type category - -category + +category gene to disease or phenotypic feature association->category - - -category + + +category subject aspect qualifier - -subject aspect qualifier + +subject aspect qualifier gene to disease or phenotypic feature association->subject aspect qualifier - - -subject aspect qualifier + + +subject aspect qualifier object direction qualifier - -object direction qualifier + +object direction qualifier gene to disease or phenotypic feature association->object direction qualifier - - -object direction qualifier + + +object direction qualifier subject - -subject + +subject gene to disease or phenotypic feature association->subject - - -subject + + +subject object - -object + +object gene to disease or phenotypic feature association->object - - -object + + +object predicate - -predicate + +predicate gene to disease or phenotypic feature association->predicate - - -predicate + + +predicate frequency qualifier - -frequency value + +frequency value gene to disease or phenotypic feature association->frequency qualifier - - -frequency qualifier + + +frequency qualifier severity qualifier - -severity value + +severity value gene to disease or phenotypic feature association->severity qualifier - - -severity qualifier + + +severity qualifier onset qualifier - -onset + +onset gene to disease or phenotypic feature association->onset qualifier - - -onset qualifier + + +onset qualifier sex qualifier - -biological sex + +biological sex gene to disease or phenotypic feature association->sex qualifier - - -sex qualifier + + +sex qualifier has count - -integer + +integer gene to disease or phenotypic feature association->has count - - -has count + + +has count has total - -integer + +integer gene to disease or phenotypic feature association->has total - - -has total + + +has total has quotient - -double + +double gene to disease or phenotypic feature association->has quotient - - -has quotient + + +has quotient has percentage - -double + +double gene to disease or phenotypic feature association->has percentage - - -has percentage + + +has percentage association_type - -string + +string association_category - -category type + +category type gene to disease or phenotypic feature association_subject aspect qualifier - -GeneOrGeneProductOrChemicalEntityAspectEnum + +GeneOrGeneProductOrChemicalEntityAspectEnum gene to disease or phenotypic feature association_object direction qualifier - -DirectionQualifierEnum + +DirectionQualifierEnum subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + gene to disease or phenotypic feature association_subject - -gene or gene product + +gene or gene product object->relation - - + + gene to disease or phenotypic feature association_object - -disease or phenotypic feature + +disease or phenotypic feature gene to disease or phenotypic feature association_predicate - -predicate type + +predicate type diff --git a/graphviz/gene_to_expression_site_association.gv b/graphviz/gene_to_expression_site_association.gv index 795a017087..d74c2ced41 100644 --- a/graphviz/gene_to_expression_site_association.gv +++ b/graphviz/gene_to_expression_site_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,5125,283"]; + graph [bb="0,0,4940,283"]; node [label="\N"]; "gene to expression site association" [height=0.5, label="gene to expression site association", - pos="2594.4,265", + pos="2409.4,265", width=4.8024]; association [height=0.5, pos="62.394,178", width=1.7332]; "gene to expression site association" -> association [label=is_a, lp="280.39,221.5", - pos="e,102.91,191.8 2421.7,263.65 1918.8,262.31 477.63,256.12 266.39,229 213.1,222.16 153.57,206.63 112.64,194.68"]; + pos="e,102.91,191.78 2237,263.4 1762.4,261.45 458.99,253.85 266.39,229 213.11,222.12 153.58,206.6 112.64,194.66"]; id [color=blue, height=0.5, label=string, @@ -19,7 +19,7 @@ digraph { "gene to expression site association" -> id [color=blue, label=id, lp="395.39,221.5", - pos="e,210.38,189.98 2422.2,263.14 1938.2,260.46 587.79,251.07 388.39,229 316.66,221.06 298.9,215.43 229.39,196 226.29,195.13 223.09,\ + pos="e,210.38,189.98 2237.5,262.87 1782.5,259.61 569.15,249.14 388.39,229 316.67,221.01 298.9,215.43 229.39,196 226.29,195.13 223.09,\ 194.17 219.89,193.15", style=solid]; iri [color=blue, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "gene to expression site association" -> iri [color=blue, label=iri, - lp="508.39,221.5", - pos="e,315.3,190.19 2422.7,262.91 1956.3,259.71 688.61,249.23 500.39,229 426.04,221.01 407.78,214.78 335.39,196 332.02,195.12 328.54,\ -194.16 325.06,193.14", + lp="501.39,221.5", + pos="e,315.32,190.15 2237.8,262.71 1799.9,259.14 663.61,248.16 493.39,229 422.11,220.98 404.75,214.31 335.39,196 332.02,195.11 328.55,\ +194.13 325.07,193.11", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "gene to expression site association" -> name [color=blue, label=name, - lp="615.39,221.5", - pos="e,439.15,191.55 2421.9,263.3 1969.8,261.13 773.33,253.15 595.39,229 544.62,222.11 488.03,206.59 449.14,194.65", + lp="604.39,221.5", + pos="e,437.98,191.88 2237.4,263.13 1814.1,260.63 744.81,252.09 584.39,229 537.02,222.18 484.45,206.99 447.86,195.13", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "gene to expression site association" -> description [color=blue, label=description, - lp="735.89,221.5", - pos="e,585.2,194.16 2421.7,263.92 1985.6,263.28 862.22,258.72 695.39,229 660.55,222.79 622.82,209.43 594.72,198.07", + lp="717.89,221.5", + pos="e,581.52,194.51 2236.7,264 1828.4,263.5 827.02,259.17 677.39,229 647.25,222.92 615.06,210.02 590.76,198.85", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "gene to expression site association" -> "has attribute" [color=blue, label="has attribute", - lp="881.39,221.5", - pos="e,726.02,192.95 2421.6,263.77 2008.6,262.77 987.21,257.4 834.39,229 799.92,222.59 762.64,208.63 735.52,197.08", + lp="852.39,221.5", + pos="e,721.33,194.02 2236.5,264.19 1850.6,264.04 941.63,260.32 805.39,229 778.88,222.91 751.04,210.01 730.13,198.84", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "gene to expression site association" -> negated [color=blue, label=negated, - lp="1036.4,221.5", - pos="e,847.23,190.47 2421.3,264.79 2068.3,265.64 1276.1,263.47 1007.4,229 954.82,222.26 896.1,205.83 857.18,193.63", + lp="990.39,221.5", + pos="e,843.03,191.98 2237.6,262.75 1881.1,259.73 1083.8,250.64 961.39,229 923.36,222.28 881.85,207.56 852.49,195.83", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "gene to expression site association" -> qualifiers [color=blue, label=qualifiers, - lp="1175.9,221.5", - pos="e,996.36,193.22 2423.6,262.14 2067,257.94 1266,246.67 1142.4,229 1095.4,222.29 1043.4,207.89 1006,196.26", + lp="1101.9,221.5", + pos="e,982.39,194.95 2237.1,263.21 1900.7,261.11 1179.3,253.77 1068.4,229 1041.6,223.01 1013.3,210.63 991.57,199.69", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "gene to expression site association" -> publications [color=blue, label=publications, - lp="1322.4,221.5", - pos="e,1147.2,192.74 2423.9,261.98 2093.5,257.69 1388.3,246.6 1278.4,229 1236.2,222.25 1189.8,207.76 1156.7,196.1", + lp="1204.4,221.5", + pos="e,1122.5,195.81 2238.1,262.58 1907.3,259.38 1208.8,250.15 1160.4,229 1148,223.6 1137.2,213.49 1128.9,203.77", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,303 +100,303 @@ digraph { width=2.0943]; "gene to expression site association" -> "has evidence" [color=blue, label="has evidence", - lp="1482.9,221.5", - pos="e,1306,193.53 2421.5,264.22 2146.2,263.64 1620.7,258.53 1436.4,229 1394.7,222.32 1348.9,208.33 1315.5,196.84", + lp="1302.9,221.5", + pos="e,1256.9,195.94 2238.9,261.86 1922.1,257.46 1273.2,246.37 1256.4,229 1250.3,222.7 1250.5,213.81 1253.1,205.27", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1469.4,178", - width=3.015]; + label=string, + pos="1399.4,178", + width=1.0652]; "gene to expression site association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1639.9,221.5", - pos="e,1496.6,195.62 2423.8,261.9 2155,258.03 1655.2,248.33 1575.4,229 1551,223.09 1525.5,211.25 1505.6,200.58", + lp="1421.9,221.5", + pos="e,1376.1,192.38 2236.5,264.44 1945.8,264.31 1387.4,260.01 1357.4,229 1348.1,219.4 1356.3,208.05 1367.8,198.59", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1704.4,178", - width=3.015]; + label=string, + pos="1494.4,178", + width=1.0652]; "gene to expression site association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1813.4,221.5", - pos="e,1704.4,196.16 2423.4,262.29 2176.3,259.09 1745.5,250.46 1718.4,229 1711.4,223.46 1707.7,214.7 1705.8,206.06", + lp="1591.4,221.5", + pos="e,1489.8,196.16 2237.1,263.35 1979.8,261.54 1522.1,254.7 1496.4,229 1490.5,223.13 1488.7,214.67 1488.8,206.37", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1939.4,178", - width=3.015]; + label=string, + pos="1669.4,178", + width=1.0652]; "gene to expression site association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2022.9,221.5", - pos="e,1922.7,195.92 2425.5,261.03 2230.4,256.75 1933.7,247.27 1916.4,229 1909.8,222.04 1911.9,212.84 1916.9,204.23", + lp="1812.9,221.5", + pos="e,1677.1,196.1 2237.2,263.07 2044.1,260.83 1751.9,253.4 1706.4,229 1696.3,223.59 1688.2,214.08 1682.2,204.79", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2121.4,178", + pos="1895.4,178", width=1.5346]; "gene to expression site association" -> timepoint [color=blue, label=timepoint, - lp="2180.4,221.5", - pos="e,2125,196.29 2430.9,259.14 2312.4,254.29 2169,245.17 2145.4,229 2137.4,223.54 2132,214.69 2128.4,205.94", + lp="1977.4,221.5", + pos="e,1906.3,196.07 2236.7,263.98 2125.7,261.52 1993.2,253.26 1942.4,229 1930.8,223.44 1920.6,213.64 1912.7,204.18", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2233.4,178", + pos="2007.4,178", width=1.0652]; "gene to expression site association" -> "original subject" [color=blue, label="original subject", - lp="2280.4,221.5", - pos="e,2224,195.81 2432.6,258.64 2339.8,253.84 2239,245 2224.4,229 2218.6,222.62 2218.5,213.83 2220.7,205.39", + lp="2083.4,221.5", + pos="e,2009.6,196.16 2252.7,257.32 2155.6,251.85 2045.8,242.75 2027.4,229 2020,223.46 2015.3,214.7 2012.3,206.06", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2347.4,178", + pos="2133.4,178", width=1.5887]; "gene to expression site association" -> "original predicate" [color=blue, label="original predicate", - lp="2408.9,221.5", - pos="e,2341.3,196.26 2435,257.97 2394.4,252.94 2358.6,244.16 2345.4,229 2340,222.82 2338.9,214.42 2339.6,206.27", + lp="2217.9,221.5", + pos="e,2136.1,196.03 2259.8,255.93 2214.5,250.84 2172,242.54 2154.4,229 2147,223.31 2142.2,214.53 2139,205.9", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2461.4,178", + pos="2267.4,178", width=1.0652]; "gene to expression site association" -> "original object" [color=blue, label="original object", - lp="2538.9,221.5", - pos="e,2466.5,195.98 2521.3,248.57 2509.1,243.72 2497.2,237.35 2487.4,229 2480,222.74 2474.5,213.87 2470.4,205.33", + lp="2348.9,221.5", + pos="e,2273.9,196.05 2333.9,248.74 2320.9,243.86 2308.1,237.44 2297.4,229 2289.4,222.75 2283.1,213.76 2278.4,205.13", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2594.4,178", + pos="2400.4,178", width=2.1304]; "gene to expression site association" -> "subject category" [color=blue, label="subject category", - lp="2653.9,221.5", - pos="e,2594.4,196.18 2594.4,246.8 2594.4,235.16 2594.4,219.55 2594.4,206.24", + lp="2465.9,221.5", + pos="e,2402.2,196.18 2407.6,246.8 2406.3,235.16 2404.7,219.55 2403.3,206.24", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2765.4,178", + pos="2571.4,178", width=2.1304]; "gene to expression site association" -> "object category" [color=blue, label="object category", - lp="2788.9,221.5", - pos="e,2751.9,196.04 2668.2,248.68 2684,243.72 2700.3,237.28 2714.4,229 2725.8,222.34 2736.5,212.6 2745.1,203.48", + lp="2601.9,221.5", + pos="e,2560.9,196.11 2486.3,248.87 2501.3,243.95 2516.4,237.48 2529.4,229 2539.2,222.62 2547.9,213.27 2554.8,204.38", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="2898.4,178", + pos="2704.4,178", width=1.0652]; "gene to expression site association" -> "subject closure" [color=blue, label="subject closure", - lp="2923.9,221.5", - pos="e,2886.8,195.3 2727,253.43 2776.7,247.85 2826.5,239.87 2848.4,229 2860.6,222.94 2871.6,212.74 2880.2,203.13", + lp="2734.9,221.5", + pos="e,2694.6,195.77 2525.7,251.62 2585.7,244.55 2649,235.78 2661.4,229 2672.2,223.12 2681.5,213.4 2688.6,204.09", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="2998.4,178", + pos="2812.4,178", width=1.0652]; "gene to expression site association" -> "object closure" [color=blue, label="object closure", - lp="3042.4,221.5", - pos="e,2996.9,196.12 2718.2,252.35 2737.7,250.54 2757.6,248.71 2776.4,247 2821.7,242.88 2944.3,256.78 2980.4,229 2987.6,223.41 2992,214.65 \ -2994.6,206.01", + lp="2855.4,221.5", + pos="e,2810.5,196.14 2533.2,252.36 2552.7,250.55 2572.6,248.72 2591.4,247 2636.3,242.9 2757.5,256.21 2793.4,229 2800.7,223.44 2805.2,\ +214.68 2808,206.04", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3131.4,178", + pos="2945.4,178", width=2.1304]; "gene to expression site association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3199.9,221.5", - pos="e,3124.3,196.05 2715.2,252.08 2735.6,250.25 2756.6,248.48 2776.4,247 2811.9,244.34 3065.3,246.33 3096.4,229 3106.1,223.59 3113.7,\ -214.2 3119.4,205.02", + lp="3013.9,221.5", + pos="e,2938,196.06 2530.2,252.09 2550.6,250.26 2571.6,248.48 2591.4,247 2626.7,244.35 2878.4,246.02 2909.4,229 2919.2,223.6 2927.1,214.22 \ +2932.9,205.03", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3323.4,178", + pos="3138.4,178", width=2.1304]; "gene to expression site association" -> "object category closure" [color=blue, label="object category closure", - lp="3390.9,221.5", - pos="e,3317.4,196.09 2713.3,251.89 2734.3,250.04 2756,248.31 2776.4,247 2805,245.17 3266.5,243.18 3291.4,229 3300.8,223.64 3307.9,214.27 \ -3312.9,205.07", + lp="3204.9,221.5", + pos="e,3132,196.11 2528.3,251.89 2549.3,250.04 2571,248.31 2591.4,247 2619.9,245.17 3080.5,242.98 3105.4,229 3114.9,223.66 3122.2,214.29 \ +3127.4,205.09", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3513.4,178", + pos="3328.4,178", width=1.0652]; "gene to expression site association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3563.4,221.5", - pos="e,3506.4,196.17 2712.3,251.82 2733.6,249.95 2755.6,248.23 2776.4,247 2815.3,244.68 3444,247.46 3478.4,229 3488.2,223.74 3495.8,214.38 \ -3501.5,205.17", + lp="3377.4,221.5", + pos="e,3321.3,195.69 2527.3,251.82 2548.6,249.95 2570.6,248.23 2591.4,247 2630.3,244.69 3258,247.2 3292.4,229 3302.6,223.62 3310.6,213.93 \ +3316.4,204.5", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3672.4,178", + pos="3487.4,178", width=1.0652]; "gene to expression site association" -> "object namespace" [color=blue, label="object namespace", - lp="3716.4,221.5", - pos="e,3665,195.72 2711.8,251.78 2733.3,249.9 2755.5,248.19 2776.4,247 2824,244.28 3593,250.93 3635.4,229 3645.7,223.66 3653.9,213.98 \ -3659.9,204.54", + lp="3530.4,221.5", + pos="e,3479.7,195.74 2526.8,251.78 2548.3,249.9 2570.5,248.19 2591.4,247 2639,244.28 3406.9,250.63 3449.4,229 3459.8,223.68 3468.2,213.99 \ +3474.4,204.56", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3823.4,178", + pos="3638.4,178", width=1.0652]; "gene to expression site association" -> "subject label closure" [color=blue, label="subject label closure", - lp="3876.4,221.5", - pos="e,3815.4,195.76 2711.8,251.73 2733.3,249.85 2755.5,248.16 2776.4,247 2832.3,243.89 3734.3,254.02 3784.4,229 3795.1,223.65 3803.7,\ -213.83 3810.2,204.3", + lp="3690.4,221.5", + pos="e,3630.1,195.77 2526.8,251.73 2548.3,249.85 2570.5,248.16 2591.4,247 2647.3,243.9 3548.2,253.69 3598.4,229 3609.2,223.67 3618.1,\ +213.85 3624.7,204.31", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="3994.4,178", + pos="3809.4,178", width=1.0652]; "gene to expression site association" -> "object label closure" [color=blue, label="object label closure", - lp="4041.9,221.5", - pos="e,3986.1,195.78 2711.3,251.73 2732.9,249.84 2755.3,248.14 2776.4,247 2809.1,245.23 3925,243.4 3954.4,229 3965.2,223.68 3974.1,213.86 \ -3980.7,204.32", + lp="3855.9,221.5", + pos="e,3800.8,195.79 2526.3,251.73 2547.9,249.84 2570.3,248.14 2591.4,247 2624,245.23 3738.9,243.21 3768.4,229 3779.4,223.7 3788.4,213.88 \ +3795.2,204.34", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4138.4,178", + pos="3953.4,178", width=2.347]; "gene to expression site association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4197.9,221.5", - pos="e,4135.4,196 2711.3,251.69 2732.9,249.81 2755.3,248.12 2776.4,247 2813.5,245.02 4084.2,249.28 4115.4,229 4123.5,223.7 4128.8,214.72 \ -4132.3,205.82", + lp="4011.9,221.5", + pos="e,3950.1,196.03 2526.3,251.69 2547.9,249.81 2570.3,248.12 2591.4,247 2628.5,245.02 3898.1,249.01 3929.4,229 3937.7,223.67 3943.3,\ +214.56 3946.9,205.56", style=solid]; type [height=0.5, - pos="4272.4,178", + pos="4087.4,178", width=0.86659]; "gene to expression site association" -> type [color=blue, label=type, - lp="4294.4,221.5", - pos="e,4277.5,196.18 2711.3,251.67 2732.9,249.79 2755.3,248.11 2776.4,247 2797.1,245.91 4256.7,243.62 4271.4,229 4277.4,223.09 4279,214.51 \ -4278.6,206.12", + lp="4108.4,221.5", + pos="e,4092.1,196.23 2526.3,251.67 2547.9,249.79 2570.3,248.11 2591.4,247 2612.1,245.91 4070.5,243.47 4085.4,229 4091.4,223.14 4093.2,\ +214.58 4093,206.19", style=solid]; category [height=0.5, - pos="4373.4,178", + pos="4188.4,178", width=1.4263]; "gene to expression site association" -> category [color=blue, label=category, - lp="4371.9,221.5", - pos="e,4359.8,195.45 2711.3,251.66 2732.9,249.78 2755.3,248.11 2776.4,247 2819.1,244.76 4274.4,243.95 4314.4,229 4329,223.56 4342.4,212.8 \ -4352.8,202.65", + lp="4185.9,221.5", + pos="e,4174.5,195.46 2526.3,251.66 2547.9,249.78 2570.3,248.11 2591.4,247 2634,244.76 4088.3,243.77 4128.4,229 4143.1,223.56 4156.8,212.81 \ +4167.4,202.66", style=solid]; "stage qualifier" [height=0.5, - pos="4520.4,178", + pos="4335.4,178", width=2.1484]; "gene to expression site association" -> "stage qualifier" [color=blue, label="stage qualifier", - lp="4503.9,221.5", - pos="e,4492.7,195.08 2711.3,251.65 2732.9,249.77 2755.3,248.1 2776.4,247 2866.9,242.28 4318.8,248.23 4407.4,229 4434.1,223.21 4462.1,\ -210.83 4483.6,199.84", + lp="4318.9,221.5", + pos="e,4307.9,194.84 2526.3,251.65 2547.9,249.77 2570.3,248.1 2591.4,247 2681.8,242.28 4132.9,248.07 4221.4,229 4248.6,223.15 4277.2,\ +210.55 4299,199.47", style=solid]; "quantifier qualifier" [height=0.5, - pos="4713.4,178", + pos="4528.4,178", width=2.7081]; "gene to expression site association" -> "quantifier qualifier" [color=blue, label="quantifier qualifier", - lp="4687.4,221.5", - pos="e,4675.9,194.73 2710.8,251.68 2732.6,249.78 2755.2,248.1 2776.4,247 2974.3,236.78 4363.9,260.96 4559.4,229 4596.3,222.96 4636.5,\ -209.69 4666.5,198.33", + lp="4502.4,221.5", + pos="e,4490.9,194.73 2525.8,251.68 2547.6,249.78 2570.2,248.1 2591.4,247 2789.3,236.78 4178.9,260.96 4374.4,229 4411.3,222.96 4451.5,\ +209.69 4481.5,198.33", style=solid]; subject [height=0.5, - pos="4873.4,178", + pos="4688.4,178", width=1.2277]; "gene to expression site association" -> subject [color=blue, label=subject, - lp="4830.4,221.5", - pos="e,4848.8,193.17 2710.8,251.66 2732.6,249.77 2755.2,248.09 2776.4,247 2886.4,241.37 4650.7,251.91 4758.4,229 4787.1,222.9 4817.4,\ -209.36 4839.7,197.92", + lp="4645.4,221.5", + pos="e,4663.8,193.17 2525.8,251.66 2547.6,249.77 2570.2,248.09 2591.4,247 2701.4,241.37 4465.7,251.91 4573.4,229 4602.1,222.9 4632.4,\ +209.36 4654.7,197.92", style=solid]; object [height=0.5, - pos="4916.4,91", + pos="4731.4,91", width=1.0832]; "gene to expression site association" -> object [color=blue, label=object, - lp="4966.4,178", - pos="e,4929.8,108.09 2710.8,251.65 2732.6,249.76 2755.2,248.08 2776.4,247 2892,241.11 4747.8,256.09 4860.4,229 4892.3,221.33 4906,221.67 \ -4926.4,196 4945.8,171.57 4948.3,156.9 4939.4,127 4938.4,123.55 4936.9,120.13 4935.1,116.85", + lp="4781.4,178", + pos="e,4744.8,108.09 2525.8,251.65 2547.6,249.76 2570.2,248.08 2591.4,247 2707,241.11 4562.8,256.09 4675.4,229 4707.3,221.33 4721,221.67 \ +4741.4,196 4760.8,171.57 4763.3,156.9 4754.4,127 4753.4,123.55 4751.9,120.13 4750.1,116.85", style=solid]; predicate [height=0.5, - pos="5070.4,178", + pos="4885.4,178", width=1.5165]; "gene to expression site association" -> predicate [color=blue, label=predicate, - lp="5043.4,221.5", - pos="e,5046.6,194.36 2710.8,251.64 2732.6,249.75 2755.2,248.08 2776.4,247 2898,240.83 4848.9,256.76 4967.4,229 4992.3,223.17 5018.2,210.57 \ -5037.8,199.49", + lp="4858.4,221.5", + pos="e,4861.6,194.36 2525.8,251.64 2547.6,249.75 2570.2,248.08 2591.4,247 2713,240.83 4663.9,256.76 4782.4,229 4807.3,223.17 4833.2,210.57 \ +4852.8,199.49", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2823.4,265", + pos="2638.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2954.4,265", + pos="2769.4,265", width=2.0762]; "gene to expression site association_stage qualifier" [color=blue, height=0.5, label="life stage", - pos="3101.4,265", + pos="2916.4,265", width=1.4985]; "gene to expression site association_quantifier qualifier" [color=blue, height=0.5, label="ontology class", - pos="3250.4,265", + pos="3065.4,265", width=2.1304]; subject -> object [label=relation, - lp="4911.4,134.5", - pos="e,4898.5,107.23 4874.5,159.55 4875.7,149.57 4878.2,137.07 4883.4,127 4885.6,122.68 4888.5,118.52 4891.7,114.66"]; + lp="4726.4,134.5", + pos="e,4713.5,107.23 4689.5,159.55 4690.7,149.57 4693.2,137.07 4698.4,127 4700.6,122.68 4703.5,118.52 4706.7,114.66"]; relation [height=0.5, - pos="4861.4,18", + pos="4676.4,18", width=1.2999]; - subject -> relation [pos="e,4862.7,36.188 4872.1,159.79 4870,132.48 4866,78.994 4863.5,46.38", + subject -> relation [pos="e,4677.7,36.188 4687.1,159.79 4685,132.48 4681,78.994 4678.5,46.38", style=dotted]; "gene to expression site association_subject" [color=blue, height=0.5, label="gene or gene product", - pos="3455.4,265", + pos="3270.4,265", width=3.0692]; - object -> relation [pos="e,4874.2,35.54 4903.9,73.889 4897,64.939 4888.2,53.617 4880.4,43.584", + object -> relation [pos="e,4689.2,35.54 4718.9,73.889 4712,64.939 4703.2,53.617 4695.4,43.584", style=dotted]; "gene to expression site association_object" [color=blue, height=0.5, label="anatomical entity", - pos="3675.4,265", + pos="3490.4,265", width=2.5456]; "gene to expression site association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3863.4,265", + pos="3678.4,265", width=2.1665]; } diff --git a/graphviz/gene_to_expression_site_association.svg b/graphviz/gene_to_expression_site_association.svg index fb508d8871..1c3c489a7d 100644 --- a/graphviz/gene_to_expression_site_association.svg +++ b/graphviz/gene_to_expression_site_association.svg @@ -4,16 +4,16 @@ - + %3 - + gene to expression site association - -gene to expression site association + +gene to expression site association @@ -24,8 +24,8 @@ gene to expression site association->association - - + + is_a @@ -37,7 +37,7 @@ gene to expression site association->id - + id @@ -50,9 +50,9 @@ gene to expression site association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ gene to expression site association->name - - -name + + +name @@ -76,9 +76,9 @@ gene to expression site association->description - - -description + + +description @@ -89,9 +89,9 @@ gene to expression site association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ gene to expression site association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ gene to expression site association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ gene to expression site association->publications - - -publications + + +publications @@ -141,401 +141,401 @@ gene to expression site association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string gene to expression site association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string gene to expression site association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string gene to expression site association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type gene to expression site association->timepoint - - -timepoint + + +timepoint original subject - -string + +string gene to expression site association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie gene to expression site association->original predicate - - -original predicate + + +original predicate original object - -string + +string gene to expression site association->original object - - -original object + + +original object subject category - -ontology class + +ontology class gene to expression site association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class gene to expression site association->object category - - -object category + + +object category subject closure - -string + +string gene to expression site association->subject closure - - -subject closure + + +subject closure object closure - -string + +string gene to expression site association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class gene to expression site association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class gene to expression site association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string gene to expression site association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string gene to expression site association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string gene to expression site association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string gene to expression site association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source gene to expression site association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type gene to expression site association->type - - -type + + +type category - -category + +category gene to expression site association->category - - -category + + +category stage qualifier - -stage qualifier + +stage qualifier gene to expression site association->stage qualifier - - -stage qualifier + + +stage qualifier quantifier qualifier - -quantifier qualifier + +quantifier qualifier gene to expression site association->quantifier qualifier - - -quantifier qualifier + + +quantifier qualifier subject - -subject + +subject gene to expression site association->subject - - -subject + + +subject object - -object + +object gene to expression site association->object - - -object + + +object predicate - -predicate + +predicate gene to expression site association->predicate - - -predicate + + +predicate association_type - -string + +string association_category - -category type + +category type gene to expression site association_stage qualifier - -life stage + +life stage gene to expression site association_quantifier qualifier - -ontology class + +ontology class subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + gene to expression site association_subject - -gene or gene product + +gene or gene product object->relation - - + + gene to expression site association_object - -anatomical entity + +anatomical entity gene to expression site association_predicate - -predicate type + +predicate type diff --git a/graphviz/gene_to_gene_association.gv b/graphviz/gene_to_gene_association.gv index bc6e45e42b..eacdf5a898 100644 --- a/graphviz/gene_to_gene_association.gv +++ b/graphviz/gene_to_gene_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4788.4,283"]; + graph [bb="0,0,4570.4,283"]; node [label="\N"]; "gene to gene association" [height=0.5, label="gene to gene association", - pos="2492.4,265", + pos="2274.4,265", width=3.4844]; association [height=0.5, pos="62.394,178", width=1.7332]; "gene to gene association" -> association [label=is_a, - lp="281.39,221.5", - pos="e,103.12,191.79 2366.9,263.66 1927.8,262.26 475.16,255.63 267.39,229 213.85,222.14 154.03,206.61 112.9,194.67"]; + lp="280.39,221.5", + pos="e,102.91,191.77 2149.2,263.44 1739.2,261.38 452.03,253.06 266.39,229 213.11,222.09 153.58,206.57 112.65,194.64"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "gene to gene association" -> id [color=blue, label=id, - lp="398.39,221.5", - pos="e,210.38,190 2367.4,263.26 1945.2,260.58 587,250.37 391.39,229 318.35,221.02 300.2,215.65 229.39,196 226.29,195.14 223.09,194.17 \ -219.89,193.16", + lp="396.39,221.5", + pos="e,210.38,189.98 2149.5,263.02 1756.7,259.75 562.92,248.34 389.39,229 317.23,220.96 299.34,215.5 229.39,196 226.29,195.13 223.09,\ +194.17 219.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "gene to gene association" -> iri [color=blue, label=iri, - lp="515.39,221.5", - pos="e,315.29,190.23 2367.7,263.05 1961.3,259.78 691.29,248.12 507.39,229 429.97,220.95 410.81,215.26 335.39,196 332.02,195.14 328.54,\ -194.18 325.05,193.17", + lp="509.39,221.5", + pos="e,315.3,190.2 2148.8,264.4 1799.4,265.06 821.06,263.65 501.39,229 426.61,220.89 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ +325.06,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "gene to gene association" -> name [color=blue, label=name, - lp="627.39,221.5", - pos="e,440.01,191.15 2367.4,263.22 1974.6,260.57 780.63,250.77 607.39,229 552.58,222.11 491.21,206.11 449.83,194.05", + lp="617.39,221.5", + pos="e,439.19,191.41 2149.7,263.04 1787.1,260 749.39,249.6 597.39,229 545.74,222 488.1,206.31 448.78,194.36", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "gene to gene association" -> description [color=blue, label=description, - lp="755.89,221.5", - pos="e,588.8,193.65 2367.3,263.53 1989.6,261.84 876.9,254.7 715.39,229 675.03,222.58 630.79,208.66 598.44,197.14", + lp="739.89,221.5", + pos="e,586.19,194.12 2149.2,263.4 1801.4,261.42 840.18,253.75 699.39,229 663.52,222.69 624.55,209.24 595.6,197.88", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "gene to gene association" -> "has attribute" [color=blue, label="has attribute", - lp="913.39,221.5", - pos="e,729.98,191.75 2367.3,263.21 2012,260.7 1012.8,251.69 866.39,229 822.26,222.16 773.51,207 739.58,195.15", + lp="887.39,221.5", + pos="e,726.83,192.67 2149.4,263.16 1823.9,260.66 967.01,251.95 840.39,229 804.17,222.43 764.8,208.24 736.39,196.65", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "gene to gene association" -> predicate [color=blue, label=predicate, - lp="1074.4,221.5", - pos="e,887.81,193.09 2366.9,264.61 2063.1,265.48 1294.7,264.05 1040.4,229 991.17,222.22 936.47,207.65 897.4,195.99", + lp="1031.4,221.5", + pos="e,880.43,194.06 2149.9,262.63 1850.8,259.03 1108.6,248.28 997.39,229 960.25,222.56 919.77,209.02 889.78,197.66", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "gene to gene association" -> negated [color=blue, label=negated, - lp="1220.4,221.5", - pos="e,1022.3,190.23 2367.2,263.68 2086.9,262.46 1416.2,256.66 1191.4,229 1135.6,222.13 1072.9,205.38 1032,193.16", + lp="1151.4,221.5", + pos="e,1015.6,192.51 2150.1,262.49 1872.9,258.81 1220.9,248.21 1122.4,229 1088.3,222.36 1051.5,208.2 1024.9,196.64", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "gene to gene association" -> qualifiers [color=blue, label=qualifiers, - lp="1356.9,221.5", - pos="e,1171.6,193.02 2366.8,263.74 2107.7,262.64 1521.5,257.02 1323.4,229 1274.6,222.11 1220.5,207.65 1181.6,196.05", + lp="1254.9,221.5", + pos="e,1151.6,195.39 2149.2,263.04 1889.4,260.59 1308.7,252.53 1221.4,229 1199.7,223.15 1177.4,211.43 1160.1,200.81", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "gene to gene association" -> publications [color=blue, label=publications, - lp="1499.4,221.5", - pos="e,1321.9,192.66 2367,263.72 2130.6,262.53 1627.2,256.71 1455.4,229 1412.5,222.09 1365.3,207.61 1331.5,196.01", + lp="1346.4,221.5", + pos="e,1286.4,196.26 2149.1,263.24 1894.1,261.17 1335.8,253.83 1302.4,229 1295.1,223.57 1290.9,214.84 1288.5,206.19", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,263 +110,264 @@ digraph { width=2.0943]; "gene to gene association" -> "has evidence" [color=blue, label="has evidence", - lp="1652.9,221.5", - pos="e,1479.4,193.55 2367.4,262.98 2158.9,260.62 1748.9,253 1606.4,229 1566,222.2 1521.6,208.38 1489.1,196.99", + lp="1444.9,221.5", + pos="e,1413.8,194.93 2149.2,263.52 1913.2,261.98 1424,255.6 1398.4,229 1390,220.25 1395.9,210.18 1405.7,201.37", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1643.4,178", - width=3.015]; + label=string, + pos="1573.4,178", + width=1.0652]; "gene to gene association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1802.9,221.5", - pos="e,1667.9,195.78 2366.8,264.76 2183.7,264.74 1853.1,260.17 1738.4,229 1716.6,223.09 1694.2,211.61 1676.7,201.13", + lp="1562.9,221.5", + pos="e,1543.3,189.28 2149.8,262.83 1936.2,260.2 1520.5,252.12 1498.4,229 1493.8,224.18 1494.8,219.62 1498.4,214 1502.8,207.12 1518,199.47 \ +1533.6,193.08", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1878.4,178", - width=3.015]; + label=string, + pos="1668.4,178", + width=1.0652]; "gene to gene association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1972.4,221.5", - pos="e,1872.6,196 2369.6,261.29 2195,256.82 1894,246.6 1877.4,229 1871.6,222.9 1870.4,214.27 1871,205.9", + lp="1729.4,221.5", + pos="e,1648.1,193.48 2151.1,261.57 1970.1,257.39 1651.9,247.45 1634.4,229 1626.3,220.46 1631.8,209.82 1640.6,200.55", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2113.4,178", - width=3.015]; + label=string, + pos="1810.4,178", + width=1.0652]; "gene to gene association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2180.9,221.5", - pos="e,2087.6,195.53 2368.7,261.98 2252.7,258.76 2094.1,250.46 2074.4,229 2066.7,220.62 2071.6,210.86 2080.1,202.2", + lp="1949.9,221.5", + pos="e,1816.9,195.93 2154.4,259.62 2036.2,254.45 1869.6,244.53 1843.4,229 1834,223.44 1826.8,214.03 1821.5,204.86", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2295.4,178", + pos="2037.4,178", width=1.5346]; "gene to gene association" -> timepoint [color=blue, label=timepoint, - lp="2332.4,221.5", - pos="e,2291.1,196.26 2382.6,256.23 2345,251.15 2309.4,242.78 2297.4,229 2292,222.83 2290.3,214.43 2290.3,206.27", + lp="2112.4,221.5", + pos="e,2046.6,196.08 2178.4,253.39 2137.3,247.54 2094.8,239.35 2077.4,229 2067.4,223.06 2058.9,213.63 2052.3,204.55", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2407.4,178", + pos="2149.4,178", width=1.0652]; "gene to gene association" -> "original subject" [color=blue, label="original subject", - lp="2430.4,221.5", - pos="e,2387.4,193.75 2404.6,252.07 2392.8,246.78 2382.1,239.36 2374.4,229 2367.7,220.01 2372.5,209.73 2380.3,200.83", + lp="2214.4,221.5", + pos="e,2148.2,196.23 2191.6,251.43 2179.1,246.26 2167.4,239.05 2158.4,229 2152.9,222.8 2150.2,214.39 2149,206.23", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2521.4,178", + pos="2274.4,178", width=1.5887]; "gene to gene association" -> "original predicate" [color=blue, label="original predicate", - lp="2556.9,221.5", - pos="e,2504.6,195.4 2490.1,246.84 2489.4,236.95 2489.6,224.45 2493.4,214 2494.7,210.42 2496.5,206.94 2498.6,203.64", + lp="2337.9,221.5", + pos="e,2274.4,196.18 2274.4,246.8 2274.4,235.16 2274.4,219.55 2274.4,206.24", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2635.4,178", + pos="2403.4,178", width=1.0652]; "gene to gene association" -> "original object" [color=blue, label="original object", - lp="2681.9,221.5", - pos="e,2634.3,196.46 2581.6,252.21 2595.9,246.98 2609.6,239.54 2620.4,229 2626.5,223.04 2630.2,214.69 2632.3,206.52", + lp="2459.9,221.5", + pos="e,2407.8,195.99 2351.9,250.8 2374.7,245.27 2395.4,238 2402.4,229 2407.4,222.62 2408.9,214.26 2408.7,206.21", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2768.4,178", + pos="2536.4,178", width=2.1304]; "gene to gene association" -> "subject category" [color=blue, label="subject category", - lp="2811.9,221.5", - pos="e,2762.2,196.16 2581.2,252.19 2649.9,242.92 2734,231.21 2737.4,229 2746.2,223.28 2752.9,214.13 2757.8,205.22", + lp="2586.9,221.5", + pos="e,2533.7,196.01 2362.9,252.17 2430.3,242.99 2512.3,231.42 2515.4,229 2522.8,223.28 2527.6,214.49 2530.7,205.86", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2939.4,178", + pos="2707.4,178", width=2.1304]; "gene to gene association" -> "object category" [color=blue, label="object category", - lp="2956.9,221.5", - pos="e,2923.7,195.63 2580.9,252.17 2596.4,250.3 2612.3,248.49 2627.4,247 2682.4,241.55 2823.8,248.87 2875.4,229 2890.4,223.21 2904.8,\ -212.62 2916.1,202.68", + lp="2728.9,221.5", + pos="e,2693.4,196.1 2362.9,252.2 2378.4,250.32 2394.4,248.51 2409.4,247 2462.8,241.64 2600.9,249.78 2650.4,229 2663.9,223.32 2676.5,213.09 \ +2686.4,203.36", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3072.4,178", + pos="2840.4,178", width=1.0652]; "gene to gene association" -> "subject closure" [color=blue, label="subject closure", - lp="3093.9,221.5", - pos="e,3059.6,195.26 2579.4,252.01 2595.4,250.11 2611.9,248.34 2627.4,247 2670.5,243.29 2976.3,245.35 3016.4,229 3030.2,223.35 3042.9,\ -212.72 3052.7,202.71", + lp="2864.9,221.5", + pos="e,2828.8,195.24 2361.4,252.03 2377.4,250.13 2393.9,248.34 2409.4,247 2451.4,243.36 2749.7,245.67 2788.4,229 2801.5,223.37 2813.2,\ +212.89 2822.2,202.97", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3172.4,178", + pos="2953.4,178", width=1.0652]; "gene to gene association" -> "object closure" [color=blue, label="object closure", - lp="3214.4,221.5", - pos="e,3170.3,196.35 2579.1,251.9 2595.1,250 2611.7,248.25 2627.4,247 2656.5,244.67 3128.5,245.77 3152.4,229 3160.1,223.61 3164.8,214.78 \ -3167.7,206.02", + lp="2988.4,221.5", + pos="e,2948,196.06 2361.1,251.91 2377.1,250.01 2393.7,248.26 2409.4,247 2437.9,244.71 2898.8,243.51 2923.4,229 2932.5,223.66 2939.1,214.42 \ +2943.8,205.32", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3305.4,178", + pos="3086.4,178", width=2.1304]; "gene to gene association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3372.9,221.5", - pos="e,3297.7,196.19 2578.7,251.87 2594.8,249.95 2611.6,248.21 2627.4,247 2662.9,244.27 3236.8,245.48 3268.4,229 3278.6,223.7 3286.6,\ -214.21 3292.6,204.9", + lp="3148.9,221.5", + pos="e,3076.5,196.26 2360.7,251.87 2376.8,249.96 2393.6,248.22 2409.4,247 2444.5,244.3 3010.5,243.95 3042.4,229 3053.7,223.68 3063.3,\ +213.92 3070.7,204.42", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3497.4,178", + pos="3279.4,178", width=2.1304]; "gene to gene association" -> "object category closure" [color=blue, label="object category closure", - lp="3563.9,221.5", - pos="e,3491.1,196.16 2578.3,251.82 2594.6,249.9 2611.5,248.17 2627.4,247 2673.8,243.59 3423.7,251.48 3464.4,229 3474,223.72 3481.2,214.36 \ -3486.5,205.16", + lp="3341.9,221.5", + pos="e,3271.1,196.24 2360.3,251.83 2376.6,249.91 2393.5,248.17 2409.4,247 2455.4,243.61 3199.1,249.71 3240.4,229 3250.8,223.76 3259.3,\ +214.28 3265.7,204.97", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3687.4,178", + pos="3469.4,178", width=1.0652]; "gene to gene association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3736.4,221.5", - pos="e,3680.3,195.72 2578,251.82 2594.3,249.88 2611.4,248.15 2627.4,247 2684.1,242.94 3601,255.38 3651.4,229 3661.6,223.66 3669.6,213.98 \ -3675.4,204.54", + lp="3515.4,221.5", + pos="e,3461.1,195.77 2360,251.82 2376.3,249.88 2393.4,248.15 2409.4,247 2465.9,242.95 3378.5,254 3429.4,229 3440.2,223.67 3449.1,213.85 \ +3455.7,204.31", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3846.4,178", + pos="3628.4,178", width=1.0652]; "gene to gene association" -> "object namespace" [color=blue, label="object namespace", - lp="3890.4,221.5", - pos="e,3838.7,195.76 2578,251.79 2594.3,249.86 2611.4,248.13 2627.4,247 2660.1,244.7 3779.1,243.8 3808.4,229 3818.9,223.71 3827.2,214.03 \ -3833.4,204.59", + lp="3669.4,221.5", + pos="e,3619.8,195.79 2360,251.79 2376.3,249.86 2393.4,248.13 2409.4,247 2474.7,242.4 3528.4,257.45 3587.4,229 3598.4,223.7 3607.4,213.88 \ +3614.2,204.34", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3997.4,178", + pos="3779.4,178", width=1.0652]; "gene to gene association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4050.4,221.5", - pos="e,3989.4,195.78 2578,251.76 2594.3,249.84 2611.4,248.11 2627.4,247 2664.3,244.44 3925.3,245.45 3958.4,229 3969.1,223.68 3977.8,213.86 \ -3984.2,204.32", + lp="3831.4,221.5", + pos="e,3770.5,195.81 2360,251.76 2376.3,249.84 2393.4,248.11 2409.4,247 2446.2,244.44 3704.1,244.81 3737.4,229 3748.5,223.72 3757.8,213.91 \ +3764.7,204.36", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4168.4,178", + pos="3950.4,178", width=1.0652]; "gene to gene association" -> "object label closure" [color=blue, label="object label closure", - lp="4216.9,221.5", - pos="e,4160.1,195.8 2577.6,251.79 2594.1,249.84 2611.3,248.11 2627.4,247 2669,244.14 4090.9,247.29 4128.4,229 4139.3,223.7 4148.1,213.88 \ -4154.7,204.34", + lp="3998.9,221.5", + pos="e,3941.8,195.81 2359.6,251.79 2376.1,249.84 2393.3,248.11 2409.4,247 2451,244.14 3871.8,247.05 3909.4,229 3920.4,223.71 3929.4,213.9 \ +3936.2,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4330.4,178", + pos="4112.4,178", width=2.347]; "gene to gene association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4378.9,221.5", - pos="e,4321.8,196.3 2577.6,251.77 2594.1,249.83 2611.3,248.1 2627.4,247 2673.5,243.86 4248.9,249.24 4290.4,229 4301.1,223.78 4309.9,214.17 \ -4316.4,204.75", + lp="4160.9,221.5", + pos="e,4103.8,196.3 2359.6,251.77 2376.1,249.83 2393.3,248.1 2409.4,247 2455.5,243.86 4030.9,249.24 4072.4,229 4083.1,223.78 4091.9,214.17 \ +4098.4,204.75", style=solid]; type [height=0.5, - pos="4464.4,178", + pos="4246.4,178", width=0.86659]; "gene to gene association" -> type [color=blue, label=type, - lp="4478.4,221.5", - pos="e,4465.2,196.18 2577.6,251.76 2594.1,249.82 2611.2,248.09 2627.4,247 2652.7,245.29 4432.6,244.79 4452.4,229 4459.2,223.54 4462.6,\ -214.93 4464.1,206.37", + lp="4260.4,221.5", + pos="e,4247.2,196.18 2359.6,251.76 2376.1,249.82 2393.2,248.09 2409.4,247 2434.7,245.29 4214.6,244.79 4234.4,229 4241.2,223.54 4244.6,\ +214.93 4246.1,206.37", style=solid]; category [height=0.5, - pos="4565.4,178", + pos="4347.4,178", width=1.4263]; "gene to gene association" -> category [color=blue, label=category, - lp="4558.9,221.5", - pos="e,4549.8,195.25 2577.6,251.76 2594.1,249.81 2611.2,248.09 2627.4,247 2679.3,243.5 4449.1,245.61 4498.4,229 4514.6,223.53 4530.1,\ -212.51 4542.1,202.2", + lp="4340.9,221.5", + pos="e,4331.8,195.25 2359.6,251.76 2376.1,249.81 2393.2,248.09 2409.4,247 2461.3,243.5 4231.1,245.61 4280.4,229 4296.6,223.53 4312.1,\ +212.51 4324.1,202.2", style=solid]; subject [height=0.5, - pos="4679.4,178", + pos="4461.4,178", width=1.2277]; "gene to gene association" -> subject [color=blue, label=subject, - lp="4655.4,221.5", - pos="e,4660.1,194.33 2577.6,251.75 2594.1,249.81 2611.2,248.09 2627.4,247 2736.4,239.66 4489.1,258.2 4594.4,229 4615.1,223.25 4636,211.09 \ -4651.9,200.2", + lp="4437.4,221.5", + pos="e,4442.1,194.33 2359.6,251.75 2376.1,249.81 2393.2,248.09 2409.4,247 2518.4,239.66 4271.1,258.2 4376.4,229 4397.1,223.25 4418,211.09 \ +4433.9,200.2", style=solid]; object [height=0.5, - pos="4722.4,91", + pos="4504.4,91", width=1.0832]; "gene to gene association" -> object [color=blue, label=object, - lp="4766.4,178", - pos="e,4735.8,108.09 2577.6,251.74 2594.1,249.8 2611.2,248.08 2627.4,247 2684.4,243.17 4631,246.46 4685.4,229 4709.7,221.2 4718,217.1 \ -4732.4,196 4746.3,175.59 4742.5,166.51 4745.4,142 4746.2,135.38 4747.3,133.39 4745.4,127 4744.4,123.55 4742.9,120.13 4741.1,116.85", + lp="4548.4,178", + pos="e,4517.8,108.09 2359.6,251.74 2376.1,249.8 2393.2,248.08 2409.4,247 2466.4,243.17 4413,246.46 4467.4,229 4491.7,221.2 4500,217.1 \ +4514.4,196 4528.3,175.59 4524.5,166.51 4527.4,142 4528.2,135.38 4529.3,133.39 4527.4,127 4526.4,123.55 4524.9,120.13 4523.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2674.4,265", + pos="2456.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2805.4,265", + pos="2587.4,265", width=2.0762]; subject -> object [label=relation, - lp="4717.4,134.5", - pos="e,4704.5,107.23 4680.5,159.55 4681.7,149.57 4684.2,137.07 4689.4,127 4691.6,122.68 4694.5,118.52 4697.7,114.66"]; + lp="4499.4,134.5", + pos="e,4486.5,107.23 4462.5,159.55 4463.7,149.57 4466.2,137.07 4471.4,127 4473.6,122.68 4476.5,118.52 4479.7,114.66"]; relation [height=0.5, - pos="4667.4,18", + pos="4449.4,18", width=1.2999]; - subject -> relation [pos="e,4668.7,36.188 4678.1,159.79 4676,132.48 4672,78.994 4669.5,46.38", + subject -> relation [pos="e,4450.7,36.188 4460.1,159.79 4458,132.48 4454,78.994 4451.5,46.38", style=dotted]; "gene to gene association_subject" [color=blue, height=0.5, label="gene or gene product", - pos="3008.4,265", + pos="2790.4,265", width=3.0692]; - object -> relation [pos="e,4680.2,35.54 4709.9,73.889 4703,64.939 4694.2,53.617 4686.4,43.584", + object -> relation [pos="e,4462.2,35.54 4491.9,73.889 4485,64.939 4476.2,53.617 4468.4,43.584", style=dotted]; "gene to gene association_object" [color=blue, height=0.5, label="gene or gene product", - pos="3247.4,265", + pos="3029.4,265", width=3.0692]; } diff --git a/graphviz/gene_to_gene_association.svg b/graphviz/gene_to_gene_association.svg index ff3af7c11c..23b2a2fdfa 100644 --- a/graphviz/gene_to_gene_association.svg +++ b/graphviz/gene_to_gene_association.svg @@ -4,16 +4,16 @@ - + %3 - + gene to gene association - -gene to gene association + +gene to gene association @@ -24,9 +24,9 @@ gene to gene association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ gene to gene association->id - - -id + + +id @@ -50,9 +50,9 @@ gene to gene association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ gene to gene association->name - - -name + + +name @@ -76,9 +76,9 @@ gene to gene association->description - - -description + + +description @@ -89,9 +89,9 @@ gene to gene association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ gene to gene association->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ gene to gene association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ gene to gene association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ gene to gene association->publications - - -publications + + +publications @@ -154,344 +154,344 @@ gene to gene association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string gene to gene association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string gene to gene association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string gene to gene association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type gene to gene association->timepoint - - -timepoint + + +timepoint original subject - -string + +string gene to gene association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie gene to gene association->original predicate - - -original predicate + + +original predicate original object - -string + +string gene to gene association->original object - - -original object + + +original object subject category - -ontology class + +ontology class gene to gene association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class gene to gene association->object category - - -object category + + +object category subject closure - -string + +string gene to gene association->subject closure - - -subject closure + + +subject closure object closure - -string + +string gene to gene association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class gene to gene association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class gene to gene association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string gene to gene association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string gene to gene association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string gene to gene association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string gene to gene association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source gene to gene association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type gene to gene association->type - - -type + + +type category - -category + +category gene to gene association->category - - -category + + +category subject - -subject + +subject gene to gene association->subject - - -subject + + +subject object - -object + +object gene to gene association->object - - -object + + +object association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + gene to gene association_subject - -gene or gene product + +gene or gene product object->relation - - + + gene to gene association_object - -gene or gene product + +gene or gene product diff --git a/graphviz/gene_to_gene_coexpression_association.gv b/graphviz/gene_to_gene_coexpression_association.gv index 314949b9bd..2de7c18e52 100644 --- a/graphviz/gene_to_gene_coexpression_association.gv +++ b/graphviz/gene_to_gene_coexpression_association.gv @@ -1,22 +1,22 @@ digraph { - graph [bb="0,0,5965.3,283"]; + graph [bb="0,0,5747.3,283"]; node [label="\N"]; "gene to gene coexpression association" [height=0.5, label="gene to gene coexpression association", - pos="3038.4,265", + pos="2820.4,265", width=5.2356]; "gene to gene association" [height=0.5, pos="125.44,178", width=3.4844]; "gene to gene coexpression association" -> "gene to gene association" [label=is_a, lp="519.44,221.5", - pos="e,204.13,192.09 2850.1,264.26 2343.7,264.49 960.81,261.99 505.44,229 405.24,221.74 291.07,205.65 214.25,193.68"]; + pos="e,204.13,192.06 2632.1,263.96 2156.7,263.42 916.85,259.07 505.44,229 405.25,221.68 291.07,205.6 214.25,193.64"]; "gene expression mixin" [height=0.5, pos="383.44,178", width=3.1955]; "gene to gene coexpression association" -> "gene expression mixin" [label=uses, - lp="650.94,221.5", - pos="e,441.05,193.59 2850.8,263.24 2323.4,260.81 851.84,252.04 634.44,229 571.58,222.34 501.07,207.64 450.82,195.89"]; + lp="649.94,221.5", + pos="e,441.07,193.62 2633.1,262.95 2139.7,259.91 828.95,249.94 633.44,229 571.06,222.32 501.12,207.71 451.11,196"]; id [color=blue, height=0.5, label=string, @@ -24,9 +24,9 @@ digraph { width=1.0652]; "gene to gene coexpression association" -> id [color=blue, label=id, - lp="768.44,221.5", - pos="e,583.43,189.98 2850.8,263.16 2342.9,260.58 965.91,251.58 761.44,229 689.7,221.08 671.95,215.43 602.44,196 599.33,195.13 596.13,\ -194.17 592.94,193.15", + lp="767.44,221.5", + pos="e,583.43,189.97 2632.9,262.84 2159.9,259.62 943.06,249.44 760.44,229 689.15,221.02 671.52,215.35 602.44,196 599.33,195.13 596.13,\ +194.16 592.94,193.14", style=solid]; iri [color=blue, height=0.5, @@ -35,9 +35,9 @@ digraph { width=1.2277]; "gene to gene coexpression association" -> iri [color=blue, label=iri, - lp="881.44,221.5", - pos="e,688.35,190.19 2850.8,262.91 2360.7,259.8 1066.7,249.71 873.44,229 799.08,221.03 780.83,214.78 708.44,196 705.06,195.12 701.59,\ -194.16 698.1,193.14", + lp="872.44,221.5", + pos="e,688.36,190.13 2633.3,262.68 2177.8,259.19 1036.7,248.57 864.44,229 794.02,221 776.94,214.18 708.44,196 705.07,195.11 701.59,194.12 \ +698.11,193.1", style=solid]; name [color=blue, height=0.5, @@ -46,8 +46,8 @@ digraph { width=1.5707]; "gene to gene coexpression association" -> name [color=blue, label=name, - lp="988.44,221.5", - pos="e,812.19,191.56 2850.4,263.35 2375.2,261.33 1151.5,253.78 968.44,229 917.66,222.12 861.07,206.6 822.18,194.66", + lp="974.44,221.5", + pos="e,810.74,192 2632.9,263.16 2192.5,260.82 1117,252.71 954.44,229 907.94,222.22 856.42,207.1 820.46,195.25", style=solid]; description [color=blue, height=0.5, @@ -56,8 +56,8 @@ digraph { width=2.0943]; "gene to gene coexpression association" -> description [color=blue, label=description, - lp="1108.9,221.5", - pos="e,958.24,194.16 2850.1,264.04 2391.3,263.64 1240.4,259.57 1068.4,229 1033.6,222.8 995.86,209.44 967.76,198.08", + lp="1085.9,221.5", + pos="e,953.78,194.76 2632,264.23 2206.7,264.18 1197.2,260.68 1045.4,229 1016.7,223 986.14,210.32 962.93,199.23", style=solid]; "has attribute" [color=blue, height=0.5, @@ -66,8 +66,8 @@ digraph { width=1.4443]; "gene to gene coexpression association" -> "has attribute" [color=blue, label="has attribute", - lp="1254.4,221.5", - pos="e,1099.1,192.96 2850.3,263.89 2415.4,263.15 1365.4,258.29 1207.4,229 1173,222.61 1135.7,208.64 1108.6,197.09", + lp="1217.4,221.5", + pos="e,1092.8,194.26 2631.7,264.62 2228.5,265.26 1308.8,262.93 1170.4,229 1146,223.01 1120.6,210.41 1101.4,199.36", style=solid]; negated [color=blue, height=0.5, @@ -76,8 +76,8 @@ digraph { width=1.2999]; "gene to gene coexpression association" -> negated [color=blue, label=negated, - lp="1409.4,221.5", - pos="e,1220.3,190.48 2851.9,262.29 2449.1,258.28 1522.8,247.19 1380.4,229 1327.9,222.28 1269.1,205.85 1230.2,193.64", + lp="1350.4,221.5", + pos="e,1214.4,192.46 2633,263.09 2259.4,260.76 1446.8,252.98 1321.4,229 1287.2,222.45 1250.2,208.21 1223.7,196.6", style=solid]; qualifiers [color=blue, height=0.5, @@ -86,8 +86,8 @@ digraph { width=2.1304]; "gene to gene coexpression association" -> qualifiers [color=blue, label=qualifiers, - lp="1548.9,221.5", - pos="e,1369.4,193.23 2852.2,262.19 2474.7,258.16 1644.2,247.34 1515.4,229 1468.5,222.31 1416.5,207.91 1379.1,196.28", + lp="1453.9,221.5", + pos="e,1350.2,195.21 2631.9,264.15 2276.8,263.72 1534.2,259.16 1420.4,229 1398.6,223.2 1376.2,211.36 1358.8,200.66", style=solid]; publications [color=blue, height=0.5, @@ -96,8 +96,8 @@ digraph { width=1.7332]; "gene to gene coexpression association" -> publications [color=blue, label=publications, - lp="1695.4,221.5", - pos="e,1520.3,192.76 2852.4,262.05 2501.5,257.97 1766.6,247.36 1651.4,229 1609.3,222.28 1562.9,207.78 1529.7,196.12", + lp="1546.4,221.5", + pos="e,1485.8,196.32 2631.8,264.56 2278.3,264.84 1547.3,261.46 1502.4,229 1495,223.64 1490.7,214.93 1488.1,206.26", style=solid]; "has evidence" [color=blue, height=0.5, @@ -106,321 +106,322 @@ digraph { width=2.0943]; "gene to gene coexpression association" -> "has evidence" [color=blue, label="has evidence", - lp="1855.9,221.5", - pos="e,1679,193.55 2849.9,264.59 2556.4,264.49 2003.9,259.99 1809.4,229 1767.8,222.36 1722,208.37 1688.6,196.87", + lp="1644.9,221.5", + pos="e,1613.4,195.05 2634.5,261.98 2296.9,257.85 1616.2,247.29 1598.4,229 1590.1,220.38 1595.8,210.33 1605.4,201.51", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1842.4,178", - width=3.015]; + label=string, + pos="1772.4,178", + width=1.0652]; "gene to gene coexpression association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2011.9,221.5", - pos="e,1869.4,195.64 2852,262.18 2563.4,258.73 2032.5,249.66 1947.4,229 1923.2,223.12 1897.9,211.28 1878.3,200.6", + lp="1762.9,221.5", + pos="e,1742.3,189.48 2631.7,264.86 2320.5,265.35 1730.3,261.89 1698.4,229 1693.8,224.21 1694.9,219.63 1698.4,214 1702.7,207.24 1717.6,\ +199.65 1732.8,193.28", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2077.4,178", - width=3.015]; + label=string, + pos="1867.4,178", + width=1.0652]; "gene to gene coexpression association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2184.4,221.5", - pos="e,2076.7,196.1 2851.2,262.85 2583,260.38 2118.4,252.69 2089.4,229 2082.7,223.45 2079.3,214.81 2077.8,206.27", + lp="1929.4,221.5", + pos="e,1847.5,193.59 2632,263.96 2353.5,262.96 1861.6,257.18 1834.4,229 1826.3,220.61 1831.7,209.99 1840.2,200.7", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2312.4,178", - width=3.015]; + label=string, + pos="2009.4,178", + width=1.0652]; "gene to gene coexpression association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2393.9,221.5", - pos="e,2294.7,195.83 2852.8,261.69 2636.8,258.06 2306.7,249.23 2287.4,229 2280.6,221.87 2283.2,212.53 2288.7,203.85", + lp="2150.9,221.5", + pos="e,2016.5,196.09 2632.1,264.14 2418.9,262.95 2094.6,256.55 2044.4,229 2034.7,223.64 2027,214.27 2021.4,205.07", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2494.4,178", + pos="2235.4,178", width=1.5346]; "gene to gene coexpression association" -> timepoint [color=blue, label=timepoint, - lp="2550.4,221.5", - pos="e,2497,196.26 2854.5,261.07 2715.1,257.29 2543,248.66 2515.4,229 2507.8,223.52 2502.9,214.66 2499.8,205.91", + lp="2314.4,221.5", + pos="e,2245.4,196.1 2641.7,259.2 2496.8,254.19 2311.6,244.8 2279.4,229 2268.2,223.48 2258.6,213.68 2251.3,204.21", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2606.4,178", + pos="2347.4,178", width=1.0652]; "gene to gene coexpression association" -> "original subject" [color=blue, label="original subject", - lp="2649.4,221.5", - pos="e,2595.3,195.28 2854.1,261.08 2739.9,257.3 2611.6,248.67 2593.4,229 2587.3,222.33 2588,213.1 2591.2,204.39", + lp="2419.4,221.5", + pos="e,2348.2,196.11 2640.3,259.7 2522.1,255.26 2385.5,246.41 2363.4,229 2356.3,223.39 2352.3,214.63 2350.1,205.99", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2720.4,178", + pos="2473.4,178", width=1.5887]; "gene to gene coexpression association" -> "original predicate" [color=blue, label="original predicate", - lp="2777.9,221.5", - pos="e,2712.5,195.83 2875.4,255.89 2800.7,250.46 2726,241.89 2714.4,229 2708.8,222.71 2708.3,214.04 2709.8,205.68", + lp="2552.9,221.5", + pos="e,2474.3,196.02 2662.9,255.05 2584.6,249.22 2503.6,240.54 2489.4,229 2482.4,223.29 2478.4,214.5 2476.2,205.87", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2834.4,178", + pos="2602.4,178", width=1.0652]; "gene to gene coexpression association" -> "original object" [color=blue, label="original object", - lp="2908.9,221.5", - pos="e,2838.1,196.37 2925.5,250.59 2895.9,245.24 2869.1,238.14 2857.4,229 2850.1,223.23 2845,214.58 2841.5,206.09", + lp="2686.9,221.5", + pos="e,2609.4,196.01 2709.8,250.35 2678.1,244.86 2648.6,237.74 2635.4,229 2626.6,223.1 2619.5,213.92 2614.2,205.02", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2967.4,178", + pos="2735.4,178", width=2.1304]; "gene to gene coexpression association" -> "subject category" [color=blue, label="subject category", - lp="3027.9,221.5", - pos="e,2963.6,196.01 2988.3,247.52 2980.4,242.76 2973.3,236.7 2968.4,229 2964.2,222.26 2962.8,213.93 2962.9,206.01", + lp="2809.9,221.5", + pos="e,2737.2,196.38 2774.1,247.55 2765.3,242.7 2756.8,236.59 2750.4,229 2745,222.56 2741.6,214.22 2739.4,206.2", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3138.4,178", + pos="2906.4,178", width=2.1304]; "gene to gene coexpression association" -> "object category" [color=blue, label="object category", - lp="3159.9,221.5", - pos="e,3122.5,195.89 3063.7,247.1 3071.5,241.57 3080,235.25 3087.4,229 3097,220.99 3106.9,211.56 3115.4,203.06", + lp="2937.9,221.5", + pos="e,2895.6,196.26 2847.3,247.08 2854.9,241.74 2862.8,235.52 2869.4,229 2876.9,221.69 2884,212.79 2889.9,204.54", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3271.4,178", + pos="3039.4,178", width=1.0652]; "gene to gene coexpression association" -> "subject closure" [color=blue, label="subject closure", - lp="3294.9,221.5", - pos="e,3259.1,195.04 3158.1,250.96 3179.3,245.87 3200.5,238.8 3219.4,229 3231.9,222.54 3243.4,212.16 3252.4,202.52", + lp="3069.9,221.5", + pos="e,3029.8,195.52 2942.5,251.19 2961.7,246.03 2980.7,238.88 2997.4,229 3007.9,222.82 3017,213.05 3024,203.78", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3370.4,178", + pos="3152.4,178", width=1.0652]; "gene to gene coexpression association" -> "object closure" [color=blue, label="object closure", - lp="3414.4,221.5", - pos="e,3369.2,196.03 3172.8,252.34 3255.1,244.65 3346,234.95 3353.4,229 3360.5,223.3 3364.7,214.52 3367.1,205.89", + lp="3191.4,221.5", + pos="e,3148.7,196.17 2951.2,252.02 3031.6,244.17 3120.9,234.39 3128.4,229 3136.3,223.4 3141.7,214.52 3145.3,205.79", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3503.4,178", + pos="3285.4,178", width=2.1304]; "gene to gene coexpression association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3571.9,221.5", - pos="e,3496.3,195.96 3172.6,252.33 3194,250.52 3215.8,248.69 3236.4,247 3288,242.79 3423.5,254.64 3468.4,229 3478.1,223.48 3485.7,214.08 \ -3491.4,204.91", + lp="3350.9,221.5", + pos="e,3276.7,196 2954.6,252.36 2976,250.54 2997.8,248.7 3018.4,247 3068.9,242.84 3200.7,252.71 3245.4,229 3255.9,223.47 3264.5,213.94 \ +3271.1,204.67", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3696.4,178", + pos="3478.4,178", width=2.1304]; "gene to gene coexpression association" -> "object category closure" [color=blue, label="object category closure", - lp="3762.9,221.5", - pos="e,3690.1,196.08 3168.8,251.99 3191.4,250.15 3214.6,248.4 3236.4,247 3283.8,243.97 3622.1,252.38 3663.4,229 3672.9,223.62 3680.2,\ -214.25 3685.5,205.05", + lp="3542.9,221.5", + pos="e,3471.1,196.12 2950.8,252 2973.4,250.15 2996.6,248.4 3018.4,247 3065.5,243.98 3400.9,251.38 3442.4,229 3452.4,223.61 3460.3,214.1 \ +3466.1,204.81", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3886.4,178", + pos="3668.4,178", width=1.0652]; "gene to gene coexpression association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3935.4,221.5", - pos="e,3879.1,196.17 3167.5,251.86 3190.4,250.01 3214.1,248.28 3236.4,247 3270.5,245.04 3820.3,245 3850.4,229 3860.5,223.68 3868.4,214.18 \ -3874.2,204.88", + lp="3715.4,221.5", + pos="e,3660.7,195.7 2949.5,251.86 2972.4,250.01 2996.1,248.28 3018.4,247 3052.4,245.04 3600.2,244.56 3630.4,229 3640.9,223.63 3649.2,\ +213.94 3655.5,204.51", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4045.4,178", + pos="3827.4,178", width=1.0652]; "gene to gene coexpression association" -> "object namespace" [color=blue, label="object namespace", - lp="4088.4,221.5", - pos="e,4037.7,195.73 3167,251.79 3190.1,249.93 3214,248.23 3236.4,247 3279.2,244.67 3969.3,248.49 4007.4,229 4017.9,223.66 4026.3,213.98 \ -4032.5,204.54", + lp="3869.4,221.5", + pos="e,3819.1,195.75 2949,251.79 2972.1,249.93 2996,248.23 3018.4,247 3061.1,244.67 3749.1,247.96 3787.4,229 3798.3,223.64 3807.1,213.81 \ +3813.7,204.28", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4196.4,178", + pos="3978.4,178", width=1.0652]; "gene to gene coexpression association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4248.4,221.5", - pos="e,4188.1,195.76 3166.4,251.76 3189.7,249.89 3213.8,248.19 3236.4,247 3287.5,244.31 4110.6,251.59 4156.4,229 4167.3,223.66 4176.1,\ -213.84 4182.7,204.3", + lp="4029.4,221.5", + pos="e,3969.8,195.77 2948.4,251.76 2971.7,249.89 2995.8,248.19 3018.4,247 3069.4,244.31 3891.5,251.29 3937.4,229 3948.4,223.67 3957.5,\ +213.85 3964.2,204.32", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4367.4,178", + pos="4149.4,178", width=1.0652]; "gene to gene coexpression association" -> "object label closure" [color=blue, label="object label closure", - lp="4413.9,221.5", - pos="e,4358.8,195.79 3166.2,251.73 3189.5,249.86 3213.7,248.16 3236.4,247 3296.9,243.91 4271.9,255.36 4326.4,229 4337.4,223.69 4346.5,\ -213.87 4353.3,204.33", + lp="4196.9,221.5", + pos="e,4140.5,195.8 2948.2,251.73 2971.5,249.86 2995.7,248.16 3018.4,247 3078.9,243.91 4052.8,255.01 4107.4,229 4118.6,223.7 4127.8,213.89 \ +4134.8,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4508.4,178", + pos="4290.4,178", width=2.347]; "gene to gene coexpression association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4569.9,221.5", - pos="e,4506,196.44 3165.9,251.71 3189.3,249.83 3213.6,248.14 3236.4,247 3271.1,245.26 4458.6,248.44 4487.4,229 4495.3,223.72 4500.2,214.9 \ -4503.3,206.13", + lp="4351.9,221.5", + pos="e,4288.4,196.42 2947.9,251.71 2971.3,249.83 2995.6,248.14 3018.4,247 3053.2,245.26 4241.8,248.71 4270.4,229 4278.2,223.69 4282.9,\ +214.87 4285.8,206.1", style=solid]; type [height=0.5, - pos="4642.4,178", + pos="4424.4,178", width=0.86659]; "gene to gene coexpression association" -> type [color=blue, label=type, - lp="4666.4,221.5", - pos="e,4648.4,196.12 3165.6,251.7 3189.2,249.82 3213.5,248.13 3236.4,247 3256,246.04 4629.7,242.91 4643.4,229 4649.3,223.03 4650.6,214.43 \ -4650,206.05", + lp="4448.4,221.5", + pos="e,4430.4,196.12 2947.6,251.7 2971.2,249.82 2995.5,248.13 3018.4,247 3038,246.04 4411.7,242.91 4425.4,229 4431.3,223.03 4432.6,214.43 \ +4432,206.05", style=solid]; category [height=0.5, - pos="4743.4,178", + pos="4525.4,178", width=1.4263]; "gene to gene coexpression association" -> category [color=blue, label=category, - lp="4742.9,221.5", - pos="e,4730.4,195.44 3165.6,251.69 3189.2,249.81 3213.5,248.12 3236.4,247 3276.7,245.03 4648.8,243.42 4686.4,229 4700.5,223.59 4713.5,\ -212.98 4723.4,202.93", + lp="4524.9,221.5", + pos="e,4512.4,195.44 2947.6,251.69 2971.2,249.81 2995.5,248.12 3018.4,247 3058.7,245.03 4430.8,243.42 4468.4,229 4482.5,223.59 4495.5,\ +212.98 4505.4,202.93", style=solid]; subject [height=0.5, - pos="4857.4,178", + pos="4639.4,178", width=1.2277]; "gene to gene coexpression association" -> subject [color=blue, label=subject, - lp="4837.4,221.5", - pos="e,4839.4,194.55 3165.6,251.68 3189.2,249.8 3213.5,248.12 3236.4,247 3322,242.83 4696.3,253.33 4778.4,229 4797.7,223.3 4816.8,211.43 \ -4831.4,200.69", + lp="4619.4,221.5", + pos="e,4621.4,194.55 2947.6,251.68 2971.2,249.8 2995.5,248.12 3018.4,247 3104,242.83 4478.3,253.33 4560.4,229 4579.7,223.3 4598.8,211.43 \ +4613.4,200.69", style=solid]; object [height=0.5, - pos="4900.4,91", + pos="4682.4,91", width=1.0832]; "gene to gene coexpression association" -> object [color=blue, label=object, - lp="4944.4,178", - pos="e,4913.8,108.09 3165.4,251.69 3189,249.8 3213.4,248.11 3236.4,247 3281.7,244.81 4824.6,243.8 4867.4,229 4890.2,221.13 4897.3,216.2 \ -4910.4,196 4923.9,175.3 4920.5,166.51 4923.4,142 4924.2,135.38 4925.3,133.39 4923.4,127 4922.4,123.55 4920.9,120.13 4919.2,116.85", + lp="4726.4,178", + pos="e,4695.8,108.09 2947.4,251.69 2971,249.8 2995.4,248.11 3018.4,247 3063.7,244.81 4606.6,243.8 4649.4,229 4672.2,221.13 4679.3,216.2 \ +4692.4,196 4705.9,175.3 4702.5,166.51 4705.4,142 4706.2,135.38 4707.3,133.39 4705.4,127 4704.4,123.55 4702.9,120.13 4701.2,116.85", style=solid]; predicate [height=0.5, - pos="5054.4,178", + pos="4836.4,178", width=1.5165]; "gene to gene coexpression association" -> predicate [color=blue, label=predicate, - lp="5027.4,221.5", - pos="e,5030.6,194.35 3165.4,251.68 3189,249.79 3213.4,248.11 3236.4,247 3331.6,242.42 4858.7,250.83 4951.4,229 4976.3,223.14 5002.2,210.55 \ -5021.8,199.46", + lp="4809.4,221.5", + pos="e,4812.6,194.35 2947.4,251.68 2971,249.79 2995.4,248.11 3018.4,247 3113.6,242.42 4640.7,250.83 4733.4,229 4758.3,223.14 4784.2,210.55 \ +4803.8,199.46", style=solid]; "quantifier qualifier" [height=0.5, - pos="5224.4,178", + pos="5006.4,178", width=2.7081]; "gene to gene coexpression association" -> "quantifier qualifier" [color=blue, label="quantifier qualifier", - lp="5195.4,221.5", - pos="e,5186,194.61 3165.4,251.67 3189,249.78 3213.4,248.1 3236.4,247 3439.4,237.3 4864.7,260.83 5065.4,229 5103.6,222.95 5145.2,209.6 \ -5176.3,198.22", + lp="4977.4,221.5", + pos="e,4968,194.61 2947.4,251.67 2971,249.78 2995.4,248.1 3018.4,247 3221.4,237.3 4646.7,260.83 4847.4,229 4885.6,222.95 4927.2,209.6 \ +4958.3,198.22", style=solid]; "expression site" [color=blue, height=0.5, label="anatomical entity", - pos="5431.4,178", + pos="5213.4,178", width=2.5456]; "gene to gene coexpression association" -> "expression site" [color=blue, label="expression site", - lp="5385.9,221.5", - pos="e,5392.2,194.37 3165.1,251.67 3188.8,249.78 3213.3,248.09 3236.4,247 3349.1,241.67 5154.9,246.03 5266.4,229 5306.4,222.9 5350.1,\ -209.32 5382.5,197.85", + lp="5167.9,221.5", + pos="e,5174.2,194.37 2947.1,251.67 2970.8,249.78 2995.3,248.09 3018.4,247 3131.1,241.67 4936.9,246.03 5048.4,229 5088.4,222.9 5132.1,\ +209.32 5164.5,197.85", style=solid]; "stage qualifier" [color=blue, height=0.5, label="life stage", - pos="5595.4,178", + pos="5377.4,178", width=1.4985]; "gene to gene coexpression association" -> "stage qualifier" [color=blue, label="stage qualifier", - lp="5555.9,221.5", - pos="e,5563.8,192.71 3165.1,251.66 3188.8,249.76 3213.3,248.08 3236.4,247 3359,241.25 5323.4,249.02 5444.4,229 5482.6,222.68 5524.3,208.3 \ -5554.1,196.57", + lp="5337.9,221.5", + pos="e,5345.8,192.71 2947.1,251.66 2970.8,249.76 2995.3,248.08 3018.4,247 3141,241.25 5105.4,249.02 5226.4,229 5264.6,222.68 5306.3,208.3 \ +5336.1,196.57", style=solid]; "phenotypic state" [color=blue, height=0.5, label="disease or phenotypic feature", - pos="5816.4,178", + pos="5598.4,178", width=4.1344]; "gene to gene coexpression association" -> "phenotypic state" [color=blue, label="phenotypic state", - lp="5750.4,221.5", - pos="e,5765.2,194.99 3165.1,251.65 3188.8,249.75 3213.3,248.08 3236.4,247 3500,234.7 5349.5,261.48 5611.4,229 5660.6,222.9 5715.1,209.27 \ -5755.5,197.78", + lp="5532.4,221.5", + pos="e,5547.2,194.99 2947.1,251.65 2970.8,249.75 2995.3,248.08 3018.4,247 3282,234.7 5131.5,261.48 5393.4,229 5442.6,222.9 5497.1,209.27 \ +5537.5,197.78", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3283.4,265", + pos="3065.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3414.4,265", + pos="3196.4,265", width=2.0762]; subject -> object [label=relation, - lp="4895.4,134.5", - pos="e,4882.5,107.23 4858.5,159.55 4859.7,149.57 4862.2,137.07 4867.4,127 4869.7,122.68 4872.6,118.52 4875.8,114.66"]; + lp="4677.4,134.5", + pos="e,4664.5,107.23 4640.5,159.55 4641.7,149.57 4644.2,137.07 4649.4,127 4651.7,122.68 4654.6,118.52 4657.8,114.66"]; relation [height=0.5, - pos="4845.4,18", + pos="4627.4,18", width=1.2999]; - subject -> relation [pos="e,4846.7,36.188 4856.1,159.79 4854.1,132.48 4850,78.994 4847.5,46.38", + subject -> relation [pos="e,4628.7,36.188 4638.1,159.79 4636.1,132.48 4632,78.994 4629.5,46.38", style=dotted]; "gene to gene association_subject" [color=blue, height=0.5, label="gene or gene product", - pos="3617.4,265", + pos="3399.4,265", width=3.0692]; - object -> relation [pos="e,4858.3,35.54 4888,73.889 4881,64.939 4872.3,53.617 4864.5,43.584", + object -> relation [pos="e,4640.3,35.54 4670,73.889 4663,64.939 4654.3,53.617 4646.5,43.584", style=dotted]; "gene to gene association_object" [color=blue, height=0.5, label="gene or gene product", - pos="3856.4,265", + pos="3638.4,265", width=3.0692]; "gene to gene coexpression association_predicate" [color=blue, height=0.5, label="predicate type", - pos="4062.4,265", + pos="3844.4,265", width=2.1665]; "gene expression mixin_quantifier qualifier" [color=blue, height=0.5, label="ontology class", - pos="4235.4,265", + pos="4017.4,265", width=2.1304]; } diff --git a/graphviz/gene_to_gene_coexpression_association.svg b/graphviz/gene_to_gene_coexpression_association.svg index 521216a62e..aed39fba8f 100644 --- a/graphviz/gene_to_gene_coexpression_association.svg +++ b/graphviz/gene_to_gene_coexpression_association.svg @@ -4,16 +4,16 @@ - + %3 - + gene to gene coexpression association - -gene to gene coexpression association + +gene to gene coexpression association @@ -24,8 +24,8 @@ gene to gene coexpression association->gene to gene association - - + + is_a @@ -37,9 +37,9 @@ gene to gene coexpression association->gene expression mixin - - -uses + + +uses @@ -50,9 +50,9 @@ gene to gene coexpression association->id - - -id + + +id @@ -63,9 +63,9 @@ gene to gene coexpression association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ gene to gene coexpression association->name - - -name + + +name @@ -89,9 +89,9 @@ gene to gene coexpression association->description - - -description + + +description @@ -102,9 +102,9 @@ gene to gene coexpression association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ gene to gene coexpression association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ gene to gene coexpression association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ gene to gene coexpression association->publications - - -publications + + +publications @@ -154,421 +154,421 @@ gene to gene coexpression association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string gene to gene coexpression association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string gene to gene coexpression association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string gene to gene coexpression association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type gene to gene coexpression association->timepoint - - -timepoint + + +timepoint original subject - -string + +string gene to gene coexpression association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie gene to gene coexpression association->original predicate - - -original predicate + + +original predicate original object - -string + +string gene to gene coexpression association->original object - - -original object + + +original object subject category - -ontology class + +ontology class gene to gene coexpression association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class gene to gene coexpression association->object category - - -object category + + +object category subject closure - -string + +string gene to gene coexpression association->subject closure - - -subject closure + + +subject closure object closure - -string + +string gene to gene coexpression association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class gene to gene coexpression association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class gene to gene coexpression association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string gene to gene coexpression association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string gene to gene coexpression association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string gene to gene coexpression association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string gene to gene coexpression association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source gene to gene coexpression association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type gene to gene coexpression association->type - - -type + + +type category - -category + +category gene to gene coexpression association->category - - -category + + +category subject - -subject + +subject gene to gene coexpression association->subject - - -subject + + +subject object - -object + +object gene to gene coexpression association->object - - -object + + +object predicate - -predicate + +predicate gene to gene coexpression association->predicate - - -predicate + + +predicate quantifier qualifier - -quantifier qualifier + +quantifier qualifier gene to gene coexpression association->quantifier qualifier - - -quantifier qualifier + + +quantifier qualifier expression site - -anatomical entity + +anatomical entity gene to gene coexpression association->expression site - - -expression site + + +expression site stage qualifier - -life stage + +life stage gene to gene coexpression association->stage qualifier - - -stage qualifier + + +stage qualifier phenotypic state - -disease or phenotypic feature + +disease or phenotypic feature gene to gene coexpression association->phenotypic state - - -phenotypic state + + +phenotypic state association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + gene to gene association_subject - -gene or gene product + +gene or gene product object->relation - - + + gene to gene association_object - -gene or gene product + +gene or gene product gene to gene coexpression association_predicate - -predicate type + +predicate type gene expression mixin_quantifier qualifier - -ontology class + +ontology class diff --git a/graphviz/gene_to_gene_family_association.gv b/graphviz/gene_to_gene_family_association.gv index 03144018d8..cfc5bd61e3 100644 --- a/graphviz/gene_to_gene_family_association.gv +++ b/graphviz/gene_to_gene_family_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4748,283"]; + graph [bb="0,0,4563,283"]; node [label="\N"]; "gene to gene family association" [height=0.5, label="gene to gene family association", - pos="2468.4,265", + pos="2283.4,265", width=4.3691]; association [height=0.5, pos="62.394,178", width=1.7332]; "gene to gene family association" -> association [label=is_a, lp="280.39,221.5", - pos="e,102.91,191.79 2311.3,263.54 1841.5,261.88 467.08,254.85 266.39,229 213.1,222.13 153.57,206.61 112.64,194.66"]; + pos="e,102.91,191.77 2126.7,263.29 1684.8,261.01 448.41,252.58 266.39,229 213.11,222.1 153.58,206.57 112.65,194.64"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "gene to gene family association" -> id [color=blue, label=id, - lp="396.39,221.5", - pos="e,210.38,189.98 2311.8,263.05 1860.6,260.07 578.1,249.86 389.39,229 317.23,221.02 299.34,215.5 229.39,196 226.29,195.13 223.09,194.17 \ -219.89,193.15", + lp="395.39,221.5", + pos="e,210.38,189.98 2127.2,262.79 1704.5,259.26 558.54,248.06 388.39,229 316.67,220.97 298.9,215.43 229.39,196 226.29,195.13 223.09,\ +194.17 219.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "gene to gene family association" -> iri [color=blue, label=iri, - lp="509.39,221.5", - pos="e,315.3,190.2 2312.2,262.82 1878.3,259.33 678.89,248.07 501.39,229 426.6,220.97 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ -325.06,193.15", + lp="501.39,221.5", + pos="e,315.32,190.15 2126,264.68 1749.9,265.7 807.07,264.51 493.39,229 422.11,220.93 404.75,214.31 335.39,196 332.02,195.11 328.55,194.13 \ +325.07,193.11", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "gene to gene family association" -> name [color=blue, label=name, - lp="616.39,221.5", - pos="e,439.35,191.54 2311.8,263.15 1892.3,260.59 763.69,251.65 596.39,229 545.26,222.08 488.24,206.51 449.14,194.57", + lp="604.39,221.5", + pos="e,437.98,191.87 2126.9,262.97 1735.3,260.09 734.18,250.67 584.39,229 537.02,222.15 484.46,206.96 447.86,195.11", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "gene to gene family association" -> description [color=blue, label=description, - lp="736.89,221.5", - pos="e,585.45,194.14 2311.3,263.69 1907.3,262.51 852.6,256.76 696.39,229 661.33,222.77 623.33,209.4 595.03,198.06", + lp="717.89,221.5", + pos="e,581.77,194.62 2126.4,263.74 1749.8,262.67 816.5,257.17 677.39,229 647.36,222.92 615.28,210.09 591.01,198.95", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "gene to gene family association" -> "has attribute" [color=blue, label="has attribute", - lp="882.39,221.5", - pos="e,725.98,192.82 2311.6,263.52 1930.7,261.94 977.64,255.38 835.39,229 800.43,222.52 762.57,208.39 735.2,196.8", + lp="852.39,221.5", + pos="e,721.33,194.01 2126.1,263.87 1771.6,263.05 931.14,258.03 805.39,229 778.89,222.88 751.04,209.98 730.13,198.82", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "gene to gene family association" -> negated [color=blue, label=negated, - lp="1038.4,221.5", - pos="e,847.59,190.46 2311.1,264.31 1987.5,264.29 1257,260.6 1009.4,229 956.09,222.2 896.47,205.66 857.14,193.46", + lp="990.39,221.5", + pos="e,843.03,191.96 2127.5,262.49 1802.5,258.95 1073.3,248.91 961.39,229 923.37,222.23 881.85,207.52 852.5,195.8", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "gene to gene family association" -> qualifiers [color=blue, label=qualifiers, - lp="1178.9,221.5", - pos="e,996.68,193.07 2311.1,264.36 2010.8,264.29 1365.8,260.34 1145.4,229 1097.6,222.2 1044.5,207.74 1006.5,196.11", + lp="1101.9,221.5", + pos="e,982.4,194.93 2127,262.83 1822,260.07 1168.8,251.57 1068.4,229 1041.6,222.97 1013.3,210.59 991.57,199.66", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "gene to gene family association" -> publications [color=blue, label=publications, - lp="1326.4,221.5", - pos="e,1148.1,192.71 2311.1,264.32 2035.4,264.05 1475.7,259.59 1282.4,229 1239.3,222.18 1191.8,207.69 1157.8,196.06", + lp="1202.4,221.5", + pos="e,1121.9,195.78 2127.9,262.3 1829.4,258.6 1201.7,248.55 1158.4,229 1146.3,223.57 1135.9,213.45 1128,203.73", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,277 +100,277 @@ digraph { width=2.0943]; "gene to gene family association" -> "has evidence" [color=blue, label="has evidence", - lp="1480.9,221.5", - pos="e,1305.9,193.61 2311.5,263.61 2065,262.17 1598.3,255.85 1434.4,229 1393.5,222.3 1348.6,208.48 1315.7,197.06", + lp="1300.9,221.5", + pos="e,1255.9,195.88 2126,264.31 1845.2,264.09 1284.1,259.77 1254.4,229 1248.2,222.63 1248.8,213.73 1251.7,205.2", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1469.4,178", - width=3.015]; + label=string, + pos="1399.4,178", + width=1.0652]; "gene to gene family association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1635.9,221.5", - pos="e,1495.5,195.59 2313.9,261.45 2076.2,257.01 1641.1,246.6 1571.4,229 1547.9,223.07 1523.5,211.31 1504.4,200.68", + lp="1419.9,221.5", + pos="e,1375.2,192.24 2126.3,263.67 1868.5,262.36 1381.6,256.25 1355.4,229 1345.9,219.09 1354.7,207.6 1366.9,198.13", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1704.4,178", - width=3.015]; + label=string, + pos="1494.4,178", + width=1.0652]; "gene to gene family association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1807.4,221.5", - pos="e,1702.1,196.41 2313.4,261.78 2098.7,257.99 1734.4,248.68 1712.4,229 1706.1,223.34 1703.4,214.82 1702.5,206.41", + lp="1589.4,221.5", + pos="e,1489,196.04 2127.3,262.54 1903.5,259.68 1515.9,251.48 1494.4,229 1488.6,222.94 1487.2,214.32 1487.7,205.94", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1939.4,178", - width=3.015]; + label=string, + pos="1669.4,178", + width=1.0652]; "gene to gene family association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2015.9,221.5", - pos="e,1918.7,195.97 2318.1,259.63 2157.3,254.2 1923.3,243.81 1909.4,229 1902.4,221.54 1905.6,212.18 1912,203.58", + lp="1809.9,221.5", + pos="e,1676.1,196.02 2128.6,261.66 1969.4,258.13 1739.5,249.53 1703.4,229 1693.8,223.55 1686.4,214.16 1680.9,204.98", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2121.4,178", + pos="1895.4,178", width=1.5346]; "gene to gene family association" -> timepoint [color=blue, label=timepoint, - lp="2171.4,221.5", - pos="e,2121.9,196.47 2329.3,256.52 2245.3,250.77 2151.6,241.65 2136.4,229 2129.6,223.41 2125.9,214.91 2123.8,206.49", + lp="1972.4,221.5", + pos="e,1904.8,195.92 2132.4,259.85 2055.4,255.54 1971,246.78 1937.4,229 1926.7,223.32 1917.5,213.63 1910.6,204.28", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2233.4,178", + pos="2007.4,178", width=1.0652]; "gene to gene family association" -> "original subject" [color=blue, label="original subject", - lp="2270.4,221.5", - pos="e,2219.6,194.92 2318.1,259.68 2271.8,254.97 2229.2,245.95 2214.4,229 2208.1,221.83 2209.9,212.39 2214.3,203.65", + lp="2076.4,221.5", + pos="e,2007.3,196.33 2136.1,258.59 2086.2,253.83 2038.5,245.06 2020.4,229 2013.9,223.25 2010.5,214.72 2008.7,206.31", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2347.4,178", + pos="2133.4,178", width=1.5887]; "gene to gene family association" -> "original predicate" [color=blue, label="original predicate", - lp="2397.9,221.5", - pos="e,2336.3,195.76 2381.5,249.91 2359.9,244.58 2341.1,237.66 2334.4,229 2329.1,222.16 2329.6,213.39 2332.4,205.11", + lp="2207.9,221.5", + pos="e,2132.9,196.42 2197,249.86 2173.7,244.42 2152.6,237.44 2144.4,229 2138.6,222.99 2135.5,214.63 2134,206.47", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2461.4,178", + pos="2267.4,178", width=1.0652]; "gene to gene family association" -> "original object" [color=blue, label="original object", - lp="2516.9,221.5", - pos="e,2462.8,196.18 2467,246.8 2466,235.16 2464.7,219.55 2463.6,206.24", + lp="2327.9,221.5", + pos="e,2270.6,196.18 2280.2,246.8 2278,235.16 2275,219.55 2272.5,206.24", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2594.4,178", + pos="2400.4,178", width=2.1304]; "gene to gene family association" -> "subject category" [color=blue, label="subject category", - lp="2642.9,221.5", - pos="e,2590.6,196.4 2539.6,248.91 2551.5,244.01 2563,237.55 2572.4,229 2579.1,222.84 2583.9,214.24 2587.3,205.9", + lp="2452.9,221.5", + pos="e,2398.4,196.3 2353.3,248.8 2364.4,243.93 2375,237.49 2383.4,229 2389.5,222.8 2393.5,214.29 2396,206.04", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2765.4,178", + pos="2571.4,178", width=2.1304]; "gene to gene family association" -> "object category" [color=blue, label="object category", - lp="2785.9,221.5", - pos="e,2750.6,195.73 2585.2,252.88 2634,246.99 2684.5,238.91 2706.4,229 2720,222.83 2733,212.54 2743.3,202.9", + lp="2593.9,221.5", + pos="e,2557.8,195.72 2399.8,252.84 2447,247 2495.4,238.98 2516.4,229 2529.3,222.88 2541.3,212.74 2550.8,203.17", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="2898.4,178", + pos="2704.4,178", width=1.0652]; "gene to gene family association" -> "subject closure" [color=blue, label="subject closure", - lp="2921.9,221.5", - pos="e,2886,195.55 2580.7,252.32 2598.9,250.49 2617.7,248.66 2635.4,247 2682,242.63 2802.6,248.14 2845.4,229 2858.3,223.21 2870.1,212.91 \ -2879.2,203.16", + lp="2728.9,221.5", + pos="e,2692.6,195.53 2395.7,252.37 2414,250.53 2432.7,248.69 2450.4,247 2495.5,242.71 2612.3,247.96 2653.4,229 2665.9,223.24 2677.1,213.08 \ +2685.9,203.42", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="2998.4,178", + pos="2812.4,178", width=1.0652]; "gene to gene family association" -> "object closure" [color=blue, label="object closure", - lp="3042.4,221.5", - pos="e,2997,196.24 2577.9,252.07 2597.1,250.21 2616.8,248.43 2635.4,247 2673.7,244.06 2949.6,251.88 2980.4,229 2987.7,223.54 2992.1,214.81 \ -2994.7,206.16", + lp="2851.4,221.5", + pos="e,2808.5,196.4 2393.4,252.05 2412.4,250.2 2431.9,248.43 2450.4,247 2487.8,244.1 2756,249.56 2787.4,229 2795.6,223.61 2801.3,214.65 \ +2805.1,205.79", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3131.4,178", + pos="2945.4,178", width=2.1304]; "gene to gene family association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3200.9,221.5", - pos="e,3124.4,196.12 2577,251.95 2596.4,250.08 2616.5,248.33 2635.4,247 2686.5,243.4 3051.4,253.56 3096.4,229 3106.2,223.67 3113.8,214.3 \ -3119.4,205.1", + lp="3010.9,221.5", + pos="e,2936.8,196.17 2392,251.96 2411.4,250.09 2431.5,248.33 2450.4,247 2500.9,243.44 2860.2,251.81 2905.4,229 2916,223.63 2924.8,213.99 \ +2931.3,204.6", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3323.4,178", + pos="3138.4,178", width=2.1304]; "gene to gene family association" -> "object category closure" [color=blue, label="object category closure", - lp="3390.9,221.5", - pos="e,3317.7,196.11 2576.1,251.85 2595.8,249.97 2616.2,248.24 2635.4,247 2671.8,244.65 3260.7,247.19 3292.4,229 3301.6,223.71 3308.4,\ -214.48 3313.3,205.38", + lp="3202.9,221.5", + pos="e,3131.1,196.18 2391.1,251.86 2410.8,249.97 2431.2,248.24 2450.4,247 2486.6,244.66 3070.4,245.96 3102.4,229 3112.4,223.69 3120.3,\ +214.19 3126.1,204.89", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3513.4,178", + pos="3328.4,178", width=1.0652]; "gene to gene family association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3563.4,221.5", - pos="e,3506.4,196.19 2575.6,251.8 2595.5,249.91 2616.1,248.19 2635.4,247 2682.2,244.13 3437.1,251.08 3478.4,229 3488.2,223.76 3495.9,\ -214.4 3501.5,205.19", + lp="3375.4,221.5", + pos="e,3320.7,195.73 2390.6,251.8 2410.5,249.91 2431.1,248.19 2450.4,247 2497,244.13 3248.8,250.19 3290.4,229 3300.8,223.67 3309.2,213.99 \ +3315.4,204.55", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3672.4,178", + pos="3487.4,178", width=1.0652]; "gene to gene family association" -> "object namespace" [color=blue, label="object namespace", - lp="3716.4,221.5", - pos="e,3665,195.74 2575.6,251.75 2595.5,249.86 2616,248.16 2635.4,247 2690.9,243.68 3586,254.45 3635.4,229 3645.7,223.68 3653.9,213.99 \ -3659.9,204.56", + lp="3529.4,221.5", + pos="e,3479.1,195.77 2390.6,251.75 2410.5,249.86 2431,248.16 2450.4,247 2505.7,243.69 3397.7,253.45 3447.4,229 3458.2,223.67 3467.1,213.85 \ +3473.7,204.31", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3823.4,178", + pos="3638.4,178", width=1.0652]; "gene to gene family association" -> "subject label closure" [color=blue, label="subject label closure", - lp="3876.4,221.5", - pos="e,3815.4,195.77 2575.2,251.75 2595.2,249.85 2615.9,248.14 2635.4,247 2667.3,245.13 3755.8,243.23 3784.4,229 3795.1,223.66 3803.8,\ -213.84 3810.2,204.31", + lp="3689.4,221.5", + pos="e,3629.8,195.79 2390.2,251.75 2410.2,249.85 2430.9,248.14 2450.4,247 2482.2,245.13 3568.7,242.86 3597.4,229 3608.4,223.69 3617.4,\ +213.88 3624.2,204.34", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="3994.4,178", + pos="3809.4,178", width=1.0652]; "gene to gene family association" -> "object label closure" [color=blue, label="object label closure", - lp="4041.9,221.5", - pos="e,3986.1,195.79 2575.2,251.72 2595.2,249.82 2615.9,248.12 2635.4,247 2672,244.89 3921.5,245.1 3954.4,229 3965.3,223.69 3974.1,213.87 \ -3980.7,204.33", + lp="3856.9,221.5", + pos="e,3800.5,195.81 2390.2,251.72 2410.2,249.82 2430.9,248.12 2450.4,247 2486.9,244.9 3734.3,244.68 3767.4,229 3778.5,223.72 3787.8,\ +213.9 3794.7,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4147.4,178", + pos="3962.4,178", width=2.347]; "gene to gene family association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4200.9,221.5", - pos="e,4141.4,196.18 2575.2,251.7 2595.2,249.8 2615.9,248.11 2635.4,247 2676.4,244.67 4079.4,248.96 4115.4,229 4124.9,223.75 4131.9,214.39 \ -4137,205.18", + lp="4015.9,221.5", + pos="e,3956.4,196.18 2390.2,251.7 2410.2,249.8 2430.9,248.11 2450.4,247 2491.4,244.67 3894.4,248.96 3930.4,229 3939.9,223.75 3946.9,214.39 \ +3952,205.18", style=solid]; type [height=0.5, - pos="4281.4,178", + pos="4096.4,178", width=0.86659]; "gene to gene family association" -> type [color=blue, label=type, - lp="4299.4,221.5", - pos="e,4284.1,195.98 2574.7,251.72 2594.9,249.81 2615.8,248.11 2635.4,247 2658.1,245.72 4257.3,244.03 4274.4,229 4280.9,223.32 4283.4,\ -214.65 4284.1,206.12", + lp="4114.4,221.5", + pos="e,4099.1,195.98 2389.7,251.72 2409.9,249.81 2430.8,248.11 2450.4,247 2473.1,245.72 4072.3,244.03 4089.4,229 4095.9,223.32 4098.4,\ +214.65 4099.1,206.12", style=solid]; category [height=0.5, - pos="4382.4,178", + pos="4197.4,178", width=1.4263]; "gene to gene family association" -> category [color=blue, label=category, - lp="4377.9,221.5", - pos="e,4367.7,195.48 2574.7,251.72 2594.9,249.81 2615.8,248.1 2635.4,247 2682.1,244.38 4275.3,244.63 4319.4,229 4334.6,223.59 4349,212.84 \ -4360.1,202.68", + lp="4192.9,221.5", + pos="e,4182.7,195.48 2389.7,251.72 2409.9,249.81 2430.8,248.1 2450.4,247 2497.1,244.38 4090.3,244.63 4134.4,229 4149.6,223.59 4164,212.84 \ +4175.1,202.68", style=solid]; subject [height=0.5, - pos="4496.4,178", + pos="4311.4,178", width=1.2277]; "gene to gene family association" -> subject [color=blue, label=subject, - lp="4473.4,221.5", - pos="e,4477.7,194.32 2574.7,251.71 2594.9,249.8 2615.8,248.1 2635.4,247 2734,241.49 4318.4,255.93 4413.4,229 4433.6,223.29 4453.7,211.3 \ -4469.2,200.49", + lp="4288.4,221.5", + pos="e,4292.7,194.32 2389.7,251.71 2409.9,249.8 2430.8,248.1 2450.4,247 2549,241.49 4133.4,255.93 4228.4,229 4248.6,223.29 4268.7,211.3 \ +4284.2,200.49", style=solid]; object [height=0.5, - pos="4539.4,91", + pos="4354.4,91", width=1.0832]; "gene to gene family association" -> object [color=blue, label=object, - lp="4583.4,178", - pos="e,4552.8,108.09 2574.7,251.7 2594.9,249.79 2615.8,248.09 2635.4,247 2687.2,244.12 4454.1,245.12 4503.4,229 4527.3,221.18 4535.3,\ -216.87 4549.4,196 4563.2,175.52 4559.5,166.51 4562.4,142 4563.2,135.38 4564.3,133.39 4562.4,127 4561.4,123.55 4559.9,120.13 4558.1,\ + lp="4398.4,178", + pos="e,4367.8,108.09 2389.7,251.7 2409.9,249.79 2430.8,248.09 2450.4,247 2502.2,244.12 4269.1,245.12 4318.4,229 4342.3,221.18 4350.3,\ +216.87 4364.4,196 4378.2,175.52 4374.5,166.51 4377.4,142 4378.2,135.38 4379.3,133.39 4377.4,127 4376.4,123.55 4374.9,120.13 4373.1,\ 116.85", style=solid]; predicate [height=0.5, - pos="4693.4,178", + pos="4508.4,178", width=1.5165]; "gene to gene family association" -> predicate [color=blue, label=predicate, - lp="4666.4,221.5", - pos="e,4669.6,194.36 2574.7,251.69 2594.9,249.78 2615.8,248.09 2635.4,247 2743.8,240.99 4484.7,253.82 4590.4,229 4615.3,223.16 4641.2,\ -210.56 4660.8,199.48", + lp="4480.4,221.5", + pos="e,4484.6,194.36 2389.7,251.69 2409.9,249.78 2430.8,248.09 2450.4,247 2558.8,240.99 4299.7,253.82 4405.4,229 4430.3,223.16 4456.2,\ +210.56 4475.8,199.48", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2682.4,265", + pos="2497.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2813.4,265", + pos="2628.4,265", width=2.0762]; subject -> object [label=relation, - lp="4534.4,134.5", - pos="e,4521.5,107.23 4497.5,159.55 4498.7,149.57 4501.2,137.07 4506.4,127 4508.6,122.68 4511.5,118.52 4514.7,114.66"]; + lp="4349.4,134.5", + pos="e,4336.5,107.23 4312.5,159.55 4313.7,149.57 4316.2,137.07 4321.4,127 4323.6,122.68 4326.5,118.52 4329.7,114.66"]; relation [height=0.5, - pos="4484.4,18", + pos="4299.4,18", width=1.2999]; - subject -> relation [pos="e,4485.7,36.188 4495.1,159.79 4493,132.48 4489,78.994 4486.5,46.38", + subject -> relation [pos="e,4300.7,36.188 4310.1,159.79 4308,132.48 4304,78.994 4301.5,46.38", style=dotted]; "gene to gene family association_subject" [color=blue, height=0.5, label=gene, - pos="2939.4,265", + pos="2754.4,265", width=0.92075]; - object -> relation [pos="e,4497.2,35.54 4526.9,73.889 4520,64.939 4511.2,53.617 4503.4,43.584", + object -> relation [pos="e,4312.2,35.54 4341.9,73.889 4335,64.939 4326.2,53.617 4318.4,43.584", style=dotted]; "gene to gene family association_object" [color=blue, height=0.5, label="gene family", - pos="3055.4,265", + pos="2870.4,265", width=1.8054]; "gene to gene family association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3216.4,265", + pos="3031.4,265", width=2.1665]; } diff --git a/graphviz/gene_to_gene_family_association.svg b/graphviz/gene_to_gene_family_association.svg index b00349156d..b72f449b4c 100644 --- a/graphviz/gene_to_gene_family_association.svg +++ b/graphviz/gene_to_gene_family_association.svg @@ -4,16 +4,16 @@ - + %3 - + gene to gene family association - -gene to gene family association + +gene to gene family association @@ -24,8 +24,8 @@ gene to gene family association->association - - + + is_a @@ -37,9 +37,9 @@ gene to gene family association->id - - -id + + +id @@ -50,9 +50,9 @@ gene to gene family association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ gene to gene family association->name - - -name + + +name @@ -76,9 +76,9 @@ gene to gene family association->description - - -description + + +description @@ -89,9 +89,9 @@ gene to gene family association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ gene to gene family association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ gene to gene family association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ gene to gene family association->publications - - -publications + + +publications @@ -141,363 +141,363 @@ gene to gene family association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string gene to gene family association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string gene to gene family association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string gene to gene family association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type gene to gene family association->timepoint - - -timepoint + + +timepoint original subject - -string + +string gene to gene family association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie gene to gene family association->original predicate - - -original predicate + + +original predicate original object - -string + +string gene to gene family association->original object - - -original object + + +original object subject category - -ontology class + +ontology class gene to gene family association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class gene to gene family association->object category - - -object category + + +object category subject closure - -string + +string gene to gene family association->subject closure - - -subject closure + + +subject closure object closure - -string + +string gene to gene family association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class gene to gene family association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class gene to gene family association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string gene to gene family association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string gene to gene family association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string gene to gene family association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string gene to gene family association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source gene to gene family association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type gene to gene family association->type - - -type + + +type category - -category + +category gene to gene family association->category - - -category + + +category subject - -subject + +subject gene to gene family association->subject - - -subject + + +subject object - -object + +object gene to gene family association->object - - -object + + +object predicate - -predicate + +predicate gene to gene family association->predicate - - -predicate + + +predicate association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + gene to gene family association_subject - -gene + +gene object->relation - - + + gene to gene family association_object - -gene family + +gene family gene to gene family association_predicate - -predicate type + +predicate type diff --git a/graphviz/gene_to_gene_homology_association.gv b/graphviz/gene_to_gene_homology_association.gv index 3aab775d34..5e00466d81 100644 --- a/graphviz/gene_to_gene_homology_association.gv +++ b/graphviz/gene_to_gene_homology_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4853.4,283"]; + graph [bb="0,0,4668.4,283"]; node [label="\N"]; "gene to gene homology association" [height=0.5, label="gene to gene homology association", - pos="2594.4,265", + pos="2409.4,265", width=4.8024]; "gene to gene association" [height=0.5, pos="125.44,178", width=3.4844]; "gene to gene homology association" -> "gene to gene association" [label=is_a, lp="406.44,221.5", - pos="e,187.32,193.67 2422.6,262.94 1939.5,259.74 591.68,249.09 392.44,229 325.77,222.28 250.85,207.61 197.38,195.89"]; + pos="e,187.59,193.7 2237.9,262.67 1783.9,258.93 573.03,247.34 392.44,229 325.88,222.24 251.1,207.62 197.65,195.92"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "gene to gene homology association" -> id [color=blue, label=id, - lp="522.44,221.5", - pos="e,336.43,189.98 2422.7,262.95 1958.6,259.85 702.07,249.63 515.44,229 443.27,221.02 425.38,215.5 355.44,196 352.33,195.13 349.13,\ -194.17 345.93,193.15", + lp="521.44,221.5", + pos="e,336.43,189.98 2237.7,262.66 1803.2,258.99 682.54,247.83 514.44,229 442.71,220.97 424.95,215.43 355.44,196 352.33,195.13 349.13,\ +194.17 345.94,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "gene to gene homology association" -> iri [color=blue, label=iri, - lp="635.44,221.5", - pos="e,441.35,190.2 2422.7,262.7 1976.5,259.07 802.86,247.84 627.44,229 552.65,220.97 534.26,214.85 461.44,196 458.06,195.13 454.58,194.16 \ -451.1,193.15", + lp="627.44,221.5", + pos="e,441.36,190.15 2236.5,264.72 1850.5,265.67 928.87,264.03 619.44,229 548.16,220.93 530.8,214.31 461.44,196 458.07,195.11 454.59,\ +194.13 451.11,193.11", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "gene to gene homology association" -> name [color=blue, label=name, - lp="742.44,221.5", - pos="e,565.4,191.54 2422.4,263.06 1991.3,260.37 887.73,251.38 722.44,229 671.3,222.08 614.29,206.51 575.18,194.57", + lp="730.44,221.5", + pos="e,564.03,191.87 2237.6,262.86 1835.9,259.84 858.3,250.39 710.44,229 663.07,222.15 610.5,206.96 573.91,195.11", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "gene to gene homology association" -> description [color=blue, label=description, - lp="862.94,221.5", - pos="e,711.49,194.14 2422,263.65 2007.3,262.36 976.71,256.42 822.44,229 787.38,222.77 749.38,209.4 721.08,198.06", + lp="843.94,221.5", + pos="e,707.82,194.62 2236.8,263.7 1850.8,262.52 940.66,256.79 803.44,229 773.4,222.92 741.32,210.09 717.05,198.95", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "gene to gene homology association" -> "has attribute" [color=blue, label="has attribute", - lp="1008.4,221.5", - pos="e,852.02,192.82 2421.9,263.45 2031.2,261.76 1101.8,255.02 961.44,229 926.48,222.52 888.61,208.39 861.24,196.8", + lp="978.44,221.5", + pos="e,847.38,194.01 2236.7,263.83 1873.7,262.9 1055.4,257.61 931.44,229 904.93,222.88 877.09,209.98 856.18,198.82", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "gene to gene homology association" -> negated [color=blue, label=negated, - lp="1164.4,221.5", - pos="e,973.64,190.46 2421.4,264.31 2090.5,264.17 1379.1,260.1 1135.4,229 1082.1,222.2 1022.5,205.66 983.19,193.46", + lp="1115.4,221.5", + pos="e,969.14,192.07 2238.3,262.34 1906.2,258.71 1196.7,248.73 1086.4,229 1048.8,222.26 1007.7,207.62 978.54,195.91", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "gene to gene homology association" -> qualifiers [color=blue, label=qualifiers, - lp="1304.9,221.5", - pos="e,1122.7,193.07 2421.5,264.35 2114.9,264.15 1488.1,259.81 1271.4,229 1223.6,222.2 1170.6,207.74 1132.5,196.11", + lp="1225.9,221.5", + pos="e,1107.9,194.93 2237.8,262.76 1926.5,259.97 1291.4,251.57 1192.4,229 1166,222.98 1138.2,210.6 1116.9,199.66", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "gene to gene homology association" -> publications [color=blue, label=publications, - lp="1452.4,221.5", - pos="e,1274.2,192.71 2421.6,264.3 2140.9,263.88 1598.2,259.03 1408.4,229 1365.3,222.18 1317.8,207.69 1283.8,196.06", + lp="1326.4,221.5", + pos="e,1247.6,196.26 2238.4,262.2 1933.7,258.51 1324.9,248.71 1282.4,229 1271,223.68 1261.2,213.91 1253.6,204.41", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,276 +100,275 @@ digraph { width=2.0943]; "gene to gene homology association" -> "has evidence" [color=blue, label="has evidence", - lp="1606.9,221.5", - pos="e,1431.9,193.61 2422,263.52 2171.9,261.9 1721,255.3 1560.4,229 1519.6,222.3 1474.7,208.48 1441.7,197.06", + lp="1424.9,221.5", + pos="e,1381,195.82 2236.6,264.31 1950.7,263.96 1407.7,259.28 1378.4,229 1372.1,222.49 1373,213.45 1376.5,204.85", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1595.4,178", - width=3.015]; + label=string, + pos="1525.4,178", + width=1.0652]; "gene to gene homology association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1761.9,221.5", - pos="e,1621.5,195.59 2425.2,261.18 2184.7,256.59 1765.7,246.24 1697.4,229 1673.9,223.07 1649.5,211.31 1630.4,200.68", + lp="1543.9,221.5", + pos="e,1500.6,191.89 2237,263.61 1975.3,262.15 1505.2,255.79 1479.4,229 1469.5,218.73 1479.3,207.01 1492.3,197.49", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1830.4,178", - width=3.015]; + label=string, + pos="1620.4,178", + width=1.0652]; "gene to gene homology association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1933.4,221.5", - pos="e,1828.2,196.41 2424.5,261.51 2208.2,257.55 1860,248.23 1838.4,229 1832.1,223.34 1829.4,214.82 1828.5,206.41", + lp="1713.4,221.5", + pos="e,1614.1,196.03 2238.3,262.37 2012.2,259.35 1639.5,251.05 1618.4,229 1612.6,222.93 1611.5,214.31 1612.3,205.94", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2065.4,178", - width=3.015]; + label=string, + pos="1795.4,178", + width=1.0652]; "gene to gene homology association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2141.9,221.5", - pos="e,2044.7,195.97 2430.6,259.17 2270.6,253.62 2049,243.4 2035.4,229 2028.4,221.54 2031.6,212.18 2038.1,203.58", + lp="1933.9,221.5", + pos="e,1801.5,196 2239.6,261.56 2080.6,258.03 1862.3,249.48 1827.4,229 1818.2,223.58 1811.2,214.32 1806.1,205.24", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2247.4,178", + pos="2021.4,178", width=1.5346]; "gene to gene homology association" -> timepoint [color=blue, label=timepoint, - lp="2297.4,221.5", - pos="e,2248,196.47 2445.2,255.81 2364,250.03 2277.1,241.14 2262.4,229 2255.7,223.41 2251.9,214.91 2249.8,206.49", + lp="2096.4,221.5", + pos="e,2030.2,195.91 2244.4,259.49 2170.6,255.04 2093.2,246.26 2061.4,229 2051.1,223.36 2042.4,213.81 2035.9,204.56", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2359.4,178", + pos="2133.4,178", width=1.0652]; "gene to gene homology association" -> "original subject" [color=blue, label="original subject", - lp="2396.4,221.5", - pos="e,2345.7,194.92 2433.2,258.48 2391.3,253.49 2354,244.6 2340.4,229 2334.2,221.83 2336,212.39 2340.4,203.65", + lp="2200.4,221.5", + pos="e,2132.6,196.27 2250,258 2203.7,253.07 2161.1,244.34 2144.4,229 2138.1,223.19 2135,214.63 2133.6,206.24", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2473.4,178", + pos="2259.4,178", width=1.5887]; "gene to gene homology association" -> "original predicate" [color=blue, label="original predicate", - lp="2523.9,221.5", - pos="e,2462.4,195.76 2505.8,249.47 2485,244.2 2466.9,237.42 2460.4,229 2455.2,222.16 2455.7,213.39 2458.4,205.11", + lp="2330.9,221.5", + pos="e,2257.7,196.34 2317.9,249.63 2295.2,244.31 2275.2,237.45 2267.4,229 2261.8,222.91 2259.3,214.52 2258.3,206.36", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2587.4,178", + pos="2388.4,178", width=1.0652]; "gene to gene homology association" -> "original object" [color=blue, label="original object", - lp="2642.9,221.5", - pos="e,2588.9,196.18 2593,246.8 2592.1,235.16 2590.8,219.55 2589.7,206.24", + lp="2451.9,221.5", + pos="e,2392.7,196.18 2405.2,246.8 2402.3,235.16 2398.5,219.55 2395.2,206.24", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2720.4,178", + pos="2521.4,178", width=2.1304]; "gene to gene homology association" -> "subject category" [color=blue, label="subject category", - lp="2768.9,221.5", - pos="e,2716.6,196.4 2666.5,248.57 2678.1,243.72 2689.3,237.35 2698.4,229 2705.2,222.84 2710,214.24 2713.3,205.9", + lp="2575.9,221.5", + pos="e,2520.5,196.22 2479.3,248.51 2489.8,243.67 2499.7,237.32 2507.4,229 2513.2,222.79 2516.7,214.38 2518.7,206.22", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2891.4,178", + pos="2692.4,178", width=2.1304]; "gene to gene homology association" -> "object category" [color=blue, label="object category", - lp="2911.9,221.5", - pos="e,2876.6,195.73 2716.7,252.22 2763.8,246.39 2811.3,238.55 2832.4,229 2846.1,222.83 2859,212.54 2869.3,202.9", + lp="2716.9,221.5", + pos="e,2679,196.2 2530.6,252.14 2575.2,246.39 2619.7,238.62 2639.4,229 2651.7,223.02 2663,213.21 2672,203.86", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3024.4,178", + pos="2825.4,178", width=1.0652]; "gene to gene homology association" -> "subject closure" [color=blue, label="subject closure", - lp="3047.9,221.5", - pos="e,3012,195.52 2718.3,252.41 2737.7,250.6 2757.6,248.75 2776.4,247 2819.8,242.98 2931.8,246.91 2971.4,229 2984.4,223.17 2996.1,212.86 \ -3005.3,203.12", + lp="2851.9,221.5", + pos="e,2814.2,195.49 2533.3,252.43 2639.3,242.5 2775,229.67 2776.4,229 2788.6,223.19 2799.4,213.03 2807.8,203.37", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3124.4,178", + pos="2938.4,178", width=1.0652]; "gene to gene homology association" -> "object closure" [color=blue, label="object closure", - lp="3168.4,221.5", - pos="e,3123,196.23 2715.3,252.05 2735.7,250.22 2756.7,248.46 2776.4,247 2813.1,244.29 3077,250.93 3106.4,229 3113.8,223.54 3118.1,214.8 \ -3120.7,206.15", + lp="2974.4,221.5", + pos="e,2933.7,195.95 2530.3,252.08 2550.7,250.25 2571.7,248.48 2591.4,247 2626.8,244.35 2880.3,247.81 2910.4,229 2919.2,223.52 2925.5,\ +214.26 2929.8,205.18", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3257.4,178", + pos="3071.4,178", width=2.1304]; "gene to gene homology association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3326.9,221.5", - pos="e,3250.4,196.11 2713.8,251.94 2734.7,250.09 2756.2,248.35 2776.4,247 2825.9,243.69 3178.9,252.79 3222.4,229 3232.2,223.66 3239.8,\ -214.29 3245.5,205.1", + lp="3134.9,221.5", + pos="e,3061.8,196.19 2528.8,251.96 2549.7,250.11 2571.2,248.36 2591.4,247 2639.9,243.74 2984.7,250.17 3028.4,229 3039.5,223.65 3048.8,\ +214.02 3055.9,204.62", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3449.4,178", + pos="3264.4,178", width=2.1304]; "gene to gene homology association" -> "object category closure" [color=blue, label="object category closure", - lp="3516.9,221.5", - pos="e,3443.7,196.1 2712.8,251.82 2734,249.96 2755.8,248.25 2776.4,247 2812.1,244.84 3387.5,246.79 3418.4,229 3427.6,223.71 3434.5,214.48 \ -3439.4,205.37", + lp="3326.9,221.5", + pos="e,3256.5,196.2 2527.8,251.82 2549,249.96 2570.8,248.25 2591.4,247 2626.7,244.86 3195,245.13 3226.4,229 3236.7,223.71 3245,214.22 \ +3251.2,204.92", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3639.4,178", + pos="3454.4,178", width=1.0652]; "gene to gene homology association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3689.4,221.5", - pos="e,3632.5,196.19 2712.3,251.75 2733.6,249.89 2755.7,248.19 2776.4,247 2822.4,244.36 3563.9,250.69 3604.4,229 3614.3,223.76 3621.9,\ -214.4 3627.5,205.19", + lp="3500.4,221.5", + pos="e,3446.1,195.75 2527.3,251.75 2548.6,249.89 2570.7,248.19 2591.4,247 2637.1,244.37 3373.4,249.26 3414.4,229 3425.3,223.65 3434.1,\ +213.82 3440.7,204.29", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3798.4,178", + pos="3613.4,178", width=1.0652]; "gene to gene homology association" -> "object namespace" [color=blue, label="object namespace", - lp="3842.4,221.5", - pos="e,3791.1,195.73 2711.8,251.73 2733.3,249.86 2755.5,248.17 2776.4,247 2831.1,243.95 3712.8,254.08 3761.4,229 3771.8,223.68 3780,213.99 \ -3786,204.56", + lp="3654.4,221.5", + pos="e,3604.8,195.78 2526.8,251.74 2548.3,249.86 2570.5,248.17 2591.4,247 2645.9,243.96 3523.4,252.77 3572.4,229 3583.4,223.68 3592.5,\ +213.86 3599.2,204.32", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3949.4,178", + pos="3764.4,178", width=1.0652]; "gene to gene homology association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4002.4,221.5", - pos="e,3941.4,195.77 2711.3,251.74 2733,249.85 2755.4,248.15 2776.4,247 2807.9,245.28 3882.2,243.05 3910.4,229 3921.2,223.66 3929.8,213.84 \ -3936.2,204.31", + lp="3816.4,221.5", + pos="e,3755.5,195.8 2526.3,251.74 2548,249.85 2570.4,248.15 2591.4,247 2654.2,243.58 3665.7,256 3722.4,229 3733.6,223.71 3742.8,213.89 \ +3749.8,204.35", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4120.4,178", + pos="3935.4,178", width=1.0652]; "gene to gene homology association" -> "object label closure" [color=blue, label="object label closure", - lp="4167.9,221.5", - pos="e,4112.1,195.79 2711.3,251.7 2733,249.82 2755.4,248.13 2776.4,247 2812.6,245.06 4047.9,244.92 4080.4,229 4091.3,223.69 4100.1,213.87 \ -4106.7,204.33", + lp="3983.9,221.5", + pos="e,3926.8,195.8 2526.3,251.7 2548,249.82 2570.4,248.13 2591.4,247 2627.6,245.07 3861.8,244.71 3894.4,229 3905.4,223.7 3914.5,213.89 \ +3921.3,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4273.4,178", + pos="4088.4,178", width=2.347]; "gene to gene homology association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4326.9,221.5", - pos="e,4267.5,196.18 2711.3,251.67 2733,249.79 2755.4,248.11 2776.4,247 2817.1,244.86 4205.9,248.76 4241.4,229 4250.9,223.75 4258,214.39 \ -4263,205.18", + lp="4141.9,221.5", + pos="e,4082.8,196.16 2526.3,251.67 2548,249.79 2570.4,248.11 2591.4,247 2632.1,244.85 4022,249.02 4057.4,229 4066.7,223.78 4073.5,214.56 \ +4078.4,205.45", style=solid]; type [height=0.5, - pos="4407.4,178", + pos="4222.4,178", width=0.86659]; "gene to gene homology association" -> type [color=blue, label=type, - lp="4425.4,221.5", - pos="e,4410.1,195.98 2711.3,251.65 2733,249.77 2755.4,248.1 2776.4,247 2799,245.83 4383.5,243.9 4400.4,229 4406.9,223.32 4409.4,214.65 \ -4410.1,206.12", + lp="4240.4,221.5", + pos="e,4225.1,195.98 2526.3,251.65 2548,249.77 2570.4,248.1 2591.4,247 2614,245.83 4198.5,243.9 4215.4,229 4221.9,223.32 4224.4,214.65 \ +4225.1,206.12", style=solid]; category [height=0.5, - pos="4508.4,178", + pos="4323.4,178", width=1.4263]; "gene to gene homology association" -> category [color=blue, label=category, - lp="4503.9,221.5", - pos="e,4493.7,195.48 2710.8,251.69 2732.6,249.8 2755.2,248.1 2776.4,247 2822.7,244.59 4401.7,244.5 4445.4,229 4460.7,223.59 4475,212.84 \ -4486.2,202.68", + lp="4318.9,221.5", + pos="e,4308.7,195.48 2525.8,251.69 2547.6,249.8 2570.2,248.1 2591.4,247 2637.7,244.59 4216.7,244.5 4260.4,229 4275.7,223.59 4290,212.84 \ +4301.2,202.68", style=solid]; subject [height=0.5, - pos="4622.4,178", + pos="4437.4,178", width=1.2277]; "gene to gene homology association" -> subject [color=blue, label=subject, - lp="4599.4,221.5", - pos="e,4603.7,194.32 2710.8,251.68 2732.6,249.79 2755.2,248.1 2776.4,247 2874.3,241.94 4445.2,255.71 4539.4,229 4559.6,223.29 4579.8,\ -211.3 4595.2,200.49", + lp="4414.4,221.5", + pos="e,4418.7,194.32 2525.8,251.68 2547.6,249.79 2570.2,248.1 2591.4,247 2689.3,241.94 4260.2,255.71 4354.4,229 4374.6,223.29 4394.8,\ +211.3 4410.2,200.49", style=solid]; predicate [height=0.5, - pos="4739.4,178", + pos="4554.4,178", width=1.5165]; "gene to gene homology association" -> predicate [color=blue, label=predicate, - lp="4707.4,221.5", - pos="e,4714.3,194.12 2710.8,251.67 2732.6,249.78 2755.2,248.09 2776.4,247 2879.3,241.71 4528.9,251.28 4629.4,229 4656.2,223.07 4684.3,\ -210.16 4705.4,198.95", + lp="4522.4,221.5", + pos="e,4529.3,194.12 2525.8,251.67 2547.6,249.78 2570.2,248.09 2591.4,247 2694.3,241.71 4343.9,251.28 4444.4,229 4471.2,223.07 4499.3,\ +210.16 4520.4,198.95", style=solid]; object [height=0.5, - pos="4689.4,91", + pos="4504.4,91", width=1.0832]; "gene to gene homology association" -> object [color=blue, label=object, - lp="4831.4,178", - pos="e,4719.3,102.76 2710.8,251.66 2732.6,249.77 2755.2,248.09 2776.4,247 2885.7,241.41 4639.8,257.46 4745.4,229 4774.1,221.28 4788.5,\ -221.64 4803.4,196 4826.1,157.11 4770,124.49 4728.7,106.65", + lp="4646.4,178", + pos="e,4534.3,102.76 2525.8,251.66 2547.6,249.77 2570.2,248.09 2591.4,247 2700.7,241.41 4454.8,257.46 4560.4,229 4589.1,221.28 4603.5,\ +221.64 4618.4,196 4641.1,157.11 4585,124.49 4543.7,106.65", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2823.4,265", + pos="2638.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2954.4,265", + pos="2769.4,265", width=2.0762]; subject -> object [label=relation, - lp="4688.4,134.5", - pos="e,4676.8,108.05 4635.4,160.61 4645.3,147.95 4659.3,130.24 4670.5,115.98"]; + lp="4503.4,134.5", + pos="e,4491.8,108.05 4450.4,160.61 4460.3,147.95 4474.3,130.24 4485.5,115.98"]; relation [height=0.5, - pos="4634.4,18", + pos="4449.4,18", width=1.2999]; - subject -> relation [pos="e,4633.1,36.188 4623.7,159.79 4625.8,132.48 4629.9,78.994 4632.4,46.38", + subject -> relation [pos="e,4448.1,36.188 4438.7,159.79 4440.8,132.48 4444.9,78.994 4447.4,46.38", style=dotted]; "gene to gene homology association_subject" [color=blue, height=0.5, label="gene or gene product", - pos="3157.4,265", + pos="2972.4,265", width=3.0692]; "gene to gene homology association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3363.4,265", + pos="3178.4,265", width=2.1665]; - object -> relation [pos="e,4647.3,35.54 4677,73.889 4670,64.939 4661.3,53.617 4653.5,43.584", + object -> relation [pos="e,4462.3,35.54 4492,73.889 4485,64.939 4476.3,53.617 4468.5,43.584", style=dotted]; "gene to gene homology association_object" [color=blue, height=0.5, label="gene or gene product", - pos="3569.4,265", + pos="3384.4,265", width=3.0692]; } diff --git a/graphviz/gene_to_gene_homology_association.svg b/graphviz/gene_to_gene_homology_association.svg index 8897657210..d673268d59 100644 --- a/graphviz/gene_to_gene_homology_association.svg +++ b/graphviz/gene_to_gene_homology_association.svg @@ -4,16 +4,16 @@ - + %3 - + gene to gene homology association - -gene to gene homology association + +gene to gene homology association @@ -24,8 +24,8 @@ gene to gene homology association->gene to gene association - - + + is_a @@ -37,9 +37,9 @@ gene to gene homology association->id - + -id +id @@ -50,9 +50,9 @@ gene to gene homology association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ gene to gene homology association->name - - -name + + +name @@ -76,9 +76,9 @@ gene to gene homology association->description - - -description + + +description @@ -89,9 +89,9 @@ gene to gene homology association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ gene to gene homology association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ gene to gene homology association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ gene to gene homology association->publications - - -publications + + +publications @@ -141,363 +141,363 @@ gene to gene homology association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string gene to gene homology association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string gene to gene homology association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string gene to gene homology association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type gene to gene homology association->timepoint - - -timepoint + + +timepoint original subject - -string + +string gene to gene homology association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie gene to gene homology association->original predicate - - -original predicate + + +original predicate original object - -string + +string gene to gene homology association->original object - - -original object + + +original object subject category - -ontology class + +ontology class gene to gene homology association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class gene to gene homology association->object category - - -object category + + +object category subject closure - -string + +string gene to gene homology association->subject closure - - -subject closure + + +subject closure object closure - -string + +string gene to gene homology association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class gene to gene homology association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class gene to gene homology association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string gene to gene homology association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string gene to gene homology association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string gene to gene homology association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string gene to gene homology association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source gene to gene homology association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type gene to gene homology association->type - - -type + + +type category - -category + +category gene to gene homology association->category - - -category + + +category subject - -subject + +subject gene to gene homology association->subject - - -subject + + +subject predicate - -predicate + +predicate gene to gene homology association->predicate - - -predicate + + +predicate object - -object + +object gene to gene homology association->object - - -object + + +object association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + gene to gene homology association_subject - -gene or gene product + +gene or gene product gene to gene homology association_predicate - -predicate type + +predicate type object->relation - - + + gene to gene homology association_object - -gene or gene product + +gene or gene product diff --git a/graphviz/gene_to_gene_product_relationship.gv b/graphviz/gene_to_gene_product_relationship.gv index f51da91455..0f2fa39b11 100644 --- a/graphviz/gene_to_gene_product_relationship.gv +++ b/graphviz/gene_to_gene_product_relationship.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4922.1,283"]; + graph [bb="0,0,4737.1,283"]; node [label="\N"]; "gene to gene product relationship" [height=0.5, label="gene to gene product relationship", - pos="2642.5,265", + pos="2457.5,265", width=4.676]; "sequence feature relationship" [height=0.5, pos="149.49,178", width=4.1524]; "gene to gene product relationship" -> "sequence feature relationship" [label=is_a, lp="454.49,221.5", - pos="e,218.76,194 2475,262.83 1995.7,259.27 640.47,247.66 440.49,229 368.23,222.26 286.91,207.68 228.64,196"]; + pos="e,218.76,193.98 2289.1,264.39 1871.7,264.82 797.13,262.54 440.49,229 368.24,222.21 286.91,207.64 228.64,195.97"]; id [color=blue, height=0.5, label=string, @@ -18,8 +18,8 @@ digraph { width=1.0652]; "gene to gene product relationship" -> id [color=blue, label=id, - lp="570.49,221.5", - pos="e,384.47,189.98 2474.9,262.98 2014.2,259.91 750.68,249.7 563.49,229 491.32,221.02 473.43,215.5 403.49,196 400.38,195.13 397.18,194.17 \ + lp="569.49,221.5", + pos="e,384.48,189.98 2290.5,262.69 1859.4,259.07 731.2,247.9 562.49,229 490.76,220.97 473,215.43 403.49,196 400.38,195.13 397.18,194.17 \ 393.98,193.15", style=solid]; iri [color=blue, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "gene to gene product relationship" -> iri [color=blue, label=iri, - lp="683.49,221.5", - pos="e,489.4,190.2 2475.2,262.74 2032.4,259.14 851.49,247.91 675.49,229 600.7,220.97 582.31,214.85 509.49,196 506.11,195.13 502.63,194.16 \ -499.15,193.15", + lp="675.49,221.5", + pos="e,489.41,190.15 2288.8,264.71 1905.5,265.68 978.07,264.16 667.49,229 596.2,220.93 578.85,214.31 509.49,196 506.11,195.11 502.64,\ +194.13 499.16,193.11", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "gene to gene product relationship" -> name [color=blue, label=name, - lp="790.49,221.5", - pos="e,613.44,191.54 2474.7,263.08 2046.8,260.43 936.33,251.45 770.49,229 719.35,222.08 662.34,206.51 623.23,194.57", + lp="778.49,221.5", + pos="e,612.07,191.87 2290.1,262.89 1891.2,259.91 906.9,250.47 758.49,229 711.11,222.15 658.55,206.96 621.95,195.11", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "gene to gene product relationship" -> description [color=blue, label=description, - lp="910.99,221.5", - pos="e,759.54,194.14 2474.3,263.66 2062.3,262.4 1025.3,256.51 870.49,229 835.43,222.77 797.43,209.4 769.13,198.06", + lp="891.99,221.5", + pos="e,755.87,194.62 2289.6,263.71 1906.2,262.56 989.27,256.9 851.49,229 821.45,222.92 789.37,210.09 765.1,198.95", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "gene to gene product relationship" -> "has attribute" [color=blue, label="has attribute", - lp="1056.5,221.5", - pos="e,900.07,192.82 2474.7,263.47 2086.8,261.82 1150.4,255.13 1009.5,229 974.52,222.52 936.66,208.39 909.29,196.8", + lp="1026.5,221.5", + pos="e,895.42,194.01 2289.5,263.84 1929,262.95 1104,257.74 979.49,229 952.98,222.88 925.14,209.98 904.22,198.82", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "gene to gene product relationship" -> negated [color=blue, label=negated, - lp="1212.5,221.5", - pos="e,1021.7,190.46 2474.2,264.31 2145.4,264.2 1428.3,260.25 1183.5,229 1130.2,222.2 1070.6,205.66 1031.2,193.46", + lp="1164.5,221.5", + pos="e,1017.1,191.96 2290.7,262.37 1960.5,258.73 1246.1,248.69 1135.5,229 1097.5,222.23 1055.9,207.52 1026.6,195.8", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "gene to gene product relationship" -> qualifiers [color=blue, label=qualifiers, - lp="1353,221.5", - pos="e,1170.8,193.07 2474,264.35 2169.1,264.19 1537.2,259.96 1319.5,229 1271.7,222.2 1218.6,207.74 1180.6,196.11", + lp="1276,221.5", + pos="e,1156.5,194.93 2290.4,262.73 1981.1,259.87 1341.8,251.31 1242.5,229 1215.7,222.97 1187.4,210.59 1165.7,199.66", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "gene to gene product relationship" -> publications [color=blue, label=publications, - lp="1500.5,221.5", - pos="e,1322.2,192.71 2474.2,264.31 2194.8,263.93 1647.2,259.19 1456.5,229 1413.4,222.18 1365.9,207.69 1331.9,196.06", + lp="1376.5,221.5", + pos="e,1296,195.78 2291.2,262.17 1988.7,258.36 1375.3,248.31 1332.5,229 1320.4,223.57 1310,213.45 1302.1,203.73", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,276 +100,276 @@ digraph { width=2.0943]; "gene to gene product relationship" -> "has evidence" [color=blue, label="has evidence", - lp="1655,221.5", - pos="e,1480,193.61 2474.4,263.55 2225.3,261.98 1770,255.45 1608.5,229 1567.6,222.3 1522.7,208.48 1489.8,197.06", + lp="1475,221.5", + pos="e,1430,195.88 2289.2,264.3 2005.1,263.97 1457.8,259.37 1428.5,229 1422.3,222.63 1422.9,213.73 1425.8,205.2", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1643.5,178", - width=3.015]; + label=string, + pos="1573.5,178", + width=1.0652]; "gene to gene product relationship" -> "knowledge source" [color=blue, label="knowledge source", - lp="1810,221.5", - pos="e,1669.6,195.59 2477.7,261.26 2238,256.71 1814.2,246.35 1745.5,229 1722,223.07 1697.5,211.31 1678.5,200.68", + lp="1594,221.5", + pos="e,1549.3,192.24 2289.4,263.62 2029.1,262.18 1555.4,255.87 1529.5,229 1519.9,219.09 1528.8,207.6 1541,198.13", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1878.5,178", - width=3.015]; + label=string, + pos="1668.5,178", + width=1.0652]; "gene to gene product relationship" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1981.5,221.5", - pos="e,1876.2,196.41 2477.1,261.59 2261.3,257.69 1908.2,248.37 1886.5,229 1880.1,223.34 1877.5,214.82 1876.6,206.41", + lp="1763.5,221.5", + pos="e,1663.1,196.04 2290.6,262.4 2065.4,259.41 1689.6,251.12 1668.5,229 1662.7,222.94 1661.3,214.32 1661.7,205.94", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2113.5,178", - width=3.015]; + label=string, + pos="1843.5,178", + width=1.0652]; "gene to gene product relationship" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2190,221.5", - pos="e,2092.8,195.97 2482.7,259.3 2322.4,253.79 2097.1,243.52 2083.5,229 2076.5,221.54 2079.7,212.18 2086.1,203.58", + lp="1984,221.5", + pos="e,1850.2,196.02 2292.5,261.43 2133.8,257.76 1912.8,249.1 1877.5,229 1867.9,223.55 1860.5,214.16 1855,204.98", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2295.5,178", + pos="2069.5,178", width=1.5346]; "gene to gene product relationship" -> timepoint [color=blue, label=timepoint, - lp="2345.5,221.5", - pos="e,2296,196.47 2496,256.01 2414,250.23 2325.3,241.28 2310.5,229 2303.7,223.41 2300,214.91 2297.8,206.49", + lp="2146.5,221.5", + pos="e,2078.9,195.92 2297.2,259.31 2222.8,254.83 2143.8,246.08 2111.5,229 2100.7,223.32 2091.6,213.63 2084.7,204.28", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2407.5,178", + pos="2181.5,178", width=1.0652]; "gene to gene product relationship" -> "original subject" [color=blue, label="original subject", - lp="2444.5,221.5", - pos="e,2393.7,194.92 2484.3,258.83 2441.1,253.92 2402.4,244.98 2388.5,229 2382.2,221.83 2384,212.39 2388.4,203.65", + lp="2250.5,221.5", + pos="e,2181.4,196.33 2302.7,257.85 2255.6,252.94 2211.7,244.26 2194.5,229 2188,223.25 2184.5,214.72 2182.8,206.31", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2521.5,178", + pos="2307.5,178", width=1.5887]; "gene to gene product relationship" -> "original predicate" [color=blue, label="original predicate", - lp="2572,221.5", - pos="e,2510.4,195.76 2554.5,249.65 2533.4,244.35 2515.1,237.52 2508.5,229 2503.2,222.16 2503.7,213.39 2506.5,205.11", + lp="2382,221.5", + pos="e,2306.9,196.42 2370,249.6 2347.1,244.19 2326.5,237.3 2318.5,229 2312.7,222.99 2309.6,214.63 2308.1,206.47", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2635.5,178", + pos="2441.5,178", width=1.0652]; "gene to gene product relationship" -> "original object" [color=blue, label="original object", - lp="2691,221.5", - pos="e,2636.9,196.18 2641.1,246.8 2640.1,235.16 2638.8,219.55 2637.7,206.24", + lp="2502,221.5", + pos="e,2444.7,196.18 2454.2,246.8 2452.1,235.16 2449.1,219.55 2446.6,206.24", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2768.5,178", + pos="2574.5,178", width=2.1304]; "gene to gene product relationship" -> "subject category" [color=blue, label="subject category", - lp="2817,221.5", - pos="e,2764.7,196.4 2714.2,248.69 2726,243.82 2737.3,237.42 2746.5,229 2753.2,222.84 2758,214.24 2761.4,205.9", + lp="2627,221.5", + pos="e,2572.5,196.3 2527.9,248.58 2538.8,243.73 2549.2,237.36 2557.5,229 2563.6,222.8 2567.6,214.29 2570.1,206.04", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2939.5,178", + pos="2745.5,178", width=2.1304]; "gene to gene product relationship" -> "object category" [color=blue, label="object category", - lp="2960,221.5", - pos="e,2924.7,195.73 2763.1,252.42 2810.7,246.57 2859.1,238.65 2880.5,229 2894.1,222.83 2907.1,212.54 2917.4,202.9", + lp="2768,221.5", + pos="e,2731.9,195.72 2577.6,252.37 2623.7,246.58 2670,238.72 2690.5,229 2703.4,222.88 2715.4,212.74 2724.9,203.17", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3072.5,178", + pos="2878.5,178", width=1.0652]; "gene to gene product relationship" -> "subject closure" [color=blue, label="subject closure", - lp="3096,221.5", - pos="e,3060.1,195.53 2763.1,252.4 2782.3,250.57 2801.9,248.72 2820.5,247 2864.7,242.89 2979,247.24 3019.5,229 3032.4,223.18 3044.2,212.87 \ -3053.3,203.13", + lp="2903,221.5", + pos="e,2866.7,195.51 2578.6,252.4 2597.6,250.59 2617.1,248.74 2635.5,247 2678.1,242.96 2788.6,247.04 2827.5,229 2840,223.21 2851.2,213.05 \ +2859.9,203.39", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3172.5,178", + pos="2986.5,178", width=1.0652]; "gene to gene product relationship" -> "object closure" [color=blue, label="object closure", - lp="3216.5,221.5", - pos="e,3171.1,196.23 2760.2,252.06 2780.3,250.23 2801,248.46 2820.5,247 2857.5,244.23 3124.7,251.18 3154.5,229 3161.8,223.54 3166.2,214.8 \ -3168.8,206.15", + lp="3025.5,221.5", + pos="e,2982.6,196.39 2575.2,252.09 2595.3,250.24 2616,248.47 2635.5,247 2671.7,244.27 2931.2,248.92 2961.5,229 2969.7,223.6 2975.3,214.64 \ +2979.1,205.78", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3305.5,178", + pos="3119.5,178", width=2.1304]; "gene to gene product relationship" -> "subject category closure" [color=blue, label="subject category closure", - lp="3375,221.5", - pos="e,3298.5,196.11 2758.7,251.96 2779.3,250.1 2800.5,248.35 2820.5,247 2870.4,243.62 3226.6,252.99 3270.5,229 3280.3,223.67 3287.9,\ -214.3 3293.5,205.1", + lp="3185,221.5", + pos="e,3110.8,196.17 2573.7,251.97 2594.3,250.11 2615.5,248.36 2635.5,247 2684.7,243.65 3035.4,251.29 3079.5,229 3090.1,223.62 3098.9,\ +213.98 3105.4,204.59", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3497.5,178", + pos="3312.5,178", width=2.1304]; "gene to gene product relationship" -> "object category closure" [color=blue, label="object category closure", - lp="3565,221.5", - pos="e,3491.8,196.1 2757.8,251.85 2778.6,249.97 2800.2,248.25 2820.5,247 2856.3,244.79 3435.4,246.9 3466.5,229 3475.7,223.71 3482.5,214.48 \ -3487.4,205.37", + lp="3377,221.5", + pos="e,3305.2,196.17 2572.8,251.85 2593.6,249.98 2615.2,248.25 2635.5,247 2671,244.81 3245,245.69 3276.5,229 3286.5,223.69 3294.4,214.19 \ +3300.2,204.89", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3687.5,178", + pos="3502.5,178", width=1.0652]; "gene to gene product relationship" -> "subject namespace" [color=blue, label="subject namespace", - lp="3737.5,221.5", - pos="e,3680.5,196.19 2757.3,251.78 2778.3,249.91 2800,248.2 2820.5,247 2866.6,244.3 3611.7,250.79 3652.5,229 3662.3,223.76 3670,214.4 \ -3675.6,205.19", + lp="3549.5,221.5", + pos="e,3494.8,195.73 2572.3,251.79 2593.3,249.91 2615,248.2 2635.5,247 2681.5,244.31 3423.4,249.92 3464.5,229 3474.9,223.67 3483.3,213.99 \ +3489.5,204.55", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3846.5,178", + pos="3661.5,178", width=1.0652]; "gene to gene product relationship" -> "object namespace" [color=blue, label="object namespace", - lp="3890.5,221.5", - pos="e,3839.1,195.73 2756.8,251.77 2778,249.88 2799.9,248.17 2820.5,247 2875.4,243.89 3760.6,254.18 3809.5,229 3819.8,223.68 3828,213.99 \ -3834,204.56", + lp="3703.5,221.5", + pos="e,3653.2,195.77 2571.8,251.77 2593,249.88 2614.9,248.17 2635.5,247 2690.2,243.89 3572.3,253.18 3621.5,229 3632.3,223.67 3641.2,213.84 \ +3647.8,204.31", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3997.5,178", + pos="3812.5,178", width=1.0652]; "gene to gene product relationship" -> "subject label closure" [color=blue, label="subject label closure", - lp="4050.5,221.5", - pos="e,3989.5,195.77 2756.8,251.73 2778,249.84 2799.9,248.15 2820.5,247 2852.1,245.25 3930.2,243.09 3958.5,229 3969.2,223.66 3977.8,213.84 \ -3984.3,204.31", + lp="3863.5,221.5", + pos="e,3803.9,195.79 2571.8,251.73 2593,249.84 2614.9,248.15 2635.5,247 2667,245.25 3743.1,242.72 3771.5,229 3782.5,223.69 3791.5,213.88 \ +3798.3,204.34", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4168.5,178", + pos="3983.5,178", width=1.0652]; "gene to gene product relationship" -> "object label closure" [color=blue, label="object label closure", - lp="4216,221.5", - pos="e,4160.2,195.79 2756.3,251.74 2777.6,249.84 2799.7,248.13 2820.5,247 2856.8,245.02 4095.8,244.97 4128.5,229 4139.3,223.69 4148.2,\ -213.87 4154.8,204.33", + lp="4031,221.5", + pos="e,3974.6,195.81 2571.3,251.74 2592.6,249.84 2614.7,248.13 2635.5,247 2671.7,245.02 3908.7,244.55 3941.5,229 3952.6,223.72 3961.9,\ +213.9 3968.8,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4321.5,178", + pos="4136.5,178", width=2.347]; "gene to gene product relationship" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4375,221.5", - pos="e,4315.5,196.18 2756.3,251.71 2777.6,249.81 2799.7,248.12 2820.5,247 2861.2,244.81 4253.8,248.81 4289.5,229 4298.9,223.75 4306,214.39 \ -4311.1,205.18", + lp="4190,221.5", + pos="e,4130.5,196.18 2571.3,251.71 2592.6,249.81 2614.7,248.12 2635.5,247 2676.2,244.81 4068.8,248.81 4104.5,229 4113.9,223.75 4121,214.39 \ +4126.1,205.18", style=solid]; type [height=0.5, - pos="4455.5,178", + pos="4270.5,178", width=0.86659]; "gene to gene product relationship" -> type [color=blue, label=type, - lp="4473.5,221.5", - pos="e,4458.2,195.98 2756.3,251.69 2777.6,249.8 2799.7,248.1 2820.5,247 2843.1,245.8 4431.5,243.93 4448.5,229 4454.9,223.32 4457.5,214.65 \ -4458.2,206.12", + lp="4288.5,221.5", + pos="e,4273.2,195.98 2571.3,251.69 2592.6,249.8 2614.7,248.1 2635.5,247 2658.1,245.8 4246.5,243.93 4263.5,229 4269.9,223.32 4272.5,214.65 \ +4273.2,206.12", style=solid]; category [height=0.5, - pos="4556.5,178", + pos="4371.5,178", width=1.4263]; "gene to gene product relationship" -> category [color=blue, label=category, - lp="4552,221.5", - pos="e,4541.7,195.48 2756.3,251.69 2777.6,249.79 2799.7,248.1 2820.5,247 2866.9,244.54 4449.7,244.53 4493.5,229 4508.7,223.59 4523.1,\ -212.84 4534.2,202.68", + lp="4367,221.5", + pos="e,4356.7,195.48 2571.3,251.69 2592.6,249.79 2614.7,248.1 2635.5,247 2681.9,244.54 4264.7,244.53 4308.5,229 4323.7,223.59 4338.1,\ +212.84 4349.2,202.68", style=solid]; subject [height=0.5, - pos="4670.5,178", + pos="4485.5,178", width=1.2277]; "gene to gene product relationship" -> subject [color=blue, label=subject, - lp="4647.5,221.5", - pos="e,4651.7,194.32 2756.3,251.68 2777.6,249.78 2799.7,248.1 2820.5,247 2918.5,241.83 4493,255.77 4587.5,229 4607.6,223.29 4627.8,211.3 \ -4643.3,200.49", + lp="4462.5,221.5", + pos="e,4466.7,194.32 2571.3,251.68 2592.6,249.78 2614.7,248.1 2635.5,247 2733.5,241.83 4308,255.77 4402.5,229 4422.6,223.29 4442.8,211.3 \ +4458.3,200.49", style=solid]; object [height=0.5, - pos="4713.5,91", + pos="4528.5,91", width=1.0832]; "gene to gene product relationship" -> object [color=blue, label=object, - lp="4757.5,178", - pos="e,4726.9,108.09 2756.3,251.67 2777.6,249.77 2799.7,248.09 2820.5,247 2872,244.3 4628.5,245.03 4677.5,229 4701.4,221.18 4709.4,216.87 \ -4723.5,196 4737.3,175.52 4733.6,166.51 4736.5,142 4737.3,135.38 4738.4,133.39 4736.5,127 4735.5,123.55 4734,120.13 4732.2,116.85", + lp="4572.5,178", + pos="e,4541.9,108.09 2571.3,251.67 2592.6,249.77 2614.7,248.09 2635.5,247 2687,244.3 4443.5,245.03 4492.5,229 4516.4,221.18 4524.4,216.87 \ +4538.5,196 4552.3,175.52 4548.6,166.51 4551.5,142 4552.3,135.38 4553.4,133.39 4551.5,127 4550.5,123.55 4549,120.13 4547.2,116.85", style=solid]; predicate [height=0.5, - pos="4867.5,178", + pos="4682.5,178", width=1.5165]; "gene to gene product relationship" -> predicate [color=blue, label=predicate, - lp="4840.5,221.5", - pos="e,4843.7,194.36 2756.3,251.66 2777.6,249.77 2799.7,248.09 2820.5,247 2928.3,241.36 4659.3,253.69 4764.5,229 4789.4,223.16 4815.3,\ -210.56 4834.9,199.48", + lp="4655.5,221.5", + pos="e,4658.7,194.36 2571.3,251.66 2592.6,249.77 2614.7,248.09 2635.5,247 2743.3,241.36 4474.3,253.69 4579.5,229 4604.4,223.16 4630.3,\ +210.56 4649.9,199.48", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2867.5,265", + pos="2682.5,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2998.5,265", + pos="2813.5,265", width=2.0762]; subject -> object [label=relation, - lp="4708.5,134.5", - pos="e,4695.6,107.23 4671.6,159.55 4672.8,149.57 4675.3,137.07 4680.5,127 4682.7,122.68 4685.6,118.52 4688.8,114.66"]; + lp="4523.5,134.5", + pos="e,4510.6,107.23 4486.6,159.55 4487.8,149.57 4490.3,137.07 4495.5,127 4497.7,122.68 4500.6,118.52 4503.8,114.66"]; relation [height=0.5, - pos="4658.5,18", + pos="4473.5,18", width=1.2999]; - subject -> relation [pos="e,4659.8,36.188 4669.2,159.79 4667.1,132.48 4663,78.994 4660.6,46.38", + subject -> relation [pos="e,4474.8,36.188 4484.2,159.79 4482.1,132.48 4478,78.994 4475.6,46.38", style=dotted]; "gene to gene product relationship_subject" [color=blue, height=0.5, label=gene, - pos="3124.5,265", + pos="2939.5,265", width=0.92075]; - object -> relation [pos="e,4671.3,35.54 4701,73.889 4694.1,64.939 4685.3,53.617 4677.5,43.584", + object -> relation [pos="e,4486.3,35.54 4516,73.889 4509.1,64.939 4500.3,53.617 4492.5,43.584", style=dotted]; "gene to gene product relationship_object" [color=blue, height=0.5, label="gene product mixin", - pos="3276.5,265", + pos="3091.5,265", width=2.7984]; "gene to gene product relationship_predicate" [color=blue, height=0.5, label="predicate type", - pos="3473.5,265", + pos="3288.5,265", width=2.1665]; } diff --git a/graphviz/gene_to_gene_product_relationship.svg b/graphviz/gene_to_gene_product_relationship.svg index 0cca85e90b..5c3fbce46b 100644 --- a/graphviz/gene_to_gene_product_relationship.svg +++ b/graphviz/gene_to_gene_product_relationship.svg @@ -4,16 +4,16 @@ - + %3 - + gene to gene product relationship - -gene to gene product relationship + +gene to gene product relationship @@ -24,8 +24,8 @@ gene to gene product relationship->sequence feature relationship - - + + is_a @@ -37,9 +37,9 @@ gene to gene product relationship->id - - -id + + +id @@ -50,9 +50,9 @@ gene to gene product relationship->iri - - -iri + + +iri @@ -63,9 +63,9 @@ gene to gene product relationship->name - - -name + + +name @@ -76,9 +76,9 @@ gene to gene product relationship->description - - -description + + +description @@ -89,9 +89,9 @@ gene to gene product relationship->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ gene to gene product relationship->negated - - -negated + + +negated @@ -115,9 +115,9 @@ gene to gene product relationship->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ gene to gene product relationship->publications - - -publications + + +publications @@ -141,363 +141,363 @@ gene to gene product relationship->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string gene to gene product relationship->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string gene to gene product relationship->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string gene to gene product relationship->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type gene to gene product relationship->timepoint - - -timepoint + + +timepoint original subject - -string + +string gene to gene product relationship->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie gene to gene product relationship->original predicate - - -original predicate + + +original predicate original object - -string + +string gene to gene product relationship->original object - - -original object + + +original object subject category - -ontology class + +ontology class gene to gene product relationship->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class gene to gene product relationship->object category - - -object category + + +object category subject closure - -string + +string gene to gene product relationship->subject closure - - -subject closure + + +subject closure object closure - -string + +string gene to gene product relationship->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class gene to gene product relationship->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class gene to gene product relationship->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string gene to gene product relationship->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string gene to gene product relationship->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string gene to gene product relationship->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string gene to gene product relationship->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source gene to gene product relationship->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type gene to gene product relationship->type - - -type + + +type category - -category + +category gene to gene product relationship->category - - -category + + +category subject - -subject + +subject gene to gene product relationship->subject - - -subject + + +subject object - -object + +object gene to gene product relationship->object - - -object + + +object predicate - -predicate + +predicate gene to gene product relationship->predicate - - -predicate + + +predicate association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + gene to gene product relationship_subject - -gene + +gene object->relation - - + + gene to gene product relationship_object - -gene product mixin + +gene product mixin gene to gene product relationship_predicate - -predicate type + +predicate type diff --git a/graphviz/gene_to_go_term_association.gv b/graphviz/gene_to_go_term_association.gv index c8ce6cae5b..259c5ebcb1 100644 --- a/graphviz/gene_to_go_term_association.gv +++ b/graphviz/gene_to_go_term_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4886.8,283"]; + graph [bb="0,0,4668.8,283"]; node [label="\N"]; "gene to go term association" [height=0.5, label="gene to go term association", - pos="2590.8,265", + pos="2372.8,265", width=3.8816]; "functional association" [height=0.5, pos="111.79,178", width=3.1053]; "gene to go term association" -> "functional association" [label=is_a, - lp="379.79,221.5", - pos="e,169.6,193.45 2451.4,263.26 1996.3,260.63 571.94,250.74 365.79,229 301.99,222.27 230.38,207.5 179.49,195.75"]; + lp="378.79,221.5", + pos="e,169.62,193.48 2233.8,263.01 1809.5,259.78 548.86,248.64 364.79,229 301.35,222.23 230.14,207.51 179.48,195.78"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "gene to go term association" -> id [color=blue, label=id, - lp="496.79,221.5", - pos="e,308.77,190 2451.5,263.17 2013.8,260.35 683.24,250.13 489.79,229 416.75,221.02 398.59,215.65 327.79,196 324.68,195.14 321.48,194.17 \ -318.28,193.16", + lp="494.79,221.5", + pos="e,308.78,189.98 2233.7,262.9 1827.3,259.49 659.28,248.11 487.79,229 415.63,220.96 397.73,215.5 327.79,196 324.68,195.13 321.48,194.17 \ +318.29,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "gene to go term association" -> iri [color=blue, label=iri, - lp="613.79,221.5", - pos="e,413.69,190.23 2451.9,262.93 2031,259.51 787.59,247.9 605.79,229 528.37,220.95 509.21,215.26 433.79,196 430.41,195.14 426.93,194.18 \ -423.45,193.17", + lp="607.79,221.5", + pos="e,413.7,190.2 2233,264.43 1872.2,265.02 915.24,263.2 599.79,229 525.01,220.89 506.61,214.85 433.79,196 430.41,195.13 426.94,194.16 \ +423.45,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "gene to go term association" -> name [color=blue, label=name, - lp="725.79,221.5", - pos="e,538.41,191.15 2451.7,263.13 2045.2,260.33 877,250.52 705.79,229 650.97,222.11 589.61,206.11 548.22,194.05", + lp="715.79,221.5", + pos="e,537.58,191.41 2233.9,262.92 1859.1,259.73 845.85,249.34 695.79,229 644.14,222 586.5,206.31 547.17,194.36", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "gene to go term association" -> description [color=blue, label=description, - lp="854.29,221.5", - pos="e,687.2,193.65 2451.3,263.47 2060.6,261.66 973.3,254.38 813.79,229 773.43,222.58 729.19,208.66 696.84,197.14", + lp="838.29,221.5", + pos="e,684.59,194.12 2233.5,263.32 1874.7,261.21 936.73,253.42 797.79,229 761.91,222.69 722.94,209.24 694,197.88", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "gene to go term association" -> "has attribute" [color=blue, label="has attribute", - lp="1011.8,221.5", - pos="e,828.38,191.75 2451.8,263.11 2084.9,260.47 1109.3,251.4 964.79,229 920.66,222.16 871.91,207 837.97,195.15", + lp="985.79,221.5", + pos="e,825.22,192.67 2233.9,263.05 1898.6,260.41 1063.6,251.63 938.79,229 902.57,222.43 863.2,208.24 834.79,196.65", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "gene to go term association" -> predicate [color=blue, label=predicate, - lp="1172.8,221.5", - pos="e,986.21,193.09 2451,264.64 2138,265.43 1389.2,263.51 1138.8,229 1089.6,222.22 1034.9,207.65 995.79,195.99", + lp="1129.8,221.5", + pos="e,978.82,194.06 2234.2,262.46 1926.6,258.7 1205.3,247.99 1095.8,229 1058.6,222.56 1018.2,209.02 988.17,197.66", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "gene to go term association" -> negated [color=blue, label=negated, - lp="1318.8,221.5", - pos="e,1120.7,190.23 2451.4,263.61 2163.3,262.27 1510.9,256.21 1289.8,229 1234,222.13 1171.3,205.38 1130.4,193.16", + lp="1249.8,221.5", + pos="e,1114,192.51 2234.5,262.31 1950,258.46 1317.7,247.89 1220.8,229 1186.7,222.36 1149.9,208.2 1123.3,196.64", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "gene to go term association" -> qualifiers [color=blue, label=qualifiers, - lp="1455.3,221.5", - pos="e,1270,193.02 2451.3,263.68 2185.7,262.44 1616.5,256.53 1421.8,229 1373,222.11 1318.9,207.65 1280,196.05", + lp="1353.3,221.5", + pos="e,1250,195.39 2233.8,262.91 1967.8,260.31 1405.6,252.12 1319.8,229 1298.1,223.15 1275.8,211.43 1258.5,200.81", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "gene to go term association" -> publications [color=blue, label=publications, - lp="1597.8,221.5", - pos="e,1420.3,192.66 2451.3,263.64 2209.6,262.3 1722.3,256.17 1553.8,229 1510.9,222.09 1463.7,207.61 1429.9,196.01", + lp="1444.8,221.5", + pos="e,1384.8,196.26 2233.6,263.12 1972.8,260.91 1433.6,253.39 1400.8,229 1393.5,223.57 1389.3,214.84 1386.9,206.19", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,264 +110,265 @@ digraph { width=2.0943]; "gene to go term association" -> "has evidence" [color=blue, label="has evidence", - lp="1751.3,221.5", - pos="e,1577.8,193.55 2451.8,262.82 2239.4,260.28 1844.2,252.47 1704.8,229 1664.4,222.2 1620,208.38 1587.5,196.99", + lp="1543.3,221.5", + pos="e,1512.2,194.93 2233.1,263.42 1992.2,261.72 1521.8,255.07 1496.8,229 1488.4,220.25 1494.3,210.18 1504.1,201.37", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1741.8,178", - width=3.015]; + label=string, + pos="1671.8,178", + width=1.0652]; "gene to go term association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1901.3,221.5", - pos="e,1766.3,195.78 2450.9,264.75 2265.4,264.49 1948.5,259.38 1836.8,229 1815,223.09 1792.6,211.61 1775.1,201.13", + lp="1661.3,221.5", + pos="e,1641.7,189.28 2234,262.65 2016.7,259.84 1618.4,251.62 1596.8,229 1592.2,224.18 1593.2,219.62 1596.8,214 1601.2,207.12 1616.4,199.47 \ +1632,193.08", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1976.8,178", - width=3.015]; + label=string, + pos="1766.8,178", + width=1.0652]; "gene to go term association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2070.8,221.5", - pos="e,1971,196 2454.4,260.93 2278.2,256.29 1992,246.15 1975.8,229 1970,222.9 1968.8,214.27 1969.4,205.9", + lp="1827.8,221.5", + pos="e,1746.5,193.48 2235.9,261.25 2053,256.89 1749.8,246.99 1732.8,229 1724.7,220.46 1730.2,209.82 1739,200.55", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2211.8,178", - width=3.015]; + label=string, + pos="1908.8,178", + width=1.0652]; "gene to go term association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2279.3,221.5", - pos="e,2186,195.53 2453.4,261.58 2338.9,258.1 2191.8,249.62 2172.8,229 2165.1,220.62 2170,210.86 2178.5,202.2", + lp="2048.3,221.5", + pos="e,1915.3,195.93 2240.7,259.08 2123.5,253.77 1967.2,244 1941.8,229 1932.4,223.44 1925.2,214.03 1919.9,204.86", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2393.8,178", + pos="2134.8,178", width=1.5346]; "gene to go term association" -> timepoint [color=blue, label=timepoint, - lp="2430.8,221.5", - pos="e,2389.5,196.26 2473.6,255.18 2438.8,250.02 2407,241.87 2395.8,229 2390.4,222.83 2388.7,214.43 2388.7,206.27", + lp="2210.8,221.5", + pos="e,2144.4,196.09 2250.8,256.11 2224.8,250.74 2198.4,242.26 2175.8,229 2165.7,223.07 2157,213.64 2150.2,204.56", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2505.8,178", + pos="2246.8,178", width=1.0652]; "gene to go term association" -> "original subject" [color=blue, label="original subject", - lp="2528.8,221.5", - pos="e,2485.7,193.75 2500.9,251.13 2490,245.91 2480.1,238.76 2472.8,229 2466.1,220.01 2470.9,209.73 2478.7,200.83", + lp="2312.8,221.5", + pos="e,2246,196.26 2288.4,250.55 2276.5,245.45 2265.4,238.5 2256.8,229 2251.2,222.83 2248.3,214.43 2247,206.27", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2619.8,178", + pos="2372.8,178", width=1.5887]; "gene to go term association" -> "original predicate" [color=blue, label="original predicate", - lp="2655.3,221.5", - pos="e,2603,195.4 2588.5,246.84 2587.8,236.95 2588,224.45 2591.8,214 2593.1,210.42 2594.9,206.94 2597,203.64", + lp="2436.3,221.5", + pos="e,2372.8,196.18 2372.8,246.8 2372.8,235.16 2372.8,219.55 2372.8,206.24", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2733.8,178", + pos="2501.8,178", width=1.0652]; "gene to go term association" -> "original object" [color=blue, label="original object", - lp="2780.3,221.5", - pos="e,2732.7,196.46 2682.3,251.35 2695.8,246.17 2708.6,238.98 2718.8,229 2724.9,223.04 2728.5,214.69 2730.7,206.52", + lp="2558.3,221.5", + pos="e,2506.2,195.99 2452.7,250.21 2474.5,244.75 2494,237.68 2500.8,229 2505.8,222.62 2507.2,214.26 2507.1,206.21", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2866.8,178", + pos="2634.8,178", width=2.1304]; "gene to go term association" -> "subject category" [color=blue, label="subject category", - lp="2910.3,221.5", - pos="e,2860.6,196.16 2688.1,252.02 2753.7,243.63 2829.4,233.2 2835.8,229 2844.5,223.28 2851.3,214.13 2856.2,205.22", + lp="2685.3,221.5", + pos="e,2632.1,196.01 2470.4,252.05 2534.6,243.82 2607.9,233.59 2613.8,229 2621.2,223.28 2626,214.49 2629.1,205.86", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3037.8,178", + pos="2805.8,178", width=2.1304]; "gene to go term association" -> "object category" [color=blue, label="object category", - lp="3055.3,221.5", - pos="e,3021.9,195.85 2689.7,252.2 2706.4,250.35 2723.6,248.55 2739.8,247 2791.7,242.04 2925.2,247.86 2973.8,229 2988.7,223.22 3003,212.74 \ -3014.2,202.86", + lp="2827.3,221.5", + pos="e,2791.7,196.08 2471.7,252.23 2488.4,250.38 2505.6,248.57 2521.8,247 2572.2,242.13 2702.2,248.69 2748.8,229 2762.3,223.29 2774.9,\ +213.06 2784.8,203.33", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3170.8,178", + pos="2938.8,178", width=1.0652]; "gene to go term association" -> "subject closure" [color=blue, label="subject closure", - lp="3192.3,221.5", - pos="e,3158,195.26 2687.7,252.01 2705,250.13 2722.9,248.37 2739.8,247 2781.4,243.63 3076.2,244.8 3114.8,229 3128.6,223.34 3141.3,212.7 \ -3151.1,202.69", + lp="2963.3,221.5", + pos="e,2927.1,195.23 2470.1,251.99 2487.3,250.12 2505.1,248.37 2521.8,247 2562.3,243.7 2849.5,245.09 2886.8,229 2899.9,223.36 2911.6,\ +212.88 2920.6,202.96", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3270.8,178", + pos="3051.8,178", width=1.0652]; "gene to go term association" -> "object closure" [color=blue, label="object closure", - lp="3312.8,221.5", - pos="e,3268.7,196.35 2686.9,251.92 2704.5,250.03 2722.7,248.28 2739.8,247 2768.1,244.89 3227.6,245.34 3250.8,229 3258.5,223.61 3263.2,\ -214.77 3266.1,206.01", + lp="3086.8,221.5", + pos="e,3046.4,196.06 2468.9,251.93 2486.5,250.04 2504.7,248.28 2521.8,247 2549.5,244.92 2997.9,243.13 3021.8,229 3030.8,223.65 3037.5,\ +214.41 3042.2,205.31", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3403.8,178", + pos="3184.8,178", width=2.1304]; "gene to go term association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3471.3,221.5", - pos="e,3396.1,196.18 2686.5,251.87 2704.2,249.97 2722.5,248.23 2739.8,247 2774.5,244.52 3335.9,245.13 3366.8,229 3376.9,223.7 3385,214.2 \ -3391,204.9", + lp="3247.3,221.5", + pos="e,3174.9,196.26 2468.5,251.87 2486.2,249.97 2504.5,248.23 2521.8,247 2556.1,244.55 3109.7,243.63 3140.8,229 3152.1,223.68 3161.7,\ +213.91 3169.1,204.41", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3595.8,178", + pos="3377.8,178", width=2.1304]; "gene to go term association" -> "object category closure" [color=blue, label="object category closure", - lp="3662.3,221.5", - pos="e,3589.5,196.16 2686.1,251.81 2703.9,249.91 2722.4,248.18 2739.8,247 2785.4,243.9 3522.8,251.11 3562.8,229 3572.3,223.72 3579.6,\ -214.36 3584.9,205.15", + lp="3440.3,221.5", + pos="e,3369.5,196.24 2468.1,251.82 2485.9,249.91 2504.4,248.18 2521.8,247 2567.1,243.92 3298.2,249.37 3338.8,229 3349.2,223.76 3357.7,\ +214.28 3364.1,204.97", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3785.8,178", + pos="3567.8,178", width=1.0652]; "gene to go term association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3834.8,221.5", - pos="e,3778.7,195.72 2686.1,251.76 2703.9,249.86 2722.4,248.15 2739.8,247 2795.8,243.31 3700.1,255.03 3749.8,229 3760,223.66 3768,213.98 \ -3773.8,204.54", + lp="3613.8,221.5", + pos="e,3559.5,195.77 2468.1,251.76 2485.9,249.86 2504.4,248.15 2521.8,247 2577.6,243.33 3477.6,253.66 3527.8,229 3538.6,223.67 3547.5,\ +213.85 3554.1,204.31", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3944.8,178", + pos="3726.8,178", width=1.0652]; "gene to go term association" -> "object namespace" [color=blue, label="object namespace", - lp="3988.8,221.5", - pos="e,3937.1,195.76 2685.7,251.77 2703.6,249.85 2722.3,248.13 2739.8,247 2772.1,244.91 3877.9,243.63 3906.8,229 3917.3,223.71 3925.6,\ -214.03 3931.8,204.59", + lp="3767.8,221.5", + pos="e,3718.2,195.79 2467.7,251.77 2485.6,249.85 2504.3,248.13 2521.8,247 2554.1,244.91 3656.7,243.06 3685.8,229 3696.8,223.69 3705.8,\ +213.88 3712.6,204.34", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4095.8,178", + pos="3877.8,178", width=1.0652]; "gene to go term association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4148.8,221.5", - pos="e,4087.8,195.78 2685.6,251.74 2703.6,249.83 2722.3,248.12 2739.8,247 2776.3,244.67 4024,245.28 4056.8,229 4067.5,223.68 4076.2,213.86 \ -4082.6,204.32", + lp="3929.8,221.5", + pos="e,3868.9,195.81 2467.6,251.74 2485.6,249.83 2504.3,248.12 2521.8,247 2558.2,244.68 3802.8,244.64 3835.8,229 3846.9,223.72 3856.2,\ +213.9 3863.1,204.36", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4266.8,178", + pos="4048.8,178", width=1.0652]; "gene to go term association" -> "object label closure" [color=blue, label="object label closure", - lp="4314.3,221.5", - pos="e,4258.5,195.8 2685.6,251.72 2703.6,249.81 2722.3,248.1 2739.8,247 2781,244.41 4189.7,247.12 4226.8,229 4237.7,223.7 4246.5,213.88 \ -4253.1,204.34", + lp="4097.3,221.5", + pos="e,4040.2,195.81 2467.6,251.72 2485.6,249.81 2504.3,248.1 2521.8,247 2563,244.41 3970.6,246.88 4007.8,229 4018.8,223.71 4027.8,213.9 \ +4034.6,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4428.8,178", + pos="4210.8,178", width=2.347]; "gene to go term association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4477.3,221.5", - pos="e,4419.9,196.31 2685.6,251.7 2703.6,249.79 2722.2,248.09 2739.8,247 2785.5,244.15 4346.5,248.81 4387.8,229 4398.6,223.79 4407.6,\ -214.18 4414.3,204.77", + lp="4259.3,221.5", + pos="e,4202.2,196.29 2467.6,251.7 2485.6,249.79 2504.2,248.09 2521.8,247 2567.5,244.15 4129.6,249.07 4170.8,229 4181.5,223.78 4190.3,\ +214.17 4196.8,204.75", style=solid]; type [height=0.5, - pos="4562.8,178", + pos="4344.8,178", width=0.86659]; "gene to go term association" -> type [color=blue, label=type, - lp="4576.8,221.5", - pos="e,4563.6,196.18 2685.2,251.73 2703.3,249.8 2722.1,248.09 2739.8,247 2764.9,245.45 4531.1,244.67 4550.8,229 4557.6,223.54 4561,214.93 \ -4562.5,206.37", + lp="4358.8,221.5", + pos="e,4345.6,196.18 2467.2,251.73 2485.3,249.8 2504.1,248.09 2521.8,247 2546.9,245.45 4313.1,244.67 4332.8,229 4339.6,223.54 4343,214.93 \ +4344.5,206.37", style=solid]; category [height=0.5, - pos="4663.8,178", + pos="4445.8,178", width=1.4263]; "gene to go term association" -> category [color=blue, label=category, - lp="4657.3,221.5", - pos="e,4648.2,195.25 2685.2,251.73 2703.3,249.8 2722.1,248.09 2739.8,247 2791.3,243.82 4547.9,245.49 4596.8,229 4613,223.53 4628.5,212.51 \ -4640.5,202.2", + lp="4439.3,221.5", + pos="e,4430.2,195.25 2467.2,251.73 2485.3,249.8 2504.1,248.09 2521.8,247 2573.3,243.82 4329.9,245.49 4378.8,229 4395,223.53 4410.5,212.51 \ +4422.5,202.2", style=solid]; subject [height=0.5, - pos="4777.8,178", + pos="4559.8,178", width=1.2277]; "gene to go term association" -> subject [color=blue, label=subject, - lp="4753.8,221.5", - pos="e,4758.5,194.33 2685.2,251.72 2703.3,249.8 2722.1,248.09 2739.8,247 2848.1,240.34 4588.2,257.99 4692.8,229 4713.5,223.25 4734.4,\ -211.09 4750.3,200.2", + lp="4535.8,221.5", + pos="e,4540.5,194.33 2467.2,251.72 2485.3,249.8 2504.1,248.09 2521.8,247 2630.1,240.34 4370.2,257.99 4474.8,229 4495.5,223.25 4516.4,\ +211.09 4532.3,200.2", style=solid]; object [height=0.5, - pos="4820.8,91", + pos="4602.8,91", width=1.0832]; "gene to go term association" -> object [color=blue, label=object, - lp="4864.8,178", - pos="e,4834.2,108.09 2685.2,251.71 2703.3,249.79 2722.1,248.08 2739.8,247 2796.5,243.53 4729.7,246.35 4783.8,229 4808.1,221.2 4816.4,\ -217.1 4830.8,196 4844.7,175.59 4840.9,166.51 4843.8,142 4844.6,135.38 4845.7,133.39 4843.8,127 4842.8,123.55 4841.3,120.13 4839.5,\ + lp="4646.8,178", + pos="e,4616.2,108.09 2467.2,251.71 2485.3,249.79 2504.1,248.08 2521.8,247 2578.5,243.53 4511.7,246.35 4565.8,229 4590.1,221.2 4598.4,\ +217.1 4612.8,196 4626.7,175.59 4622.9,166.51 4625.8,142 4626.6,135.38 4627.7,133.39 4625.8,127 4624.8,123.55 4623.3,120.13 4621.5,\ 116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2786.8,265", + pos="2568.8,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2917.8,265", + pos="2699.8,265", width=2.0762]; subject -> object [label=relation, - lp="4815.8,134.5", - pos="e,4802.9,107.23 4778.9,159.55 4780.1,149.57 4782.6,137.07 4787.8,127 4790,122.68 4792.9,118.52 4796.1,114.66"]; + lp="4597.8,134.5", + pos="e,4584.9,107.23 4560.9,159.55 4562.1,149.57 4564.6,137.07 4569.8,127 4572,122.68 4574.9,118.52 4578.1,114.66"]; relation [height=0.5, - pos="4765.8,18", + pos="4547.8,18", width=1.2999]; - subject -> relation [pos="e,4767.1,36.188 4776.5,159.79 4774.4,132.48 4770.3,78.994 4767.9,46.38", + subject -> relation [pos="e,4549.1,36.188 4558.5,159.79 4556.4,132.48 4552.3,78.994 4549.9,46.38", style=dotted]; "gene to go term association_subject" [color=blue, height=0.5, label=gene, - pos="3043.8,265", + pos="2825.8,265", width=0.92075]; - object -> relation [pos="e,4778.6,35.54 4808.3,73.889 4801.4,64.939 4792.6,53.617 4784.8,43.584", + object -> relation [pos="e,4560.6,35.54 4590.3,73.889 4583.4,64.939 4574.6,53.617 4566.8,43.584", style=dotted]; "gene to go term association_object" [color=blue, height=0.5, label="ontology class", - pos="3171.8,265", + pos="2953.8,265", width=2.1304]; } diff --git a/graphviz/gene_to_go_term_association.svg b/graphviz/gene_to_go_term_association.svg index 59c4d04d03..0a72c5e018 100644 --- a/graphviz/gene_to_go_term_association.svg +++ b/graphviz/gene_to_go_term_association.svg @@ -4,16 +4,16 @@ - + %3 - + gene to go term association - -gene to go term association + +gene to go term association @@ -24,9 +24,9 @@ gene to go term association->functional association - - -is_a + + +is_a @@ -37,9 +37,9 @@ gene to go term association->id - - -id + + +id @@ -50,9 +50,9 @@ gene to go term association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ gene to go term association->name - - -name + + +name @@ -76,9 +76,9 @@ gene to go term association->description - - -description + + +description @@ -89,9 +89,9 @@ gene to go term association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ gene to go term association->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ gene to go term association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ gene to go term association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ gene to go term association->publications - - -publications + + +publications @@ -154,344 +154,344 @@ gene to go term association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string gene to go term association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string gene to go term association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string gene to go term association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type gene to go term association->timepoint - - -timepoint + + +timepoint original subject - -string + +string gene to go term association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie gene to go term association->original predicate - - -original predicate + + +original predicate original object - -string + +string gene to go term association->original object - - -original object + + +original object subject category - -ontology class + +ontology class gene to go term association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class gene to go term association->object category - - -object category + + +object category subject closure - -string + +string gene to go term association->subject closure - - -subject closure + + +subject closure object closure - -string + +string gene to go term association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class gene to go term association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class gene to go term association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string gene to go term association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string gene to go term association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string gene to go term association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string gene to go term association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source gene to go term association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type gene to go term association->type - - -type + + +type category - -category + +category gene to go term association->category - - -category + + +category subject - -subject + +subject gene to go term association->subject - - -subject + + +subject object - -object + +object gene to go term association->object - - -object + + +object association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + gene to go term association_subject - -gene + +gene object->relation - - + + gene to go term association_object - -ontology class + +ontology class diff --git a/graphviz/gene_to_pathway_association.gv b/graphviz/gene_to_pathway_association.gv index 9179542437..f42e2ea50e 100644 --- a/graphviz/gene_to_pathway_association.gv +++ b/graphviz/gene_to_pathway_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,5125.4,283"]; + graph [bb="0,0,4907.4,283"]; node [label="\N"]; "gene to pathway association" [height=0.5, label="gene to pathway association", - pos="2761.4,265", + pos="2543.4,265", width=3.9538]; association [height=0.5, pos="62.394,178", width=1.7332]; "gene to pathway association" -> association [label=is_a, - lp="467.39,221.5", - pos="e,107.53,190.6 2619.4,263.48 2185,261.65 877.94,254.13 453.39,229 311.11,220.58 274.93,219.76 134.39,196 128.93,195.08 123.27,193.98 \ -117.62,192.8"]; + lp="466.39,221.5", + pos="e,107.54,190.59 2401.6,263.23 1995.5,260.77 832.82,251.88 452.39,229 310.56,220.47 274.49,219.71 134.39,196 128.93,195.08 123.27,\ +193.98 117.62,192.8"]; "gene to entity association mixin" [height=0.5, pos="302.39,178", width=4.4232]; "gene to pathway association" -> "gene to entity association mixin" [label=uses, - lp="615.89,221.5", - pos="e,373.72,194.11 2618.8,264.5 2202.5,265.5 993.08,265.12 599.39,229 525.93,222.26 443.23,207.76 383.79,196.11"]; + lp="614.89,221.5", + pos="e,373.78,194.14 2401.1,264.2 2014.2,264.3 948.23,261.51 598.39,229 525.3,222.21 443.04,207.75 383.82,196.12"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "gene to pathway association" -> id [color=blue, label=id, - lp="735.39,221.5", - pos="e,547.38,190 2619.9,263.07 2189.5,260.03 914.59,249.39 728.39,229 655.35,221 637.2,215.65 566.39,196 563.29,195.14 560.09,194.17 \ -556.89,193.16", + lp="733.39,221.5", + pos="e,547.38,189.98 2400.8,264.64 2031.5,265.77 1049.7,265.15 726.39,229 654.24,220.93 636.34,215.5 566.39,196 563.29,195.13 560.09,\ +194.17 556.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,9 @@ digraph { width=1.2277]; "gene to pathway association" -> iri [color=blue, label=iri, - lp="852.39,221.5", - pos="e,652.29,190.23 2619.1,264.56 2235.9,265.57 1188.2,264.85 844.39,229 766.98,220.93 747.81,215.26 672.39,196 669.02,195.14 665.54,\ -194.18 662.05,193.17", + lp="846.39,221.5", + pos="e,652.3,190.2 2401,264.3 2048,264.51 1139.4,261.76 838.39,229 763.61,220.86 745.22,214.85 672.39,196 669.02,195.13 665.54,194.16 \ +662.06,193.15", style=solid]; name [color=blue, height=0.5, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "gene to pathway association" -> name [color=blue, label=name, - lp="964.39,221.5", - pos="e,777.39,191.26 2619.9,263 2221.5,259.95 1108.4,249.67 944.39,229 889.75,222.11 828.59,206.19 787.21,194.15", + lp="954.39,221.5", + pos="e,776.19,191.4 2401.9,262.76 2036,259.28 1077.3,248.43 934.39,229 882.75,221.98 825.11,206.29 785.78,194.35", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "gene to pathway association" -> description [color=blue, label=description, - lp="1092.9,221.5", - pos="e,925.8,193.64 2619.4,263.33 2237.1,261.22 1204.7,253.3 1052.4,229 1012,222.56 967.8,208.65 935.45,197.13", + lp="1075.9,221.5", + pos="e,922.95,194.11 2401.5,263.16 2051.8,260.75 1167.3,252.39 1035.4,229 999.74,222.68 961.04,209.22 932.29,197.87", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "gene to pathway association" -> "has attribute" [color=blue, label="has attribute", - lp="1250.4,221.5", - pos="e,1067,191.74 2619.8,262.95 2262.1,259.98 1340.8,250.36 1203.4,229 1159.3,222.14 1110.5,206.98 1076.6,195.14", + lp="1222.4,221.5", + pos="e,1063.7,192.78 2401.9,262.88 2076.4,259.95 1293.4,250.72 1175.4,229 1139.8,222.44 1101.1,208.32 1073.1,196.75", style=solid]; predicate [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=2.1665]; "gene to pathway association" -> predicate [color=blue, label=predicate, - lp="1410.4,221.5", - pos="e,1224.6,193.08 2619,264.47 2315.3,264.81 1612.8,261.87 1376.4,229 1327.6,222.22 1273.5,207.75 1234.6,196.12", + lp="1366.4,221.5", + pos="e,1216.9,194.04 2402.6,262.23 2105.8,258.16 1435.1,247.09 1332.4,229 1295.9,222.57 1256.1,209.12 1226.6,197.79", style=solid]; negated [color=blue, height=0.5, @@ -87,8 +87,8 @@ digraph { width=1.2999]; "gene to pathway association" -> negated [color=blue, label=negated, - lp="1555.4,221.5", - pos="e,1359,190.21 2619.5,263.41 2341.5,261.69 1733.8,254.98 1526.4,229 1471.1,222.07 1409.1,205.34 1368.5,193.13", + lp="1484.4,221.5", + pos="e,1352,192.62 2402.9,262.08 2129.7,257.96 1545.7,247.16 1455.4,229 1422.5,222.38 1387,208.39 1361.3,196.89", style=solid]; qualifiers [color=blue, height=0.5, @@ -97,8 +97,8 @@ digraph { width=2.1304]; "gene to pathway association" -> qualifiers [color=blue, label=qualifiers, - lp="1690.9,221.5", - pos="e,1507.9,193 2619.6,263.44 2364.7,261.77 1838.8,255.16 1657.4,229 1609.4,222.07 1556,207.62 1517.8,196.03", + lp="1585.9,221.5", + pos="e,1486.9,195.38 2402,262.77 2147.5,260.01 1631.7,251.67 1552.4,229 1532,223.18 1511.4,211.62 1495.4,201.08", style=solid]; publications [color=blue, height=0.5, @@ -107,8 +107,8 @@ digraph { width=1.7332]; "gene to pathway association" -> publications [color=blue, label=publications, - lp="1831.4,221.5", - pos="e,1658.1,192.76 2619.4,263.39 2388.8,261.65 1943,254.93 1787.4,229 1746.1,222.11 1700.6,207.8 1667.9,196.25", + lp="1676.4,221.5", + pos="e,1620.9,196.02 2401.6,263.11 2152.8,260.91 1661.1,253.48 1632.4,229 1625.8,223.37 1622.8,214.71 1621.6,206.17", style=solid]; "has evidence" [color=blue, height=0.5, @@ -117,263 +117,264 @@ digraph { width=2.0943]; "gene to pathway association" -> "has evidence" [color=blue, label="has evidence", - lp="1982.9,221.5", - pos="e,1815.4,193.77 2620,262.5 2419.7,259.6 2063.5,251.39 1936.4,229 1898,222.24 1856.1,208.65 1825,197.35", + lp="1774.9,221.5", + pos="e,1747,194.37 2401.8,262.94 2174.5,260.54 1751.3,252.87 1728.4,229 1719.2,219.42 1726.7,209.02 1738.4,200.2", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1980.4,178", - width=3.015]; + label=string, + pos="1910.4,178", + width=1.0652]; "gene to pathway association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2128.9,221.5", - pos="e,2001.8,195.77 2618.9,264.91 2445.7,264.61 2164.4,259.21 2064.4,229 2045.1,223.17 2025.6,212 2010.3,201.69", + lp="1892.9,221.5", + pos="e,1881.1,189.71 2402.8,262.04 2200.1,258.5 1847.9,249.45 1828.4,229 1823.8,224.17 1824.7,219.56 1828.4,214 1831.1,209.87 1851.6,\ +201.11 1871.5,193.39", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2215.4,178", - width=3.015]; + label=string, + pos="2005.4,178", + width=1.0652]; "gene to pathway association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2296.4,221.5", - pos="e,2203.3,196.25 2624.4,260.09 2463.2,254.8 2215.7,244.25 2201.4,229 2195.4,222.6 2196,213.84 2199,205.44", + lp="2059.4,221.5", + pos="e,1982.4,192.58 2405.7,260.37 2239.2,255.3 1979.3,244.88 1964.4,229 1955.4,219.44 1963.2,208.17 1974.3,198.76", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2450.4,178", - width=3.015]; + label=string, + pos="2147.4,178", + width=1.0652]; "gene to pathway association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2504.9,221.5", - pos="e,2416.3,195.1 2625.5,259.6 2529,255.02 2413.9,246.05 2398.4,229 2389.6,219.36 2396.6,209.3 2407.9,200.75", + lp="2276.9,221.5", + pos="e,2150.7,196.22 2412,258.07 2312.7,252.52 2190.1,242.98 2170.4,229 2162.6,223.46 2157.4,214.59 2153.9,205.85", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2632.4,178", + pos="2373.4,178", width=1.5346]; "gene to pathway association" -> timepoint [color=blue, label=timepoint, - lp="2654.4,221.5", - pos="e,2621.3,195.8 2671.6,250.98 2647.9,245.61 2626.8,238.39 2619.4,229 2614.1,222.2 2614.6,213.44 2617.3,205.16", + lp="2435.4,221.5", + pos="e,2378.6,196.25 2446.1,251.82 2429.7,246.64 2413.7,239.31 2400.4,229 2392.7,223.04 2386.9,214.23 2382.7,205.66", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2744.4,178", + pos="2485.4,178", width=1.0652]; "gene to pathway association" -> "original subject" [color=blue, label="original subject", - lp="2751.4,221.5", - pos="e,2718.3,191.31 2715.2,247.95 2707.3,243.1 2700.1,236.89 2695.4,229 2688.1,216.95 2697.5,205.59 2709.8,196.74", + lp="2533.4,221.5", + pos="e,2477.4,195.83 2497.2,247.95 2489.3,243.1 2482.1,236.89 2477.4,229 2473.2,222.01 2473.1,213.51 2474.7,205.53", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2858.4,178", + pos="2611.4,178", width=1.5887]; "gene to pathway association" -> "original predicate" [color=blue, label="original predicate", - lp="2886.9,221.5", - pos="e,2842.4,195.75 2784.8,247.1 2792.2,241.53 2800.3,235.17 2807.4,229 2816.8,220.85 2826.7,211.38 2835.2,202.9", + lp="2661.9,221.5", + pos="e,2606.2,196.38 2570.2,247.16 2577.1,241.95 2584.1,235.78 2589.4,229 2594.8,222.12 2599.2,213.69 2602.6,205.72", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2972.4,178", + pos="2745.4,178", width=1.0652]; "gene to pathway association" -> "original object" [color=blue, label="original object", - lp="3016.9,221.5", - pos="e,2970.6,196.32 2871.5,253.58 2907.1,248.21 2941,240.33 2954.4,229 2961.2,223.24 2965.4,214.7 2968.1,206.3", + lp="2791.9,221.5", + pos="e,2744.3,196.25 2651.2,253.21 2685.1,247.83 2716.9,240.04 2729.4,229 2736,223.17 2739.9,214.61 2742.2,206.21", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3105.4,178", + pos="2878.4,178", width=2.1304]; "gene to pathway association" -> "subject category" [color=blue, label="subject category", - lp="3147.9,221.5", - pos="e,3098.6,196.3 2864.4,252.47 2954.8,242.34 3072.1,229.17 3072.4,229 3081.5,223.43 3088.6,214.32 3093.8,205.38", + lp="2921.9,221.5", + pos="e,2872.3,196.26 2645.8,252.47 2733.7,242.54 2846.3,229.69 2847.4,229 2856.2,223.4 2863,214.27 2867.8,205.34", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3276.4,178", + pos="3049.4,178", width=2.1304]; "gene to pathway association" -> "object category" [color=blue, label="object category", - lp="3292.9,221.5", - pos="e,3260.5,195.7 2861.1,252.12 2878.5,250.25 2896.5,248.46 2913.4,247 2979.5,241.31 3149.3,252.25 3211.4,229 3226.8,223.24 3241.5,\ -212.52 3253,202.48", + lp="3066.9,221.5", + pos="e,3033.8,195.69 2643.1,252.14 2660.5,250.27 2678.5,248.47 2695.4,247 2759.7,241.41 2925,251.9 2985.4,229 3000.5,223.29 3014.8,212.71 \ +3026.1,202.75", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3409.4,178", + pos="3182.4,178", width=1.0652]; "gene to pathway association" -> "subject closure" [color=blue, label="subject closure", - lp="3429.9,221.5", - pos="e,3396.3,195.29 2859.8,251.97 2877.6,250.08 2896.1,248.32 2913.4,247 2962.1,243.28 3307.1,247.13 3352.4,229 3366.4,223.39 3379.3,\ -212.76 3389.3,202.74", + lp="3203.9,221.5", + pos="e,3169.6,195.29 2641.8,251.98 2659.6,250.09 2678.1,248.33 2695.4,247 2743.2,243.33 3082,247.01 3126.4,229 3140.3,223.38 3152.9,212.75 \ +3162.7,202.73", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3509.4,178", + pos="3290.4,178", width=1.0652]; "gene to pathway association" -> "object closure" [color=blue, label="object closure", - lp="3551.4,221.5", - pos="e,3506.9,196.38 2859.4,251.87 2877.3,249.98 2895.9,248.25 2913.4,247 2945.3,244.72 3462.1,247.1 3488.4,229 3496.2,223.65 3501.1,\ -214.82 3504.2,206.06", + lp="3326.4,221.5", + pos="e,3285.7,196.04 2641.4,251.88 2659.3,249.99 2677.9,248.25 2695.4,247 2726.8,244.75 3235.5,245.37 3262.4,229 3271.2,223.63 3277.5,\ +214.38 3281.8,205.29", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3642.4,178", + pos="3423.4,178", width=2.1304]; "gene to pathway association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3709.9,221.5", - pos="e,3634.7,196.2 2859,251.84 2877.1,249.94 2895.8,248.21 2913.4,247 2951.8,244.36 3571.3,246.75 3605.4,229 3615.6,223.71 3623.7,214.22 \ -3629.6,204.91", + lp="3486.9,221.5", + pos="e,3413.8,196.26 2641,251.84 2659.1,249.94 2677.8,248.21 2695.4,247 2733.4,244.38 3346,245.33 3380.4,229 3391.5,223.74 3400.8,214.11 \ +3407.9,204.71", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3834.4,178", + pos="3616.4,178", width=2.1304]; "gene to pathway association" -> "object category closure" [color=blue, label="object category closure", - lp="3900.9,221.5", - pos="e,3828.1,196.16 2858.6,251.8 2876.8,249.89 2895.6,248.17 2913.4,247 2962.6,243.75 3758.2,252.82 3801.4,229 3811,223.73 3818.2,214.37 \ -3823.5,205.16", + lp="3678.9,221.5", + pos="e,3608.4,196.23 2640.6,251.8 2658.8,249.89 2677.6,248.17 2695.4,247 2744.4,243.77 3534.7,251.25 3578.4,229 3588.7,223.75 3597,214.27 \ +3603.2,204.96", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4024.4,178", + pos="3806.4,178", width=1.0652]; "gene to pathway association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4073.4,221.5", - pos="e,4017.3,195.73 2858.2,251.79 2876.5,249.87 2895.5,248.15 2913.4,247 2943.2,245.09 3961.9,242.84 3988.4,229 3998.6,223.67 4006.6,\ -213.98 4012.4,204.55", + lp="3852.4,221.5", + pos="e,3798.1,195.78 2640.2,251.79 2658.5,249.87 2677.5,248.15 2695.4,247 2754.8,243.19 3713,255.23 3766.4,229 3777.2,223.67 3786.1,213.85 \ +3792.7,204.32", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4183.4,178", + pos="3965.4,178", width=1.0652]; "gene to pathway association" -> "object namespace" [color=blue, label="object namespace", - lp="4227.4,221.5", - pos="e,4175.7,195.76 2858.2,251.76 2876.5,249.84 2895.5,248.13 2913.4,247 2947.6,244.85 4114.8,244.43 4145.4,229 4155.9,223.71 4164.2,\ -214.03 4170.4,204.59", + lp="4006.4,221.5", + pos="e,3956.8,195.8 2640.2,251.76 2658.5,249.84 2677.5,248.13 2695.4,247 2729.5,244.85 3893.6,243.83 3924.4,229 3935.4,223.7 3944.4,213.88 \ +3951.2,204.34", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4334.4,178", + pos="4116.4,178", width=1.0652]; "gene to pathway association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4387.4,221.5", - pos="e,4326.4,195.78 2858.2,251.73 2876.5,249.82 2895.5,248.11 2913.4,247 2951.7,244.61 4261,246.07 4295.4,229 4306.1,223.68 4314.8,213.86 \ -4321.2,204.32", + lp="4168.4,221.5", + pos="e,4107.5,195.81 2640.2,251.74 2658.5,249.82 2677.5,248.11 2695.4,247 2733.6,244.62 4039.8,245.41 4074.4,229 4085.5,223.72 4094.8,\ +213.91 4101.7,204.36", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4505.4,178", + pos="4287.4,178", width=1.0652]; "gene to pathway association" -> "object label closure" [color=blue, label="object label closure", - lp="4553.9,221.5", - pos="e,4497.1,195.8 2858.2,251.71 2876.5,249.8 2895.5,248.1 2913.4,247 2956.4,244.35 4426.6,247.9 4465.4,229 4476.3,223.7 4485.1,213.89 \ -4491.7,204.34", + lp="4335.9,221.5", + pos="e,4278.8,195.81 2640.2,251.71 2658.5,249.8 2677.5,248.1 2695.4,247 2738.4,244.35 4207.6,247.66 4246.4,229 4257.4,223.72 4266.4,213.9 \ +4273.2,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4667.4,178", + pos="4449.4,178", width=2.347]; "gene to pathway association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4715.9,221.5", - pos="e,4658.8,196.3 2857.8,251.74 2876.2,249.81 2895.4,248.1 2913.4,247 2960.9,244.1 4584.6,249.85 4627.4,229 4638.1,223.78 4646.9,214.17 \ -4653.4,204.75", + lp="4497.9,221.5", + pos="e,4440.8,196.3 2639.8,251.74 2658.2,249.81 2677.4,248.1 2695.4,247 2742.9,244.1 4366.6,249.85 4409.4,229 4420.1,223.78 4428.9,214.17 \ +4435.4,204.75", style=solid]; type [height=0.5, - pos="4801.4,178", + pos="4583.4,178", width=0.86659]; "gene to pathway association" -> type [color=blue, label=type, - lp="4815.4,221.5", - pos="e,4802.2,196.19 2857.8,251.73 2876.2,249.8 2895.4,248.09 2913.4,247 2939.4,245.42 4769,245.23 4789.4,229 4796.2,223.54 4799.6,214.93 \ -4801.2,206.37", + lp="4597.4,221.5", + pos="e,4584.2,196.19 2639.8,251.73 2658.2,249.8 2677.4,248.09 2695.4,247 2721.4,245.42 4551,245.23 4571.4,229 4578.2,223.54 4581.6,214.93 \ +4583.2,206.37", style=solid]; category [height=0.5, - pos="4902.4,178", + pos="4684.4,178", width=1.4263]; "gene to pathway association" -> category [color=blue, label=category, - lp="4895.9,221.5", - pos="e,4886.8,195.26 2857.8,251.72 2876.2,249.8 2895.4,248.09 2913.4,247 2966.7,243.78 4784.8,246.06 4835.4,229 4851.6,223.54 4867.1,\ -212.51 4879.1,202.2", + lp="4677.9,221.5", + pos="e,4668.8,195.26 2639.8,251.72 2658.2,249.8 2677.4,248.09 2695.4,247 2748.7,243.78 4566.8,246.06 4617.4,229 4633.6,223.54 4649.1,\ +212.51 4661.1,202.2", style=solid]; subject [height=0.5, - pos="5016.4,178", + pos="4798.4,178", width=1.2277]; "gene to pathway association" -> subject [color=blue, label=subject, - lp="4992.4,221.5", - pos="e,4997.1,194.33 2857.8,251.72 2876.2,249.79 2895.4,248.09 2913.4,247 3025.3,240.26 4823.4,258.94 4931.4,229 4952.1,223.25 4973,211.09 \ -4988.9,200.2", + lp="4774.4,221.5", + pos="e,4779.1,194.33 2639.8,251.72 2658.2,249.79 2677.4,248.09 2695.4,247 2807.3,240.26 4605.4,258.94 4713.4,229 4734.1,223.25 4755,211.09 \ +4770.9,200.2", style=solid]; object [height=0.5, - pos="5059.4,91", + pos="4841.4,91", width=1.0832]; "gene to pathway association" -> object [color=blue, label=object, - lp="5103.4,178", - pos="e,5072.8,108.09 2857.8,251.71 2876.2,249.79 2895.4,248.08 2913.4,247 2971.9,243.49 4966.6,246.89 5022.4,229 5046.7,221.21 5055,217.1 \ -5069.4,196 5083.3,175.59 5079.5,166.51 5082.4,142 5083.2,135.38 5084.3,133.39 5082.4,127 5081.4,123.55 5079.9,120.13 5078.1,116.85", + lp="4885.4,178", + pos="e,4854.8,108.09 2639.8,251.71 2658.2,249.79 2677.4,248.08 2695.4,247 2753.9,243.49 4748.6,246.89 4804.4,229 4828.7,221.21 4837,217.1 \ +4851.4,196 4865.3,175.59 4861.5,166.51 4864.4,142 4865.2,135.38 4866.3,133.39 4864.4,127 4863.4,123.55 4861.9,120.13 4860.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2960.4,265", + pos="2742.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3091.4,265", + pos="2873.4,265", width=2.0762]; subject -> object [label=relation, - lp="5054.4,134.5", - pos="e,5041.5,107.23 5017.5,159.55 5018.7,149.57 5021.2,137.07 5026.4,127 5028.6,122.68 5031.5,118.52 5034.7,114.66"]; + lp="4836.4,134.5", + pos="e,4823.5,107.23 4799.5,159.55 4800.7,149.57 4803.2,137.07 4808.4,127 4810.6,122.68 4813.5,118.52 4816.7,114.66"]; relation [height=0.5, - pos="5004.4,18", + pos="4786.4,18", width=1.2999]; - subject -> relation [pos="e,5005.7,36.188 5015.1,159.79 5013,132.48 5009,78.994 5006.5,46.38", + subject -> relation [pos="e,4787.7,36.188 4797.1,159.79 4795,132.48 4791,78.994 4788.5,46.38", style=dotted]; "gene to pathway association_subject" [color=blue, height=0.5, label="gene or gene product", - pos="3294.4,265", + pos="3076.4,265", width=3.0692]; - object -> relation [pos="e,5017.2,35.54 5046.9,73.889 5040,64.939 5031.2,53.617 5023.4,43.584", + object -> relation [pos="e,4799.2,35.54 4828.9,73.889 4822,64.939 4813.2,53.617 4805.4,43.584", style=dotted]; "gene to pathway association_object" [color=blue, height=0.5, label=pathway, - pos="3473.4,265", + pos="3255.4,265", width=1.3902]; } diff --git a/graphviz/gene_to_pathway_association.svg b/graphviz/gene_to_pathway_association.svg index 3db14ac7c7..86fb8dd682 100644 --- a/graphviz/gene_to_pathway_association.svg +++ b/graphviz/gene_to_pathway_association.svg @@ -4,16 +4,16 @@ - + %3 - + gene to pathway association - -gene to pathway association + +gene to pathway association @@ -24,9 +24,9 @@ gene to pathway association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ gene to pathway association->gene to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ gene to pathway association->id - - -id + + +id @@ -63,9 +63,9 @@ gene to pathway association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ gene to pathway association->name - - -name + + +name @@ -89,9 +89,9 @@ gene to pathway association->description - - -description + + +description @@ -102,9 +102,9 @@ gene to pathway association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ gene to pathway association->predicate - - -predicate + + +predicate @@ -128,9 +128,9 @@ gene to pathway association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ gene to pathway association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ gene to pathway association->publications - - -publications + + +publications @@ -167,344 +167,344 @@ gene to pathway association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string gene to pathway association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string gene to pathway association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string gene to pathway association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type gene to pathway association->timepoint - - -timepoint + + +timepoint original subject - -string + +string gene to pathway association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie gene to pathway association->original predicate - - -original predicate + + +original predicate original object - -string + +string gene to pathway association->original object - - -original object + + +original object subject category - -ontology class + +ontology class gene to pathway association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class gene to pathway association->object category - - -object category + + +object category subject closure - -string + +string gene to pathway association->subject closure - - -subject closure + + +subject closure object closure - -string + +string gene to pathway association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class gene to pathway association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class gene to pathway association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string gene to pathway association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string gene to pathway association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string gene to pathway association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string gene to pathway association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source gene to pathway association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type gene to pathway association->type - - -type + + +type category - -category + +category gene to pathway association->category - - -category + + +category subject - -subject + +subject gene to pathway association->subject - - -subject + + +subject object - -object + +object gene to pathway association->object - - -object + + +object association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + gene to pathway association_subject - -gene or gene product + +gene or gene product object->relation - - + + gene to pathway association_object - -pathway + +pathway diff --git a/graphviz/gene_to_phenotype_association.gv b/graphviz/gene_to_phenotype_association.gv index eb0b08e17c..135fdc8c9a 100644 --- a/graphviz/gene_to_phenotype_association.gv +++ b/graphviz/gene_to_phenotype_association.gv @@ -1,367 +1,500 @@ digraph { - graph [bb="0,0,4878.7,283"]; + graph [bb="0,0,7126.1,283"]; node [label="\N"]; "gene to phenotype association" [height=0.5, label="gene to phenotype association", - pos="2498.4,265", + pos="3944.1,265", width=4.2066]; - association [height=0.5, - pos="62.394,178", - width=1.7332]; - "gene to phenotype association" -> association [label=is_a, - lp="280.39,221.5", - pos="e,102.91,191.79 2347.1,263.6 1878.7,262.07 470.95,255.33 266.39,229 213.1,222.14 153.57,206.61 112.64,194.67"]; + "gene to disease or phenotypic feature association" [height=0.5, + pos="241.13,178", + width=6.698]; + "gene to phenotype association" -> "gene to disease or phenotypic feature association" [label=is_a, + lp="1056.1,221.5", + pos="e,401.34,191.5 3793.1,263.13 3277.1,260.02 1585.8,248.55 1042.1,229 824.25,221.17 573.47,204.23 411.4,192.24"]; + "entity to phenotypic feature association mixin" [height=0.5, + pos="724.13,178", + width=6.2286]; + "gene to phenotype association" -> "entity to phenotypic feature association mixin" [label=uses, + lp="1285.6,221.5", + pos="e,847.31,193.08 3793.1,263.58 3303.9,261.99 1765.8,254.99 1269.1,229 1128.3,221.63 967.69,206.01 857.48,194.18"]; + "gene to entity association mixin" [height=0.5, + pos="1125.1,178", + width=4.4232]; + "gene to phenotype association" -> "gene to entity association mixin" [label=uses, + lp="1436.6,221.5", + pos="e,1196,194.16 3793.1,263.26 3285,260.59 1655.4,250.44 1420.1,229 1347.1,222.35 1265,207.84 1206,196.16"]; id [color=blue, height=0.5, label=string, - pos="181.39,178", + pos="1341.1,178", width=1.0652]; "gene to phenotype association" -> id [color=blue, label=id, - lp="396.39,221.5", - pos="e,210.38,189.98 2347.6,263.13 1897.4,260.29 581.96,250.27 389.39,229 317.23,221.03 299.34,215.5 229.39,196 226.29,195.13 223.09,\ -194.17 219.89,193.15", + lp="1554.1,221.5", + pos="e,1370.1,189.97 3793.1,263.47 3301.9,261.53 1769,253.56 1547.1,229 1475.8,221.11 1458.2,215.35 1389.1,196 1386,195.13 1382.8,194.16 \ +1379.6,193.14", style=solid]; iri [color=blue, height=0.5, label="iri type", - pos="282.39,178", + pos="1442.1,178", width=1.2277]; "gene to phenotype association" -> iri [color=blue, label=iri, - lp="503.39,221.5", - pos="e,315.31,190.16 2347.5,262.98 1912.9,259.82 677.2,249.16 495.39,229 423.23,221 405.62,214.45 335.39,196 332.02,195.11 328.55,194.14 \ -325.06,193.12", + lp="1659.1,221.5", + pos="e,1475.1,190.13 3793,263.39 3316.1,261.22 1862.3,252.72 1651.1,229 1580.7,221.09 1563.6,214.18 1495.1,196 1491.8,195.11 1488.3,194.12 \ +1484.8,193.1", style=solid]; name [color=blue, height=0.5, label="label type", - pos="401.39,178", + pos="1561.1,178", width=1.5707]; "gene to phenotype association" -> name [color=blue, label=name, - lp="607.39,221.5", - pos="e,438.25,191.77 2347.3,263.35 1926.2,261.26 759.22,253.29 587.39,229 538.92,222.15 485.05,206.78 447.81,194.87", + lp="1761.1,221.5", + pos="e,1597.1,191.92 3792.8,263.83 3328.2,262.99 1942.3,258.05 1741.1,229 1694.5,222.26 1642.8,207.06 1606.8,195.18", style=solid]; description [color=blue, height=0.5, label="narrative text", - pos="551.39,178", + pos="1711.1,178", width=2.0943]; "gene to phenotype association" -> description [color=blue, label=description, - lp="723.89,221.5", - pos="e,582.77,194.4 2347.1,264.05 1940.6,263.75 844.21,260.04 683.39,229 651.71,222.88 617.7,209.83 592.13,198.6", + lp="1873.6,221.5", + pos="e,1740.7,194.79 3793.6,263.03 3326.6,259.83 1928.7,248.65 1833.1,229 1804.2,223.04 1773.4,210.36 1750,199.27", style=solid]; "has attribute" [color=blue, height=0.5, label=attribute, - pos="696.39,178", + pos="1856.1,178", width=1.4443]; "gene to phenotype association" -> "has attribute" [color=blue, label="has attribute", - lp="862.39,221.5", - pos="e,722.86,193.55 2347,264.09 1961.5,263.87 962.53,260.25 815.39,229 786.11,222.78 754.98,209.44 731.91,198.1", - style=solid]; - subject [color=blue, - height=0.5, - label="named thing", - pos="836.39,178", - width=1.9318]; - "gene to phenotype association" -> subject [color=blue, - label=subject, - lp="989.39,221.5", - pos="e,866.52,194.37 2347.3,263.57 1986.8,262.1 1096.3,255.78 963.39,229 932.94,222.86 900.37,209.9 875.84,198.71", - style=solid]; - predicate [color=blue, - height=0.5, - label="predicate type", - pos="1002.4,178", - width=2.1665]; - "gene to phenotype association" -> predicate [color=blue, - label=predicate, - lp="1068.4,221.5", - pos="e,1008.4,196.14 2347,264.19 1984.3,264.13 1090.8,260.75 1034.4,229 1025,223.69 1017.9,214.33 1012.8,205.13", - style=solid]; - object [color=blue, - height=0.5, - label="named thing", - pos="934.39,91", - width=1.9318]; - "gene to phenotype association" -> object [color=blue, - label=object, - lp="1147.4,178", - pos="e,976.03,105.47 2349.3,261.73 2082.5,257.29 1533.3,246.34 1342.4,229 1245.2,220.17 1212.5,240.02 1125.4,196 1105.2,185.79 1108.1,\ -172.77 1089.4,160 1057.3,138.07 1017,120.64 985.5,108.92", + lp="2006.1,221.5", + pos="e,1880,194.29 3793.5,263.12 3345.6,260.27 2047.8,250.2 1959.1,229 1934.3,223.05 1908.4,210.46 1888.8,199.4", style=solid]; negated [color=blue, height=0.5, label=boolean, - pos="1225.4,178", + pos="1973.1,178", width=1.2999]; "gene to phenotype association" -> negated [color=blue, label=negated, - lp="1452.4,221.5", - pos="e,1260,190.37 2348,262.71 2095.6,259.93 1597.4,251.7 1423.4,229 1369.6,221.98 1309.4,205.49 1269.6,193.36", + lp="2139.1,221.5", + pos="e,2001.5,192.49 3792.8,263.98 3383.2,263.5 2273,259.4 2110.1,229 2075.4,222.53 2037.9,208.28 2010.9,196.64", style=solid]; qualifiers [color=blue, height=0.5, label="ontology class", - pos="1366.4,178", + pos="2114.1,178", width=2.1304]; "gene to phenotype association" -> qualifiers [color=blue, label=qualifiers, - lp="1585.9,221.5", - pos="e,1408.3,193.18 2348.2,262.57 2121.2,259.7 1701.2,251.46 1552.4,229 1506.1,222.01 1454.8,207.72 1417.8,196.19", + lp="2243.6,221.5", + pos="e,2137.7,195.24 3793.6,262.83 3385.9,259.4 2286.1,248.41 2210.1,229 2187.6,223.26 2164.5,211.42 2146.6,200.71", style=solid]; publications [color=blue, height=0.5, label=publication, - pos="1523.4,178", + pos="2271.1,178", width=1.7332]; "gene to phenotype association" -> publications [color=blue, label=publications, - lp="1723.4,221.5", - pos="e,1558,193.06 2348.4,262.38 2147.9,259.39 1803.5,251.12 1679.4,229 1640.7,222.11 1598.4,208.11 1567.6,196.67", + lp="2337.1,221.5", + pos="e,2273.9,196.44 3793.6,262.94 3392.1,259.84 2324.1,249.67 2293.1,229 2285.2,223.72 2280.1,214.91 2276.9,206.14", style=solid]; "has evidence" [color=blue, height=0.5, label="evidence type", - pos="1679.4,178", + pos="2427.1,178", width=2.0943]; "gene to phenotype association" -> "has evidence" [color=blue, label="has evidence", - lp="1869.9,221.5", - pos="e,1713.8,194.06 2350.1,261.18 2182.5,257.14 1920.5,247.98 1823.4,229 1788.9,222.26 1751.4,209.05 1723.4,197.9", + lp="2435.6,221.5", + pos="e,2402.5,195.13 3793.2,263.37 3407.3,261.39 2413.5,253.88 2389.1,229 2381.1,220.76 2386.1,210.79 2394.9,201.94", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1881.4,178", - width=3.015]; + label=string, + pos="2559.1,178", + width=1.0652]; "gene to phenotype association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2009.9,221.5", - pos="e,1897.3,195.93 2346.9,264.39 2208.9,262.95 2016.2,255.89 1945.4,229 1930.4,223.32 1916.2,212.85 1904.9,202.96", + lp="2553.6,221.5", + pos="e,2530.2,189.84 3793.2,263.12 3425.6,260.62 2511.7,252.1 2489.1,229 2484.5,224.23 2485.6,219.67 2489.1,214 2493.1,207.6 2506.7,200.19 \ +2520.9,193.84", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2116.4,178", - width=3.015]; + label=string, + pos="2654.1,178", + width=1.0652]; "gene to phenotype association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2176.4,221.5", - pos="e,2093.1,195.58 2350.3,261.21 2238,257.51 2099.7,248.92 2081.4,229 2074.1,221.04 2078.2,211.47 2085.7,202.85", + lp="2721.1,221.5", + pos="e,2636.1,194.35 3793.7,262.73 3452.2,259.49 2646.3,249.67 2626.1,229 2618.6,221.28 2622.5,211.15 2629.4,202.02", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2351.4,178", - width=3.015]; + label=string, + pos="2796.1,178", + width=1.0652]; "gene to phenotype association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2385.9,221.5", - pos="e,2303,194.15 2363.9,256.71 2325.9,251.67 2291.5,243.21 2279.4,229 2269.3,217.19 2278.7,206.86 2293.6,198.69", + lp="2943.6,221.5", + pos="e,2804.8,195.72 3794.1,262.53 3501.5,259.21 2879.2,249.75 2837.1,229 2826.2,223.61 2817.1,213.78 2810.4,204.25", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2533.4,178", + pos="3023.1,178", width=1.5346]; "gene to phenotype association" -> timepoint [color=blue, label=timepoint, - lp="2534.4,221.5", - pos="e,2513.1,194.83 2495.7,246.69 2494.9,236.76 2495.1,224.26 2499.4,214 2501.1,209.95 2503.5,206.11 2506.2,202.56", + lp="3110.1,221.5", + pos="e,3035.1,195.77 3792.7,263.72 3561.1,262.42 3139.1,256.28 3075.1,229 3062.2,223.5 3050.6,213.23 3041.7,203.43", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2645.4,178", + pos="3135.1,178", width=1.0652]; "gene to phenotype association" -> "original subject" [color=blue, label="original subject", - lp="2647.4,221.5", - pos="e,2623.9,193.16 2534.2,247.4 2545.6,241.84 2558.2,235.42 2569.4,229 2570.6,228.29 2594.6,212.48 2615.4,198.82", + lp="3218.1,221.5", + pos="e,3139.5,195.97 3796.1,261.11 3576.8,256.31 3188.5,245.52 3162.1,229 3153.5,223.61 3147.5,214.49 3143.3,205.49", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2759.4,178", + pos="3260.1,178", width=1.5887]; "gene to phenotype association" -> "original predicate" [color=blue, label="original predicate", - lp="2789.9,221.5", - pos="e,2745.8,195.62 2622.3,254.63 2650.3,249.37 2679.1,241.31 2704.4,229 2717.2,222.76 2729.2,212.6 2738.7,203.05", + lp="3356.6,221.5", + pos="e,3266.5,196.03 3793.5,262.99 3614.7,260.69 3335.4,253.21 3293.1,229 3283.7,223.57 3276.4,214.18 3271.1,205", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2873.4,178", + pos="3389.1,178", width=1.0652]; "gene to phenotype association" -> "original object" [color=blue, label="original object", - lp="2917.9,221.5", - pos="e,2871.5,196.13 2606.6,252.37 2624.3,250.54 2642.3,248.69 2659.4,247 2702.7,242.72 2819.7,255.33 2854.4,229 2861.7,223.43 2866.2,\ -214.67 2869,206.03", + lp="3498.6,221.5", + pos="e,3402.6,195.15 3793,263.73 3670.1,261.61 3507.6,253.92 3447.1,229 3433,223.19 3419.9,212.54 3409.7,202.56", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3006.4,178", + pos="3522.1,178", width=2.1304]; "gene to phenotype association" -> "subject category" [color=blue, label="subject category", - lp="3048.9,221.5", - pos="e,3000,196.02 2604.4,252.08 2622.7,250.22 2641.6,248.45 2659.4,247 2694.2,244.16 2943.1,246.44 2973.4,229 2982.9,223.55 2990.1,214.16 \ -2995.4,204.98", + lp="3634.6,221.5", + pos="e,3535,195.99 3798.9,259.83 3713.3,255.52 3614.3,246.76 3575.1,229 3562.4,223.23 3550.8,213.13 3541.7,203.51", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3177.4,178", + pos="3693.1,178", width=2.1304]; "gene to phenotype association" -> "object category" [color=blue, label="object category", - lp="3195.9,221.5", - pos="e,3161.5,195.82 2603.1,251.94 2621.8,250.07 2641.2,248.32 2659.4,247 2709.6,243.35 3065,246.16 3112.4,229 3127.8,223.4 3142.6,212.7 \ -3154.1,202.62", + lp="3763.6,221.5", + pos="e,3693.8,196.34 3810.2,256.5 3766.2,251.47 3724.4,243.06 3708.1,229 3701.5,223.27 3697.7,214.73 3695.6,206.33", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3310.4,178", + pos="3826.1,178", width=1.0652]; "gene to phenotype association" -> "subject closure" [color=blue, label="subject closure", - lp="3333.9,221.5", - pos="e,3297.9,195.34 2602.2,251.88 2621.2,249.99 2640.9,248.25 2659.4,247 2725.5,242.52 3194,253.82 3255.4,229 3269.1,223.45 3281.6,212.83 \ -3291.2,202.8", + lp="3883.6,221.5", + pos="e,3822.6,196.01 3856.8,250.23 3846.1,245.14 3836.4,238.26 3829.1,229 3824.1,222.64 3822.3,214.28 3822.1,206.23", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3408.4,178", + pos="3939.1,178", width=1.0652]; "gene to phenotype association" -> "object closure" [color=blue, label="object closure", - lp="3450.4,221.5", - pos="e,3406.3,196.38 2601.8,251.84 2620.9,249.94 2640.7,248.21 2659.4,247 2699.8,244.37 3355.1,252.12 3388.4,229 3396.1,223.65 3400.8,\ -214.82 3403.7,206.06", + lp="3992.1,221.5", + pos="e,3940.1,196.18 3943.1,246.8 3942.4,235.16 3941.5,219.55 3940.7,206.24", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3541.4,178", + pos="4072.1,178", width=2.1304]; "gene to phenotype association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3608.9,221.5", - pos="e,3533.8,196.21 2601.8,251.79 2620.9,249.9 2640.7,248.18 2659.4,247 2706.3,244.03 3462.7,250.58 3504.4,229 3514.6,223.73 3522.7,\ -214.25 3528.7,204.94", + lp="4144.6,221.5", + pos="e,4066.4,196.41 4010.9,248.75 4023.2,243.84 4035.2,237.41 4045.1,229 4052.4,222.78 4058.1,214.06 4062.3,205.64", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3731.4,178", + pos="4265.1,178", width=2.1304]; "gene to phenotype association" -> "object category closure" [color=blue, label="object category closure", - lp="3798.9,221.5", - pos="e,3725.7,196.14 2601.3,251.77 2620.6,249.87 2640.6,248.15 2659.4,247 2688.3,245.23 3675.2,243.28 3700.4,229 3709.6,223.76 3716.5,\ -214.54 3721.3,205.43", + lp="4334.6,221.5", + pos="e,4259.7,196.22 4051.6,252.23 4133.2,243.12 4232.1,231.62 4236.1,229 4244.6,223.41 4250.9,214.41 4255.5,205.57", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3921.4,178", + pos="4455.1,178", width=1.0652]; "gene to phenotype association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3971.4,221.5", - pos="e,3914.7,195.72 2601.3,251.73 2620.6,249.83 2640.6,248.13 2659.4,247 2693.4,244.96 3856.3,244.96 3886.4,229 3896.5,223.66 3904.3,\ -213.97 3909.9,204.54", + lp="4506.1,221.5", + pos="e,4448.7,196.02 4050.1,252.07 4068.5,250.22 4087.3,248.44 4105.1,247 4140.3,244.15 4391.5,246.59 4422.1,229 4431.6,223.55 4438.8,\ +214.16 4444.1,204.98", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4080.4,178", + pos="4614.1,178", width=1.0652]; "gene to phenotype association" -> "object namespace" [color=blue, label="object namespace", - lp="4124.4,221.5", - pos="e,4073,195.76 2600.9,251.75 2620.3,249.83 2640.5,248.12 2659.4,247 2697.8,244.73 4009.2,246.53 4043.4,229 4053.7,223.7 4061.9,214.02 \ -4067.9,204.58", + lp="4659.1,221.5", + pos="e,4606.8,196.13 4048.8,251.91 4067.6,250.05 4086.9,248.31 4105.1,247 4157.6,243.24 4531.8,253.86 4578.1,229 4588.1,223.64 4596,214.13 \ +4601.8,204.84", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4231.4,178", + pos="4725.1,178", width=1.0652]; "gene to phenotype association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4284.4,221.5", - pos="e,4223.4,195.79 2600.9,251.73 2620.3,249.81 2640.5,248.11 2659.4,247 2701.9,244.51 4154.2,247.91 4192.4,229 4203.1,223.69 4211.8,\ -213.87 4218.2,204.33", + lp="4808.1,221.5", + pos="e,4731.5,196.07 4048,251.86 4067,249.98 4086.6,248.24 4105.1,247 4139.6,244.68 4703,253.8 4727.1,229 4733,222.98 4734.1,214.37 4733.3,\ +205.99", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4402.4,178", + pos="4820.1,178", width=1.0652]; "gene to phenotype association" -> "object label closure" [color=blue, label="object label closure", - lp="4450.9,221.5", - pos="e,4394.1,195.8 2600.9,251.71 2620.3,249.8 2640.5,248.1 2659.4,247 2706.6,244.26 4319.9,249.72 4362.4,229 4373.3,223.71 4382.1,213.89 \ -4388.7,204.35", + lp="4960.6,221.5", + pos="e,4850.6,188.95 4047.5,251.81 4066.7,249.92 4086.5,248.2 4105.1,247 4126.8,245.61 4871,244.52 4886.1,229 4899.6,215.21 4880.8,202.14 \ +4859.9,192.83", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4564.4,178", + pos="4961.1,178", width=2.347]; "gene to phenotype association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4612.9,221.5", - pos="e,4555.8,196.3 2600.9,251.69 2620.3,249.79 2640.5,248.09 2659.4,247 2711.1,244.03 4477.8,251.67 4524.4,229 4535.1,223.79 4543.9,\ -214.17 4550.4,204.76", + lp="5108.6,221.5", + pos="e,5007.2,193.16 4047.5,251.76 4066.6,249.87 4086.5,248.16 4105.1,247 4130.9,245.39 5016.1,247.43 5034.1,229 5046,216.91 5034.1,205.95 \ +5016.7,197.4", style=solid]; type [height=0.5, - pos="4726.4,178", + pos="5095.1,178", width=0.86659]; "gene to phenotype association" -> type [color=blue, label=type, - lp="4721.4,221.5", - pos="e,4718.1,195.81 2600.9,251.68 2620.3,249.77 2640.5,248.08 2659.4,247 2715.6,243.79 4635.8,253.62 4686.4,229 4697.3,223.72 4706.1,\ -213.9 4712.7,204.36", + lp="5202.1,221.5", + pos="e,5119.8,189.33 4047.1,251.76 4066.3,249.86 4086.3,248.15 4105.1,247 4135,245.18 5161.1,250.33 5182.1,229 5186.8,224.25 5185.9,219.51 \ +5182.1,214 5169.8,195.87 5156.5,204.2 5136.1,196 5133.9,195.1 5131.6,194.17 5129.3,193.22", style=solid]; category [height=0.5, - pos="4827.4,178", + pos="5196.1,178", width=1.4263]; "gene to phenotype association" -> category [color=blue, label=category, - lp="4807.9,221.5", - pos="e,4807.2,194.82 2600.9,251.68 2620.3,249.77 2640.5,248.08 2659.4,247 2717.1,243.71 4685.6,244.29 4741.4,229 4762.1,223.34 4782.9,\ -211.42 4798.9,200.65", + lp="5258.6,221.5", + pos="e,5213.6,194.94 4047.1,251.75 4066.3,249.85 4086.3,248.14 4105.1,247 4136.1,245.12 5200.4,251.12 5222.1,229 5229.4,221.63 5226.2,\ +211.83 5220,202.86", + style=solid]; + "subject aspect qualifier" [height=0.5, + pos="5384.1,178", + width=3.3039]; + "gene to phenotype association" -> "subject aspect qualifier" [color=blue, + label="subject aspect qualifier", + lp="5414.6,221.5", + pos="e,5361.4,195.77 4047.1,251.74 4066.3,249.84 4086.3,248.13 4105.1,247 4171.1,243.03 5230.3,246.05 5294.1,229 5315,223.43 5336.2,212.01 \ +5352.7,201.48", + style=solid]; + "object direction qualifier" [height=0.5, + pos="5646.1,178", + width=3.4664]; + "gene to phenotype association" -> "object direction qualifier" [color=blue, + label="object direction qualifier", + lp="5647.1,221.5", + pos="e,5609.7,195.31 4046.6,251.74 4066,249.83 4086.2,248.12 4105.1,247 4260.1,237.84 5349.2,255.8 5502.1,229 5535.9,223.07 5572.5,210.32 \ +5600.3,199.17", + style=solid]; + predicate [height=0.5, + pos="5843.1,178", + width=1.5165]; + "gene to phenotype association" -> predicate [color=blue, + label=predicate, + lp="5815.1,221.5", + pos="e,5819,194.34 4046.6,251.71 4066,249.8 4086.2,248.1 4105.1,247 4195.8,241.73 5650.7,249.66 5739.1,229 5764.2,223.14 5790.4,210.54 \ +5810.1,199.46", + style=solid]; + "frequency qualifier" [color=blue, + height=0.5, + label="frequency value", + pos="6001.1,178", + width=2.3651]; + "gene to phenotype association" -> "frequency qualifier" [color=blue, + label="frequency qualifier", + lp="5980.1,221.5", + pos="e,5965.8,194.48 4046.6,251.7 4066,249.79 4086.2,248.1 4105.1,247 4299,235.79 5661.6,261.49 5853.1,229 5888.8,222.95 5927.5,209.62 \ +5956.4,198.25", + style=solid]; + "severity qualifier" [color=blue, + height=0.5, + label="severity value", + pos="6180.1,178", + width=2.1123]; + "gene to phenotype association" -> "severity qualifier" [color=blue, + label="severity qualifier", + lp="6164.1,221.5", + pos="e,6149.5,194.61 4046.6,251.69 4066,249.78 4086.2,248.09 4105.1,247 4213.1,240.81 5945.9,249.52 6052.1,229 6082.7,223.09 6115.4,210.19 \ +6140.1,198.97", + style=solid]; + "onset qualifier" [color=blue, + height=0.5, + label=onset, + pos="6310.1,178", + width=1.011]; + "gene to phenotype association" -> "onset qualifier" [color=blue, + label="onset qualifier", + lp="6314.6,221.5", + pos="e,6292.5,193.84 4046.6,251.68 4066,249.77 4086.2,248.08 4105.1,247 4164,243.65 6172.4,245.35 6229.1,229 6249.2,223.22 6269.1,210.98 \ +6284.2,200.06", + style=solid]; + "sex qualifier" [color=blue, + height=0.5, + label="biological sex", + pos="6438.1,178", + width=2.0401]; + "gene to phenotype association" -> "sex qualifier" [color=blue, + label="sex qualifier", + lp="6443.1,221.5", + pos="e,6421.7,195.76 4046.6,251.67 4066,249.76 4086.2,248.07 4105.1,247 4167.9,243.44 6310.4,248.85 6370.1,229 6386.3,223.63 6401.8,212.83 \ +6413.9,202.64", + style=solid]; + "has count" [color=blue, + height=0.5, + label=integer, + pos="6574.1,178", + width=1.2277]; + "gene to phenotype association" -> "has count" [color=blue, + label="has count", + lp="6560.1,221.5", + pos="e,6555.4,194.34 4046.2,251.7 4065.7,249.78 4086,248.08 4105.1,247 4171.3,243.27 6427.3,246.99 6491.1,229 6511.3,223.31 6531.5,211.32 \ +6546.9,200.51", + style=solid]; + "has total" [color=blue, + height=0.5, + label=integer, + pos="6680.1,178", + width=1.2277]; + "gene to phenotype association" -> "has total" [color=blue, + label="has total", + lp="6664.6,221.5", + pos="e,6661.6,194.58 4046.2,251.7 4065.7,249.78 4086,248.07 4105.1,247 4174.3,243.11 6532.5,248.15 6599.1,229 6618.8,223.35 6638.4,211.48 \ +6653.3,200.73", + style=solid]; + "has quotient" [color=blue, + height=0.5, + label=double, + pos="6784.1,178", + width=1.1735]; + "gene to phenotype association" -> "has quotient" [color=blue, + label="has quotient", + lp="6780.1,221.5", + pos="e,6765.1,194.34 4046.2,251.69 4065.7,249.77 4086,248.07 4105.1,247 4177.1,242.96 6630.7,248.36 6700.1,229 6720.7,223.27 6741.3,211.11 \ +6757,200.22", + style=solid]; + "has percentage" [color=blue, + height=0.5, + label=double, + pos="6886.1,178", + width=1.1735]; + "gene to phenotype association" -> "has percentage" [color=blue, + label="has percentage", + lp="6909.1,221.5", + pos="e,6873.1,195.47 4046.2,251.69 4065.7,249.77 4086,248.07 4105.1,247 4180.7,242.77 6758.4,255.89 6829.1,229 6843.2,223.63 6856.2,213.03 \ +6866.1,202.97", + style=solid]; + subject [height=0.5, + pos="7008.1,178", + width=1.2277]; + "gene to phenotype association" -> subject [color=blue, + label=subject, + lp="7013.1,221.5", + pos="e,6999.8,195.82 4046.2,251.68 4065.7,249.76 4086,248.06 4105.1,247 4144.8,244.78 6932.3,246.34 6968.1,229 6979,223.73 6987.9,213.92 \ +6994.4,204.37", + style=solid]; + object [height=0.5, + pos="7051.1,91", + width=1.0832]; + "gene to phenotype association" -> object [color=blue, + label=object, + lp="7104.1,178", + pos="e,7064.5,108.09 4046.2,251.68 4065.7,249.76 4086,248.06 4105.1,247 4145.9,244.73 7008.1,249.94 7043.1,229 7083.8,204.69 7087.7,172.39 \ +7074.1,127 7073.1,123.55 7071.6,120.13 7069.9,116.85", style=solid]; - subject -> object [label=relation, - lp="919.39,134.5", - pos="e,915.56,108.34 855.29,160.61 870.2,147.68 891.19,129.47 907.8,115.07"]; - relation [height=0.5, - pos="848.39,18", - width=1.2999]; - subject -> relation [pos="e,847.09,36.188 837.7,159.79 839.78,132.48 843.84,78.994 846.31,46.38", - style=dotted]; - object -> relation [pos="e,867.35,34.647 914.45,73.533 902.81,63.922 887.97,51.669 875.3,41.213", - style=dotted]; association_type [color=blue, height=0.5, label=string, - pos="2706.4,265", + pos="4152.1,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2837.4,265", + pos="4283.1,265", width=2.0762]; + "gene to disease or phenotypic feature association_subject aspect qualifier" [color=blue, + height=0.5, + label=GeneOrGeneProductOrChemicalEntityAspectEnum, + pos="4625.1,265", + width=6.9147]; + "gene to disease or phenotypic feature association_object direction qualifier" [color=blue, + height=0.5, + label=DirectionQualifierEnum, + pos="5013.1,265", + width=3.358]; + "gene to disease or phenotypic feature association_predicate" [color=blue, + height=0.5, + label="predicate type", + pos="5230.1,265", + width=2.1665]; + subject -> object [label=relation, + lp="7046.1,134.5", + pos="e,7033.2,107.23 7009.2,159.55 7010.4,149.57 7012.9,137.07 7018.1,127 7020.4,122.68 7023.3,118.52 7026.5,114.66"]; + relation [height=0.5, + pos="6996.1,18", + width=1.2999]; + subject -> relation [pos="e,6997.4,36.188 7006.8,159.79 7004.7,132.48 7000.7,78.994 6998.2,46.38", + style=dotted]; + "gene to phenotype association_subject" [color=blue, + height=0.5, + label="gene or gene product", + pos="5436.1,265", + width=3.0692]; + object -> relation [pos="e,7008.9,35.54 7038.6,73.889 7031.7,64.939 7022.9,53.617 7015.2,43.584", + style=dotted]; + "gene to phenotype association_object" [color=blue, + height=0.5, + label="phenotypic feature", + pos="5663.1,265", + width=2.7442]; } diff --git a/graphviz/gene_to_phenotype_association.svg b/graphviz/gene_to_phenotype_association.svg index da67f70e96..9ada1271fb 100644 --- a/graphviz/gene_to_phenotype_association.svg +++ b/graphviz/gene_to_phenotype_association.svg @@ -4,482 +4,668 @@ - + %3 - + gene to phenotype association - -gene to phenotype association + +gene to phenotype association - + -association - -association +gene to disease or phenotypic feature association + +gene to disease or phenotypic feature association - + -gene to phenotype association->association - - -is_a +gene to phenotype association->gene to disease or phenotypic feature association + + +is_a - + +entity to phenotypic feature association mixin + +entity to phenotypic feature association mixin + + + +gene to phenotype association->entity to phenotypic feature association mixin + + +uses + + + +gene to entity association mixin + +gene to entity association mixin + + + +gene to phenotype association->gene to entity association mixin + + +uses + + + id - -string + +string - + gene to phenotype association->id - - -id + + +id - + iri - -iri type + +iri type - + gene to phenotype association->iri - - -iri + + +iri - + name - -label type + +label type - + gene to phenotype association->name - - -name + + +name - + description - -narrative text + +narrative text - + gene to phenotype association->description - - -description + + +description - + has attribute - -attribute + +attribute - -gene to phenotype association->has attribute - - -has attribute - - - -subject - -named thing - - - -gene to phenotype association->subject - - -subject - - - -predicate - -predicate type - - -gene to phenotype association->predicate - - -predicate - - - -object - -named thing - - - -gene to phenotype association->object - - -object +gene to phenotype association->has attribute + + +has attribute - + negated - -boolean + +boolean - + gene to phenotype association->negated - - -negated + + +negated - + qualifiers - -ontology class + +ontology class - + gene to phenotype association->qualifiers - - -qualifiers + + +qualifiers - + publications - -publication + +publication - + gene to phenotype association->publications - - -publications + + +publications - + has evidence - -evidence type + +evidence type - + gene to phenotype association->has evidence - - -has evidence + + +has evidence - + knowledge source - -information resource + +string - + gene to phenotype association->knowledge source - - -knowledge source + + +knowledge source - + primary knowledge source - -information resource + +string - + gene to phenotype association->primary knowledge source - - -primary knowledge source + + +primary knowledge source - + aggregator knowledge source - -information resource + +string - + gene to phenotype association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source - + timepoint - -time type + +time type - + gene to phenotype association->timepoint - - -timepoint + + +timepoint - + original subject - -string + +string - + gene to phenotype association->original subject - - -original subject + + +original subject - + original predicate - -uriorcurie + +uriorcurie - + gene to phenotype association->original predicate - - -original predicate + + +original predicate - + original object - -string + +string - + gene to phenotype association->original object - - -original object + + +original object - + subject category - -ontology class + +ontology class - + gene to phenotype association->subject category - - -subject category + + +subject category - + object category - -ontology class + +ontology class - + gene to phenotype association->object category - - -object category + + +object category - + subject closure - -string + +string - + gene to phenotype association->subject closure - - -subject closure + + +subject closure - + object closure - -string + +string - + gene to phenotype association->object closure - - -object closure + + +object closure - + subject category closure - -ontology class + +ontology class - + gene to phenotype association->subject category closure - - -subject category closure + + +subject category closure - + object category closure - -ontology class + +ontology class - + gene to phenotype association->object category closure - - -object category closure + + +object category closure - + subject namespace - -string + +string - + gene to phenotype association->subject namespace - - -subject namespace + + +subject namespace - + object namespace - -string + +string - + gene to phenotype association->object namespace - - -object namespace + + +object namespace - + subject label closure - -string + +string - + gene to phenotype association->subject label closure - - -subject label closure + + +subject label closure - + object label closure - -string + +string - + gene to phenotype association->object label closure - - -object label closure + + +object label closure - + retrieval source ids - -retrieval source + +retrieval source - + gene to phenotype association->retrieval source ids - - -retrieval source ids + + +retrieval source ids - + type - -type + +type - + gene to phenotype association->type - - -type + + +type - + category - -category + +category - + gene to phenotype association->category - - -category + + +category - + + +subject aspect qualifier + +subject aspect qualifier + + + +gene to phenotype association->subject aspect qualifier + + +subject aspect qualifier + + + +object direction qualifier + +object direction qualifier + + -subject->object - - -relation +gene to phenotype association->object direction qualifier + + +object direction qualifier - - -relation - -relation + + +predicate + +predicate - + -subject->relation - - +gene to phenotype association->predicate + + +predicate - + + +frequency qualifier + +frequency value + + -object->relation - - +gene to phenotype association->frequency qualifier + + +frequency qualifier + + + +severity qualifier + +severity value + + + +gene to phenotype association->severity qualifier + + +severity qualifier + + + +onset qualifier + +onset + + + +gene to phenotype association->onset qualifier + + +onset qualifier + + + +sex qualifier + +biological sex + + + +gene to phenotype association->sex qualifier + + +sex qualifier + + + +has count + +integer + + + +gene to phenotype association->has count + + +has count + + + +has total + +integer + + + +gene to phenotype association->has total + + +has total + + + +has quotient + +double + + + +gene to phenotype association->has quotient + + +has quotient + + + +has percentage + +double + + + +gene to phenotype association->has percentage + + +has percentage + + + +subject + +subject + + + +gene to phenotype association->subject + + +subject + + + +object + +object + + + +gene to phenotype association->object + + +object - + association_type - -string + +string - + association_category - -category type + +category type + + + +gene to disease or phenotypic feature association_subject aspect qualifier + +GeneOrGeneProductOrChemicalEntityAspectEnum + + + +gene to disease or phenotypic feature association_object direction qualifier + +DirectionQualifierEnum + + + +gene to disease or phenotypic feature association_predicate + +predicate type + + + +subject->object + + +relation + + + +relation + +relation + + + +subject->relation + + + + + +gene to phenotype association_subject + +gene or gene product + + + +object->relation + + + + + +gene to phenotype association_object + +phenotypic feature diff --git a/graphviz/genomic_sequence_localization.gv b/graphviz/genomic_sequence_localization.gv index 977d0a298c..c0208b7096 100644 --- a/graphviz/genomic_sequence_localization.gv +++ b/graphviz/genomic_sequence_localization.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,5599.1,283"]; + graph [bb="0,0,5414.1,283"]; node [label="\N"]; "genomic sequence localization" [height=0.5, label="genomic sequence localization", - pos="2895.5,265", + pos="2710.5,265", width=4.2066]; "sequence association" [height=0.5, pos="108.54,178", width=3.015]; "genomic sequence localization" -> "sequence association" [label=is_a, lp="372.54,221.5", - pos="e,165.17,193.42 2744.2,263.53 2233.8,261.73 594.74,254.03 358.54,229 295.61,222.33 225,207.52 174.91,195.73"]; + pos="e,165.18,193.4 2559.4,263.35 2074.3,261.06 575.86,252.15 358.54,229 295.62,222.3 225,207.49 174.91,195.71"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "genomic sequence localization" -> id [color=blue, label=id, - lp="488.54,221.5", - pos="e,302.53,189.98 2744.3,263.47 2250.6,261.51 705.1,253.45 481.54,229 409.36,221.11 391.48,215.5 321.54,196 318.43,195.13 315.23,194.17 \ -312.04,193.15", + lp="487.54,221.5", + pos="e,302.53,189.98 2559.5,263.28 2091.5,260.83 685.35,251.66 480.54,229 408.81,221.06 391.05,215.43 321.54,196 318.43,195.13 315.24,\ +194.17 312.04,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "genomic sequence localization" -> iri [color=blue, label=iri, - lp="601.54,221.5", - pos="e,407.45,190.2 2744.6,263.29 2266.8,260.83 805.81,251.53 593.54,229 518.74,221.06 500.36,214.85 427.54,196 424.16,195.13 420.69,\ -194.16 417.2,193.15", + lp="593.54,221.5", + pos="e,407.46,190.15 2559.8,263.17 2107.3,260.44 779.72,250.68 585.54,229 514.25,221.04 496.9,214.31 427.54,196 424.17,195.11 420.69,\ +194.13 417.21,193.11", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "genomic sequence localization" -> name [color=blue, label=name, - lp="708.54,221.5", - pos="e,531.13,191.46 2744.3,263.66 2279.4,262.31 890.44,256.04 688.54,229 637.24,222.13 580.03,206.47 540.92,194.5", + lp="696.54,221.5", + pos="e,530.12,191.9 2559.2,263.57 2119.4,262.02 860.69,255.32 676.54,229 629.15,222.23 576.59,207.03 540,195.16", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "genomic sequence localization" -> description [color=blue, label=description, - lp="829.04,221.5", - pos="e,677.59,194.18 2743.9,264.24 2292.9,264.55 979.05,262.55 788.54,229 753.47,222.82 715.47,209.46 687.17,198.09", + lp="810.04,221.5", + pos="e,673.66,194.53 2558.8,264.39 2132.3,265.05 942.62,263.71 769.54,229 739.39,222.95 707.2,210.06 682.9,198.87", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "genomic sequence localization" -> "has attribute" [color=blue, label="has attribute", - lp="974.54,221.5", - pos="e,818.12,192.86 2744.1,264.15 2313.8,264.19 1103.9,261.37 927.54,229 892.57,222.58 854.7,208.45 827.34,196.84", + lp="944.54,221.5", + pos="e,813.47,194.04 2559,264.62 2152.3,265.78 1057,265.44 897.54,229 871.02,222.94 843.18,210.04 822.27,198.86", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "genomic sequence localization" -> negated [color=blue, label=negated, - lp="1129.5,221.5", - pos="e,939.56,190.5 2745,262.9 2342.6,259.68 1261.1,249.26 1100.5,229 1047.6,222.32 988.42,205.82 949.3,193.59", + lp="1082.5,221.5", + pos="e,935.17,192.01 2559.5,263.43 2178.7,261.62 1199.1,254.51 1053.5,229 1015.5,222.33 973.98,207.61 944.63,195.86", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "genomic sequence localization" -> qualifiers [color=blue, label=qualifiers, - lp="1269,221.5", - pos="e,1088.4,193.14 2745.1,262.87 2364.3,259.71 1382.3,249.66 1235.5,229 1188.2,222.33 1135.7,207.86 1098.1,196.19", + lp="1193,221.5", + pos="e,1074.3,194.98 2559.1,263.95 2195.6,263.36 1293.4,258.86 1159.5,229 1132.9,223.06 1104.9,210.68 1083.4,199.73", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "genomic sequence localization" -> publications [color=blue, label=publications, - lp="1415.5,221.5", - pos="e,1239.6,192.78 2745,262.82 2386.9,259.68 1504.4,249.91 1371.5,229 1329.1,222.33 1282.4,207.82 1249.1,196.15", + lp="1295.5,221.5", + pos="e,1214.3,195.82 2559.4,263.47 2198.2,261.78 1310.5,254.99 1251.5,229 1239.3,223.62 1228.7,213.51 1220.5,203.79", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,328 +100,328 @@ digraph { width=2.0943]; "genomic sequence localization" -> "has evidence" [color=blue, label="has evidence", - lp="1576,221.5", - pos="e,1398.4,193.58 2745.5,262.36 2415.5,258.43 1646.8,247.42 1529.5,229 1487.6,222.42 1441.6,208.42 1407.9,196.9", + lp="1395,221.5", + pos="e,1349,195.95 2560,262.86 2210,259.87 1369.4,250.45 1348.5,229 1342.4,222.71 1342.7,213.83 1345.3,205.29", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1561.5,178", - width=3.015]; + label=string, + pos="1491.5,178", + width=1.0652]; "genomic sequence localization" -> "knowledge source" [color=blue, label="knowledge source", - lp="1734,221.5", - pos="e,1588.8,195.42 2744.7,263.09 2440.1,260.77 1771.4,252.97 1669.5,229 1644.4,223.09 1618.1,211.05 1597.7,200.26", + lp="1514,221.5", + pos="e,1468.2,192.4 2560.5,262.55 2230.4,258.99 1468.7,248.66 1449.5,229 1440.2,219.43 1448.4,208.07 1459.9,198.61", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1796.5,178", - width=3.015]; + label=string, + pos="1586.5,178", + width=1.0652]; "genomic sequence localization" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1907.5,221.5", - pos="e,1797.2,196.25 2744.4,263.68 2455.2,262.44 1849,256.56 1812.5,229 1805.3,223.55 1801.3,214.82 1799.1,206.17", + lp="1684.5,221.5", + pos="e,1582.3,196.23 2558.9,264.61 2260.7,265.09 1623.7,262.19 1589.5,229 1583.6,223.2 1581.6,214.76 1581.6,206.46", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2031.5,178", - width=3.015]; + label=string, + pos="1761.5,178", + width=1.0652]; "genomic sequence localization" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2117,221.5", - pos="e,2015.8,196.05 2744.2,263.4 2498,261.67 2035.5,254.96 2010.5,229 2004.1,222.25 2005.8,213.2 2010.3,204.65", + lp="1906,221.5", + pos="e,1769.3,195.66 2561.8,261.59 2312.2,257.08 1832.7,246.23 1799.5,229 1789.1,223.59 1780.8,213.89 1774.6,204.47", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2213.5,178", + pos="1988.5,178", width=1.5346]; "genomic sequence localization" -> timepoint [color=blue, label=timepoint, - lp="2275.5,221.5", - pos="e,2218,195.94 2744.4,263.64 2564.2,262.01 2282,255.24 2240.5,229 2232,223.57 2225.9,214.44 2221.8,205.45", + lp="2070.5,221.5", + pos="e,1999.1,195.68 2561,262.13 2376.6,258.91 2081.8,250.45 2035.5,229 2023.5,223.44 2013.1,213.31 2005.2,203.61", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2325.5,178", + pos="2100.5,178", width=1.0652]; "genomic sequence localization" -> "original subject" [color=blue, label="original subject", - lp="2375.5,221.5", - pos="e,2317.4,195.95 2749.9,260.08 2584.1,254.88 2334.2,244.53 2319.5,229 2313.7,222.84 2313.2,214.21 2314.7,205.84", + lp="2176.5,221.5", + pos="e,2102.7,196.27 2559.5,263.35 2396.5,261.34 2155.3,254.1 2120.5,229 2113,223.58 2108.3,214.85 2105.4,206.19", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2439.5,178", + pos="2225.5,178", width=1.5887]; "genomic sequence localization" -> "original predicate" [color=blue, label="original predicate", - lp="2505,221.5", - pos="e,2435,196.05 2745.9,262.17 2621.9,259.09 2462.6,250.86 2441.5,229 2435.8,223.02 2434,214.53 2434.1,206.24", + lp="2312,221.5", + pos="e,2228.8,196.28 2564.1,260.29 2438.6,255.9 2274.2,246.82 2248.5,229 2240.7,223.53 2235.4,214.68 2232,205.93", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2553.5,178", + pos="2354.5,178", width=1.0652]; "genomic sequence localization" -> "original object" [color=blue, label="original object", - lp="2639,221.5", - pos="e,2560.4,195.81 2752.2,259.11 2685.7,254.57 2615.4,245.83 2587.5,229 2578.1,223.3 2570.7,213.87 2565.2,204.72", + lp="2449,221.5", + pos="e,2364.3,195.88 2569.8,258.25 2501.3,253.47 2427.4,244.77 2397.5,229 2386.7,223.27 2377.4,213.57 2370.2,204.23", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2686.5,178", + pos="2487.5,178", width=2.1304]; "genomic sequence localization" -> "subject category" [color=blue, label="subject category", - lp="2764,221.5", - pos="e,2688.4,196.31 2783,252.91 2749,247.55 2717.3,239.85 2704.5,229 2697.7,223.23 2693.5,214.69 2690.9,206.29", + lp="2578,221.5", + pos="e,2493.8,196.02 2603.8,252.21 2567.9,246.63 2533.2,238.97 2518.5,229 2509.9,223.11 2503.2,213.93 2498.3,205.03", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2857.5,178", + pos="2658.5,178", width=2.1304]; "genomic sequence localization" -> "object category" [color=blue, label="object category", - lp="2885,221.5", - pos="e,2838.6,195.82 2849.1,247.74 2841.3,242.92 2834.2,236.78 2829.5,229 2824.7,220.9 2827.3,211.93 2832.5,203.84", + lp="2700,221.5", + pos="e,2647.3,196.12 2664.1,247.74 2656.3,242.92 2649.2,236.78 2644.5,229 2640.2,221.86 2640.9,213.36 2643.4,205.41", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="2990.5,178", + pos="2791.5,178", width=1.0652]; "genomic sequence localization" -> "subject closure" [color=blue, label="subject closure", - lp="3011,221.5", - pos="e,2975.7,194.83 2918.4,247.09 2925.6,241.51 2933.6,235.16 2940.5,229 2950.1,220.58 2960.1,210.78 2968.6,202.1", + lp="2823,221.5", + pos="e,2781.3,195.67 2735,247.03 2742,241.64 2749.4,235.41 2755.5,229 2762.8,221.45 2769.8,212.36 2775.6,204.01", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3090.5,178", + pos="2904.5,178", width=1.0652]; "genomic sequence localization" -> "object closure" [color=blue, label="object closure", - lp="3131.5,221.5", - pos="e,3087.6,196.31 2997.8,251.64 3028.7,246.16 3057.7,238.71 3069.5,229 3076.7,223.17 3081.4,214.5 3084.6,206.02", + lp="2944.5,221.5", + pos="e,2900.8,196.33 2810.4,251.34 2841,245.82 2869.7,238.42 2881.5,229 2888.9,223.19 2893.9,214.53 2897.4,206.04", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3223.5,178", + pos="3037.5,178", width=2.1304]; "genomic sequence localization" -> "subject category closure" [color=blue, label="subject category closure", - lp="3290,221.5", - pos="e,3215.1,196.31 3001.8,252.14 3082.9,242.94 3181.4,231.36 3185.5,229 3195.4,223.33 3203.6,213.95 3209.8,204.83", + lp="3104,221.5", + pos="e,3028.7,196.31 2820.7,252.59 2898.6,244.2 2990.6,233.51 2998.5,229 3008.6,223.33 3016.9,213.95 3023.3,204.84", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3415.5,178", + pos="3230.5,178", width=2.1304]; "genomic sequence localization" -> "object category closure" [color=blue, label="object category closure", - lp="3481,221.5", - pos="e,3408.8,196.04 3001.1,252.09 3019.6,250.23 3038.6,248.44 3056.5,247 3092.6,244.1 3350.1,246.8 3381.5,229 3391.1,223.58 3398.6,214.19 \ -3404,205", + lp="3295,221.5", + pos="e,3223.5,196.05 2816.1,252.09 2834.6,250.23 2853.6,248.44 2871.5,247 2907.5,244.11 3164,246.53 3195.5,229 3205.3,223.59 3212.9,214.21 \ +3218.5,205.02", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3605.5,178", + pos="3420.5,178", width=1.0652]; "genomic sequence localization" -> "subject namespace" [color=blue, label="subject namespace", - lp="3653.5,221.5", - pos="e,3598.1,195.67 2999.8,251.91 3018.7,250.03 3038.2,248.29 3056.5,247 3113.3,243.01 3518.2,255.51 3568.5,229 3578.8,223.59 3587,213.89 \ -3593,204.47", + lp="3467.5,221.5", + pos="e,3412.8,195.68 2814.8,251.91 2833.7,250.03 2853.2,248.29 2871.5,247 2928.2,243.01 3332.1,255.14 3382.5,229 3393,223.6 3401.3,213.91 \ +3407.5,204.48", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3764.5,178", + pos="3579.5,178", width=1.0652]; "genomic sequence localization" -> "object namespace" [color=blue, label="object namespace", - lp="3807.5,221.5", - pos="e,3756.5,195.72 2999.4,251.83 3018.4,249.95 3038,248.22 3056.5,247 3093.6,244.55 3692.4,245.76 3725.5,229 3736.2,223.6 3744.9,213.77 \ -3751.3,204.25", + lp="3621.5,221.5", + pos="e,3571.2,195.73 2814.4,251.83 2833.4,249.95 2853,248.22 2871.5,247 2908.6,244.55 3506.3,245.53 3539.5,229 3550.4,223.62 3559.2,213.79 \ +3565.8,204.26", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3915.5,178", + pos="3730.5,178", width=1.0652]; "genomic sequence localization" -> "subject label closure" [color=blue, label="subject label closure", - lp="3967.5,221.5", - pos="e,3907.2,195.75 2998.9,251.8 3018.1,249.91 3037.9,248.19 3056.5,247 3102,244.11 3834.7,249.16 3875.5,229 3886.4,223.65 3895.2,213.82 \ -3901.8,204.29", + lp="3781.5,221.5", + pos="e,3721.9,195.76 2813.9,251.8 2833.1,249.91 2852.9,248.19 2871.5,247 2916.9,244.11 3648.7,248.89 3689.5,229 3700.5,223.66 3709.6,\ +213.84 3716.3,204.3", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4086.5,178", + pos="3901.5,178", width=1.0652]; "genomic sequence localization" -> "object label closure" [color=blue, label="object label closure", - lp="4133,221.5", - pos="e,4077.9,195.78 2998.5,251.78 3017.8,249.88 3037.7,248.16 3056.5,247 3111.4,243.61 3996.1,252.96 4045.5,229 4056.5,223.68 4065.6,\ -213.86 4072.3,204.32", + lp="3948,221.5", + pos="e,3892.6,195.79 2813.5,251.78 2832.8,249.88 2852.7,248.16 2871.5,247 2926.3,243.61 3810,252.64 3859.5,229 3870.7,223.69 3879.9,213.88 \ +3886.9,204.34", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4239.5,178", + pos="4054.5,178", width=2.347]; "genomic sequence localization" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4292,221.5", - pos="e,4233.2,196.18 2998.5,251.74 3017.8,249.84 3037.7,248.14 3056.5,247 3088.4,245.07 4178.5,244.36 4206.5,229 4216.1,223.75 4223.4,\ -214.39 4228.6,205.19", + lp="4107,221.5", + pos="e,4048.2,196.18 2813.5,251.74 2832.8,249.84 2852.7,248.14 2871.5,247 2903.4,245.07 3993.5,244.36 4021.5,229 4031.1,223.75 4038.4,\ +214.39 4043.6,205.19", style=solid]; type [height=0.5, - pos="4373.5,178", + pos="4188.5,178", width=0.86659]; "genomic sequence localization" -> type [color=blue, label=type, - lp="4390.5,221.5", - pos="e,4375.9,196.02 2998.5,251.71 3017.8,249.82 3037.7,248.12 3056.5,247 3092.8,244.84 4338,252.78 4365.5,229 4372.1,223.36 4374.8,214.7 \ -4375.6,206.16", + lp="4205.5,221.5", + pos="e,4190.9,196.02 2813.5,251.71 2832.8,249.82 2852.7,248.12 2871.5,247 2907.8,244.84 4153,252.78 4180.5,229 4187.1,223.36 4189.8,214.7 \ +4190.6,206.16", style=solid]; category [height=0.5, - pos="4474.5,178", + pos="4289.5,178", width=1.4263]; "genomic sequence localization" -> category [color=blue, label=category, - lp="4470,221.5", - pos="e,4459.5,195.47 2998.1,251.75 3017.5,249.84 3037.6,248.12 3056.5,247 3131.6,242.55 4339.6,253.96 4410.5,229 4426.1,223.53 4440.8,\ -212.61 4452.2,202.37", + lp="4285,221.5", + pos="e,4274.5,195.47 2813.1,251.75 2832.5,249.84 2852.6,248.12 2871.5,247 2946.6,242.55 4154.6,253.96 4225.5,229 4241.1,223.53 4255.8,\ +212.61 4267.2,202.37", style=solid]; "start interbase coordinate" [color=blue, height=0.5, label=integer, - pos="4588.5,178", + pos="4403.5,178", width=1.2277]; "genomic sequence localization" -> "start interbase coordinate" [color=blue, label="start interbase coordinate", - lp="4633,221.5", - pos="e,4569.8,194.31 2998.1,251.74 3017.5,249.82 3037.6,248.12 3056.5,247 3136.9,242.27 4428.1,251.04 4505.5,229 4525.7,223.26 4545.9,\ -211.27 4561.3,200.47", + lp="4448,221.5", + pos="e,4384.8,194.31 2813.1,251.74 2832.5,249.82 2852.6,248.12 2871.5,247 2951.9,242.27 4243.1,251.04 4320.5,229 4340.7,223.26 4360.9,\ +211.27 4376.3,200.47", style=solid]; "end interbase coordinate" [color=blue, height=0.5, label=integer, - pos="4761.5,178", + pos="4576.5,178", width=1.2277]; "genomic sequence localization" -> "end interbase coordinate" [color=blue, label="end interbase coordinate", - lp="4835,221.5", - pos="e,4755.9,196.17 2998.1,251.71 3017.5,249.8 3037.6,248.1 3056.5,247 3103,244.31 4690,251.83 4730.5,229 4739.8,223.79 4746.6,214.57 \ -4751.5,205.46", + lp="4650,221.5", + pos="e,4570.9,196.17 2813.1,251.71 2832.5,249.8 2852.6,248.1 2871.5,247 2918,244.31 4505,251.83 4545.5,229 4554.8,223.79 4561.6,214.57 \ +4566.5,205.46", style=solid]; "genome build" [color=blue, height=0.5, label=StrandEnum, - pos="4909.5,178", + pos="4724.5,178", width=1.9318]; "genomic sequence localization" -> "genome build" [color=blue, label="genome build", - lp="4982,221.5", - pos="e,4924,195.74 2998.1,251.69 3017.5,249.78 3037.6,248.09 3056.5,247 3082.5,245.51 4910.2,247.47 4928.5,229 4935.1,222.34 4933.6,213.16 \ -4929.3,204.48", + lp="4797,221.5", + pos="e,4739,195.74 2813.1,251.69 2832.5,249.78 2852.6,248.09 2871.5,247 2897.5,245.51 4725.2,247.47 4743.5,229 4750.1,222.34 4748.6,213.16 \ +4744.3,204.48", style=solid]; strand [color=blue, height=0.5, label=StrandEnum, - pos="5066.5,178", + pos="4881.5,178", width=1.9318]; "genomic sequence localization" -> strand [color=blue, label=strand, - lp="5074,221.5", - pos="e,5060.6,196.19 2998.1,251.69 3017.5,249.78 3037.6,248.08 3056.5,247 3111.4,243.86 4986.5,255.6 5034.5,229 5044,223.76 5051.1,214.41 \ -5056.2,205.2", + lp="4889,221.5", + pos="e,4875.6,196.19 2813.1,251.69 2832.5,249.78 2852.6,248.08 2871.5,247 2926.4,243.86 4801.5,255.6 4849.5,229 4859,223.76 4866.1,214.41 \ +4871.2,205.2", style=solid]; phase [color=blue, height=0.5, label=PhaseEnum, - pos="5219.5,178", + pos="5034.5,178", width=1.8234]; "genomic sequence localization" -> phase [color=blue, label=phase, - lp="5170,221.5", - pos="e,5191.9,194.37 2998.1,251.68 3017.5,249.77 3037.6,248.08 3056.5,247 3170,240.53 4990.3,252.11 5101.5,229 5130.1,223.07 5160.3,210.13 \ -5183,198.89", + lp="4985,221.5", + pos="e,5006.9,194.37 2813.1,251.68 2832.5,249.77 2852.6,248.08 2871.5,247 2985,240.53 4805.3,252.11 4916.5,229 4945.1,223.07 4975.3,210.13 \ +4998,198.89", style=solid]; subject [height=0.5, - pos="5347.5,178", + pos="5162.5,178", width=1.2277]; "genomic sequence localization" -> subject [color=blue, label=subject, - lp="5281.5,221.5", - pos="e,5318.2,191.66 2998.1,251.67 3017.5,249.77 3037.6,248.08 3056.5,247 3175.2,240.25 5078.3,248.3 5195.5,229 5235.2,222.47 5278.7,\ -207.32 5308.9,195.4", + lp="5096.5,221.5", + pos="e,5133.2,191.66 2813.1,251.67 2832.5,249.77 2852.6,248.08 2871.5,247 2990.2,240.25 4893.3,248.3 5010.5,229 5050.2,222.47 5093.7,\ +207.32 5123.9,195.4", style=solid]; object [height=0.5, - pos="5390.5,91", + pos="5205.5,91", width=1.0832]; "genomic sequence localization" -> object [color=blue, label=object, - lp="5441.5,178", - pos="e,5403.9,108.09 2998.1,251.67 3017.5,249.76 3037.6,248.07 3056.5,247 3181.6,239.91 5188.3,251.62 5311.5,229 5353,221.38 5372.5,227.55 \ -5400.5,196 5421.3,172.66 5422.5,156.9 5413.5,127 5412.5,123.55 5411,120.13 5409.3,116.85", + lp="5256.5,178", + pos="e,5218.9,108.09 2813.1,251.67 2832.5,249.76 2852.6,248.07 2871.5,247 2996.6,239.91 5003.3,251.62 5126.5,229 5168,221.38 5187.5,227.55 \ +5215.5,196 5236.3,172.66 5237.5,156.9 5228.5,127 5227.5,123.55 5226,120.13 5224.3,116.85", style=solid]; predicate [height=0.5, - pos="5544.5,178", + pos="5359.5,178", width=1.5165]; "genomic sequence localization" -> predicate [color=blue, label=predicate, - lp="5517.5,221.5", - pos="e,5520.7,194.37 2997.6,251.7 3017.2,249.78 3037.5,248.08 3056.5,247 3188.8,239.53 5312.5,259.17 5441.5,229 5466.4,223.18 5492.3,\ -210.58 5511.9,199.49", + lp="5332.5,221.5", + pos="e,5335.7,194.37 2812.6,251.7 2832.2,249.78 2852.5,248.08 2871.5,247 3003.8,239.53 5127.5,259.17 5256.5,229 5281.4,223.18 5307.3,\ +210.58 5326.9,199.49", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3103.5,265", + pos="2918.5,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3234.5,265", + pos="3049.5,265", width=2.0762]; subject -> object [label=relation, - lp="5385.5,134.5", - pos="e,5372.6,107.23 5348.6,159.55 5349.8,149.57 5352.3,137.07 5357.5,127 5359.8,122.68 5362.7,118.52 5365.9,114.66"]; + lp="5200.5,134.5", + pos="e,5187.6,107.23 5163.6,159.55 5164.8,149.57 5167.3,137.07 5172.5,127 5174.8,122.68 5177.7,118.52 5180.9,114.66"]; relation [height=0.5, - pos="5335.5,18", + pos="5150.5,18", width=1.2999]; - subject -> relation [pos="e,5336.8,36.188 5346.2,159.79 5344.2,132.48 5340.1,78.994 5337.6,46.38", + subject -> relation [pos="e,5151.8,36.188 5161.2,159.79 5159.2,132.48 5155.1,78.994 5152.6,46.38", style=dotted]; "genomic sequence localization_subject" [color=blue, height=0.5, label="nucleic acid entity", - pos="3422.5,265", + pos="3237.5,265", width=2.6539]; - object -> relation [pos="e,5348.4,35.54 5378.1,73.889 5371.1,64.939 5362.4,53.617 5354.6,43.584", + object -> relation [pos="e,5163.4,35.54 5193.1,73.889 5186.1,64.939 5177.4,53.617 5169.6,43.584", style=dotted]; "genomic sequence localization_object" [color=blue, height=0.5, label="nucleic acid entity", - pos="3631.5,265", + pos="3446.5,265", width=2.6539]; "genomic sequence localization_predicate" [color=blue, height=0.5, label="predicate type", - pos="3823.5,265", + pos="3638.5,265", width=2.1665]; } diff --git a/graphviz/genomic_sequence_localization.svg b/graphviz/genomic_sequence_localization.svg index 1edc9a6b86..56d4feb657 100644 --- a/graphviz/genomic_sequence_localization.svg +++ b/graphviz/genomic_sequence_localization.svg @@ -4,16 +4,16 @@ - + %3 - + genomic sequence localization - -genomic sequence localization + +genomic sequence localization @@ -24,8 +24,8 @@ genomic sequence localization->sequence association - - + + is_a @@ -37,9 +37,9 @@ genomic sequence localization->id - + -id +id @@ -50,9 +50,9 @@ genomic sequence localization->iri - - -iri + + +iri @@ -63,9 +63,9 @@ genomic sequence localization->name - - -name + + +name @@ -76,9 +76,9 @@ genomic sequence localization->description - - -description + + +description @@ -89,9 +89,9 @@ genomic sequence localization->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ genomic sequence localization->negated - - -negated + + +negated @@ -115,9 +115,9 @@ genomic sequence localization->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ genomic sequence localization->publications - - -publications + + +publications @@ -141,428 +141,428 @@ genomic sequence localization->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string genomic sequence localization->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string genomic sequence localization->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string genomic sequence localization->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type genomic sequence localization->timepoint - - -timepoint + + +timepoint original subject - -string + +string genomic sequence localization->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie genomic sequence localization->original predicate - - -original predicate + + +original predicate original object - -string + +string genomic sequence localization->original object - - -original object + + +original object subject category - -ontology class + +ontology class genomic sequence localization->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class genomic sequence localization->object category - - -object category + + +object category subject closure - -string + +string genomic sequence localization->subject closure - - -subject closure + + +subject closure object closure - -string + +string genomic sequence localization->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class genomic sequence localization->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class genomic sequence localization->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string genomic sequence localization->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string genomic sequence localization->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string genomic sequence localization->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string genomic sequence localization->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source genomic sequence localization->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type genomic sequence localization->type - - -type + + +type category - -category + +category genomic sequence localization->category - - -category + + +category start interbase coordinate - -integer + +integer genomic sequence localization->start interbase coordinate - - -start interbase coordinate + + +start interbase coordinate end interbase coordinate - -integer + +integer genomic sequence localization->end interbase coordinate - - -end interbase coordinate + + +end interbase coordinate genome build - -StrandEnum + +StrandEnum genomic sequence localization->genome build - - -genome build + + +genome build strand - -StrandEnum + +StrandEnum genomic sequence localization->strand - - -strand + + +strand phase - -PhaseEnum + +PhaseEnum genomic sequence localization->phase - - -phase + + +phase subject - -subject + +subject genomic sequence localization->subject - - -subject + + +subject object - -object + +object genomic sequence localization->object - - -object + + +object predicate - -predicate + +predicate genomic sequence localization->predicate - - -predicate + + +predicate association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + genomic sequence localization_subject - -nucleic acid entity + +nucleic acid entity object->relation - - + + genomic sequence localization_object - -nucleic acid entity + +nucleic acid entity genomic sequence localization_predicate - -predicate type + +predicate type diff --git a/graphviz/genotype_as_a_model_of_disease_association.gv b/graphviz/genotype_as_a_model_of_disease_association.gv index 7032d6fc59..5446f68972 100644 --- a/graphviz/genotype_as_a_model_of_disease_association.gv +++ b/graphviz/genotype_as_a_model_of_disease_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,6110.1,283"]; + graph [bb="0,0,5892.1,283"]; node [label="\N"]; "genotype as a model of disease association" [height=0.5, label="genotype as a model of disease association", - pos="3443.9,265", + pos="3225.9,265", width=5.8314]; "genotype to disease association" [height=0.5, pos="157.94,178", width=4.3871]; "genotype as a model of disease association" -> "genotype to disease association" [label=is_a, - lp="817.94,221.5", - pos="e,269.28,190.85 3235.6,262.74 2698.5,259.23 1275.8,248.37 803.94,229 590.72,220.25 537.56,214.14 324.94,196 310.17,194.74 294.68,\ -193.31 279.33,191.83"]; + lp="816.94,221.5", + pos="e,269.28,190.84 3016,264.81 2595.7,265.59 1621,263.12 802.94,229 590.17,220.13 537.11,214.12 324.94,196 310.17,194.74 294.68,193.31 \ +279.33,191.82"]; "model to disease association mixin" [height=0.5, pos="505.94,178", width=4.7843]; "genotype as a model of disease association" -> "model to disease association mixin" [label=uses, - lp="1035.4,221.5", - pos="e,613.33,192.08 3234.7,263.21 2728.3,260.93 1447,252.91 1018.9,229 882.97,221.41 727.37,205.17 623.53,193.25"]; + lp="1034.4,221.5", + pos="e,613.62,192.09 3017.2,262.87 2544.4,259.94 1402.6,250.8 1017.9,229 882.45,221.32 727.43,205.15 623.8,193.26"]; "entity to disease association mixin" [height=0.5, pos="866.94,178", width=4.7482]; "genotype as a model of disease association" -> "entity to disease association mixin" [label=uses, - lp="1190.4,221.5", - pos="e,941.31,194.24 3233.8,264.68 2750.2,265.62 1569.7,264.09 1173.9,229 1098.1,222.28 1012.8,207.81 951.34,196.16"]; + lp="1189.4,221.5", + pos="e,941.38,194.27 3015.9,264.28 2566.9,264.25 1525.5,260.65 1172.9,229 1097.5,222.23 1012.6,207.8 951.37,196.18"]; id [color=blue, height=0.5, label=string, @@ -31,9 +31,9 @@ digraph { width=1.0652]; "genotype as a model of disease association" -> id [color=blue, label=id, - lp="1307.9,221.5", - pos="e,1122.9,189.98 3235.2,262.83 2733.8,259.69 1489.2,249.89 1300.9,229 1229.2,221.04 1211.4,215.43 1141.9,196 1138.8,195.13 1135.6,\ -194.17 1132.4,193.15", + lp="1306.9,221.5", + pos="e,1122.9,189.97 3018,262.43 2554.9,258.61 1466.6,247.75 1299.9,229 1228.6,220.98 1211,215.35 1141.9,196 1138.8,195.13 1135.6,194.16 \ +1132.4,193.14", style=solid]; iri [color=blue, height=0.5, @@ -42,9 +42,9 @@ digraph { width=1.2277]; "genotype as a model of disease association" -> iri [color=blue, label=iri, - lp="1420.9,221.5", - pos="e,1227.8,190.19 3235.9,262.54 2754.3,258.86 1590.2,248.09 1412.9,229 1338.6,220.99 1320.3,214.78 1247.9,196 1244.6,195.12 1241.1,\ -194.16 1237.6,193.14", + lp="1411.9,221.5", + pos="e,1227.9,190.13 3018.4,262.23 2574.5,258.11 1560.3,246.88 1403.9,229 1333.5,220.95 1316.4,214.18 1247.9,196 1244.6,195.11 1241.1,\ +194.12 1237.6,193.1", style=solid]; name [color=blue, height=0.5, @@ -53,8 +53,8 @@ digraph { width=1.5707]; "genotype as a model of disease association" -> name [color=blue, label=name, - lp="1527.9,221.5", - pos="e,1351.7,191.54 3235.3,262.99 2769.9,260.33 1675.1,251.73 1507.9,229 1457.2,222.09 1400.6,206.58 1361.7,194.65", + lp="1513.9,221.5", + pos="e,1350.2,191.99 3017.3,262.72 2589.5,259.65 1640.7,250.51 1493.9,229 1447.4,222.18 1395.9,207.07 1360,195.23", style=solid]; description [color=blue, height=0.5, @@ -63,8 +63,8 @@ digraph { width=2.0943]; "genotype as a model of disease association" -> description [color=blue, label=description, - lp="1648.4,221.5", - pos="e,1497.7,194.15 3234.2,263.71 2786.3,262.56 1764,256.86 1607.9,229 1573.1,222.78 1535.4,209.42 1507.3,198.07", + lp="1625.4,221.5", + pos="e,1493.3,194.75 3016.4,263.84 2605.3,262.91 1721.2,257.55 1584.9,229 1556.2,222.98 1525.6,210.3 1502.4,199.22", style=solid]; "has attribute" [color=blue, height=0.5, @@ -73,8 +73,8 @@ digraph { width=1.4443]; "genotype as a model of disease association" -> "has attribute" [color=blue, label="has attribute", - lp="1793.9,221.5", - pos="e,1638.6,192.95 3234.6,263.5 2812.9,261.94 1889.3,255.5 1746.9,229 1712.5,222.58 1675.2,208.62 1648.1,197.07", + lp="1756.9,221.5", + pos="e,1632.3,194.25 3015.8,264.2 2629.2,263.82 1833,259.31 1709.9,229 1685.5,222.98 1660.1,210.39 1640.9,199.35", style=solid]; negated [color=blue, height=0.5, @@ -83,8 +83,8 @@ digraph { width=1.2999]; "genotype as a model of disease association" -> negated [color=blue, label=negated, - lp="1948.9,221.5", - pos="e,1759.8,190.46 3233.9,264.63 2877.1,264.77 2167.4,260.86 1919.9,229 1867.4,222.23 1808.6,205.81 1769.7,193.62", + lp="1888.9,221.5", + pos="e,1753.9,192.55 3017.9,262.45 2663.5,259.25 1970.1,250.34 1859.9,229 1826.1,222.44 1789.5,208.27 1763.1,196.69", style=solid]; qualifiers [color=blue, height=0.5, @@ -93,8 +93,8 @@ digraph { width=2.1304]; "genotype as a model of disease association" -> qualifiers [color=blue, label=qualifiers, - lp="2087.4,221.5", - pos="e,1908.7,193.2 3233.8,264.77 2902.9,264.96 2275,260.88 2053.9,229 2007.2,222.26 1955.5,207.87 1918.3,196.25", + lp="1992.4,221.5", + pos="e,1889.8,195.43 3016.4,263.54 2682.7,262.02 2057.8,255.59 1958.9,229 1937.4,223.21 1915.4,211.5 1898.3,200.86", style=solid]; publications [color=blue, height=0.5, @@ -103,8 +103,8 @@ digraph { width=1.7332]; "genotype as a model of disease association" -> publications [color=blue, label=publications, - lp="2232.9,221.5", - pos="e,2059.7,192.85 3233.7,264.89 2930,265.03 2383.6,260.62 2188.9,229 2147.6,222.28 2102.1,207.95 2069.4,196.35", + lp="2083.9,221.5", + pos="e,2024.6,196.25 3016,264.04 2685.7,263.22 2078.2,257.78 2039.9,229 2032.7,223.56 2028.7,214.83 2026.5,206.18", style=solid]; "has evidence" [color=blue, height=0.5, @@ -113,307 +113,308 @@ digraph { width=2.0943]; "genotype as a model of disease association" -> "has evidence" [color=blue, label="has evidence", - lp="2391.4,221.5", - pos="e,2217.9,193.63 3234.1,263.85 2964.1,262.53 2510,256.15 2344.9,229 2304.5,222.35 2260.2,208.52 2227.6,197.09", + lp="2182.4,221.5", + pos="e,2151.8,194.88 3015.7,264.67 2707.5,264.61 2166,260.04 2135.9,229 2127.3,220.11 2133.6,209.91 2143.8,201.06", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2381.9,178", - width=3.015]; + label=string, + pos="2311.9,178", + width=1.0652]; "genotype as a model of disease association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2546.4,221.5", - pos="e,2407.5,195.61 3238.6,261.16 2977.8,256.84 2552.9,247.12 2481.9,229 2458.8,223.1 2434.9,211.34 2416.2,200.71", + lp="2300.4,221.5", + pos="e,2281.4,189.23 3016.3,263.91 2733.7,262.74 2262.6,256.62 2235.9,229 2231.3,224.2 2232.3,219.61 2235.9,214 2240.4,207 2256.1,199.25 \ +2272.1,192.84", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2616.9,178", - width=3.015]; + label=string, + pos="2406.9,178", + width=1.0652]; "genotype as a model of disease association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2717.9,221.5", - pos="e,2613.9,196.33 3237.3,261.8 3001.5,258.31 2645.2,249.64 2622.9,229 2616.8,223.32 2614.4,214.91 2613.8,206.59", + lp="2466.9,221.5", + pos="e,2386.4,193.24 3017.8,262.61 2772.2,259.91 2394,252.02 2371.9,229 2363.6,220.29 2369.6,209.43 2378.8,200.05", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2851.9,178", - width=3.015]; + label=string, + pos="2548.9,178", + width=1.0652]; "genotype as a model of disease association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2926.4,221.5", - pos="e,2830.1,195.87 3244.4,259.34 3067.4,254.19 2834.6,244.52 2819.9,229 2812.8,221.43 2816.3,212.05 2823.1,203.46", + lp="2687.4,221.5", + pos="e,2555,196.02 3018.5,262.12 2844.4,259.01 2618.3,250.76 2580.9,229 2571.7,223.61 2564.7,214.35 2559.6,205.26", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="3033.9,178", + pos="2775.9,178", width=1.5346]; "genotype as a model of disease association" -> timepoint [color=blue, label=timepoint, - lp="3080.9,221.5", - pos="e,3033.3,196.43 3254.5,257.2 3160.1,252.05 3062.6,243.34 3045.9,229 3039.4,223.36 3036.1,214.85 3034.5,206.44", + lp="2849.9,221.5", + pos="e,2784.4,195.97 3019.7,261.58 2936.1,257.5 2850.8,248.43 2814.9,229 2804.7,223.43 2796.2,213.89 2789.8,204.63", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="3145.9,178", + pos="2887.9,178", width=1.0652]; "genotype as a model of disease association" -> "original subject" [color=blue, label="original subject", - lp="3178.9,221.5", - pos="e,3130.2,194.82 3270.2,254.87 3200.4,249.39 3133.8,241.08 3122.9,229 3116.3,221.56 3118.9,211.86 3124.3,202.98", + lp="2952.9,221.5", + pos="e,2886.2,196.27 3054.4,254.62 2981.1,248.99 2909.4,240.62 2896.9,229 2890.8,223.25 2887.9,214.83 2886.8,206.52", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3259.9,178", + pos="3012.9,178", width=1.5887]; "genotype as a model of disease association" -> "original predicate" [color=blue, label="original predicate", - lp="3305.4,221.5", - pos="e,3246.1,195.8 3298.7,251.97 3272.6,246.83 3250.8,239.48 3241.9,229 3236.1,222.05 3237.4,213.06 3241.2,204.62", + lp="3083.4,221.5", + pos="e,3010.6,196.02 3082,251.88 3054,246.73 3030,239.41 3019.9,229 3014.1,222.99 3011.6,214.49 3010.9,206.2", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3373.9,178", + pos="3141.9,178", width=1.0652]; "genotype as a model of disease association" -> "original object" [color=blue, label="original object", - lp="3429.4,221.5", - pos="e,3371.4,196.07 3397.9,247.43 3390.1,242.64 3382.9,236.59 3377.9,229 3373.5,222.32 3371.8,214 3371.3,206.08", + lp="3211.4,221.5", + pos="e,3144.9,196.35 3183.2,247.27 3174.6,242.4 3166.3,236.35 3159.9,229 3154.3,222.53 3150.4,214.18 3147.7,206.16", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3506.9,178", + pos="3274.9,178", width=2.1304]; "genotype as a model of disease association" -> "subject category" [color=blue, label="subject category", - lp="3553.4,221.5", - pos="e,3501.5,196.22 3467.4,247.1 3473.6,241.81 3480,235.61 3484.9,229 3490.2,221.97 3494.5,213.49 3497.9,205.54", + lp="3332.4,221.5", + pos="e,3275.1,196.17 3251.4,247.12 3257.4,241.98 3263.1,235.86 3266.9,229 3270.8,222.15 3272.9,213.99 3274.1,206.26", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3677.9,178", + pos="3445.9,178", width=2.1304]; "genotype as a model of disease association" -> "object category" [color=blue, label="object category", - lp="3696.4,221.5", - pos="e,3661.9,195.91 3555.9,249.66 3576.8,244.69 3598,238 3616.9,229 3630.5,222.54 3643.7,212.41 3654.3,202.94", + lp="3472.4,221.5", + pos="e,3433.4,195.95 3340.7,249.91 3359.8,244.91 3379,238.15 3395.9,229 3407.6,222.72 3418.3,212.86 3426.8,203.55", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3810.9,178", + pos="3578.9,178", width=1.0652]; "genotype as a model of disease association" -> "subject closure" [color=blue, label="subject closure", - lp="3833.4,221.5", - pos="e,3797.9,195.42 3588,251.89 3662,244.94 3740,236.19 3755.9,229 3769.1,223.04 3781.3,212.72 3790.8,203", + lp="3606.4,221.5", + pos="e,3568.3,195.4 3370.9,251.93 3442.5,245.15 3516.9,236.55 3531.9,229 3543.6,223.13 3553.9,213.1 3561.9,203.55", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3909.9,178", + pos="3691.9,178", width=1.0652]; "genotype as a model of disease association" -> "object closure" [color=blue, label="object closure", - lp="3953.9,221.5", - pos="e,3908.4,196.15 3593.7,252.36 3723.8,242.23 3891.7,229.14 3891.9,229 3899.2,223.45 3903.6,214.7 3906.1,206.05", + lp="3728.9,221.5", + pos="e,3687.3,196.34 3375.1,252.31 3502.1,242.33 3664.2,229.51 3664.9,229 3673.3,223.54 3679.3,214.57 3683.5,205.72", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="4042.9,178", + pos="3824.9,178", width=2.1304]; "genotype as a model of disease association" -> "subject category closure" [color=blue, label="subject category closure", - lp="4112.4,221.5", - pos="e,4035.9,196.07 3590.6,252.1 3614.7,250.29 3639.5,248.52 3662.9,247 3701.2,244.51 3974.4,247.61 4007.9,229 4017.7,223.61 4025.3,\ -214.23 4030.9,205.04", + lp="3889.4,221.5", + pos="e,3815.6,196.13 3372.9,252.1 3396.9,250.29 3421.6,248.53 3444.9,247 3482.5,244.54 3749.3,245.79 3782.9,229 3793.8,223.58 3802.9,\ +213.93 3809.9,204.55", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="4235.9,178", + pos="4017.9,178", width=2.1304]; "genotype as a model of disease association" -> "object category closure" [color=blue, label="object category closure", - lp="4303.4,221.5", - pos="e,4229.9,196.1 3588.2,251.89 3613.1,250.06 3638.8,248.34 3662.9,247 3693,245.34 4177.8,243.87 4203.9,229 4213.3,223.65 4220.4,214.27 \ -4225.5,205.08", + lp="4081.4,221.5", + pos="e,4010.3,196.16 3370.2,251.9 3395.1,250.07 3420.8,248.34 3444.9,247 3474.7,245.35 3954.6,242.85 3980.9,229 3991.1,223.67 3999.2,\ +214.17 4005.2,204.87", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4425.9,178", + pos="4207.9,178", width=1.0652]; "genotype as a model of disease association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4475.9,221.5", - pos="e,4418.9,196.18 3587,251.8 3612.3,249.96 3638.4,248.26 3662.9,247 3703.3,244.93 4355.3,248.13 4390.9,229 4400.7,223.74 4408.4,214.38 \ -4414,205.18", + lp="4254.9,221.5", + pos="e,4199.9,195.73 3369,251.81 3394.3,249.96 3420.4,248.26 3444.9,247 3485.1,244.94 4133,247.1 4168.9,229 4179.6,223.62 4188.3,213.79 \ +4194.7,204.26", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4584.9,178", + pos="4366.9,178", width=1.0652]; "genotype as a model of disease association" -> "object namespace" [color=blue, label="object namespace", - lp="4628.9,221.5", - pos="e,4577.6,195.73 3586.4,251.75 3611.9,249.9 3638.2,248.21 3662.9,247 3712.1,244.6 4504.2,251.58 4547.9,229 4558.3,223.66 4566.4,213.98 \ -4572.5,204.55", + lp="4408.9,221.5", + pos="e,4358.6,195.76 3368.4,251.76 3393.9,249.91 3420.2,248.21 3444.9,247 3493.9,244.6 4283,250.68 4326.9,229 4337.8,223.65 4346.6,213.83 \ +4353.2,204.3", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4735.9,178", + pos="4517.9,178", width=1.0652]; "genotype as a model of disease association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4788.9,221.5", - pos="e,4727.9,195.76 3586.1,251.72 3611.7,249.86 3638.1,248.18 3662.9,247 3720.3,244.28 4645.5,254.65 4696.9,229 4707.6,223.66 4716.3,\ -213.83 4722.7,204.3", + lp="4568.9,221.5", + pos="e,4509.3,195.78 3368.1,251.72 3393.7,249.86 3420.1,248.18 3444.9,247 3502.2,244.28 4425.3,253.98 4476.9,229 4487.9,223.68 4497,213.87 \ +4503.7,204.33", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4906.9,178", + pos="4688.9,178", width=1.0652]; "genotype as a model of disease association" -> "object label closure" [color=blue, label="object label closure", - lp="4954.4,221.5", - pos="e,4898.6,195.78 3585.5,251.71 3611.3,249.84 3637.9,248.16 3662.9,247 3696.3,245.45 4836.9,243.71 4866.9,229 4877.8,223.68 4886.6,\ -213.86 4893.2,204.33", + lp="4736.4,221.5", + pos="e,4680,195.8 3367.5,251.71 3393.3,249.84 3419.9,248.16 3444.9,247 3478.3,245.46 4616.8,243.33 4646.9,229 4658.1,223.71 4667.3,213.9 \ +4674.3,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="5048.9,178", + pos="4830.9,178", width=2.347]; "genotype as a model of disease association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="5110.4,221.5", - pos="e,5046.5,196.45 3585.5,251.67 3611.3,249.81 3637.9,248.14 3662.9,247 3700.8,245.28 4996.5,250.2 5027.9,229 5035.8,223.72 5040.7,\ -214.91 5043.8,206.14", + lp="4892.4,221.5", + pos="e,4828.5,196.45 3367.5,251.67 3393.3,249.81 3419.9,248.14 3444.9,247 3482.8,245.28 4778.5,250.2 4809.9,229 4817.8,223.72 4822.7,\ +214.91 4825.8,206.14", style=solid]; type [height=0.5, - pos="5182.9,178", + pos="4964.9,178", width=0.86659]; "genotype as a model of disease association" -> type [color=blue, label=type, - lp="5206.9,221.5", - pos="e,5188.9,196.12 3585.2,251.66 3611.1,249.8 3637.8,248.12 3662.9,247 3684,246.06 5169.1,244.03 5183.9,229 5189.8,223.03 5191.1,214.44 \ -5190.5,206.05", + lp="4988.9,221.5", + pos="e,4970.9,196.12 3367.2,251.66 3393.1,249.8 3419.8,248.12 3444.9,247 3466,246.06 4951.1,244.03 4965.9,229 4971.8,223.03 4973.1,214.44 \ +4972.5,206.05", style=solid]; category [height=0.5, - pos="5283.9,178", + pos="5065.9,178", width=1.4263]; "genotype as a model of disease association" -> category [color=blue, label=category, - lp="5283.4,221.5", - pos="e,5270.9,195.44 3585.2,251.66 3611.1,249.79 3637.8,248.12 3662.9,247 3706.3,245.07 5186.4,244.54 5226.9,229 5241,223.6 5254,212.99 \ -5263.9,202.93", + lp="5065.4,221.5", + pos="e,5052.9,195.44 3367.2,251.66 3393.1,249.79 3419.8,248.12 3444.9,247 3488.3,245.07 4968.4,244.54 5008.9,229 5023,223.6 5036,212.99 \ +5045.9,202.93", style=solid]; predicate [height=0.5, - pos="5407.9,178", + pos="5189.9,178", width=1.5165]; "genotype as a model of disease association" -> predicate [color=blue, label=predicate, - lp="5389.9,221.5", - pos="e,5387,194.81 3585.2,251.64 3611.1,249.78 3637.8,248.11 3662.9,247 3754.9,242.94 5230.1,252.77 5318.9,229 5340.2,223.32 5361.7,211.41 \ -5378.3,200.63", + lp="5171.9,221.5", + pos="e,5169,194.81 3367.2,251.64 3393.1,249.78 3419.8,248.11 3444.9,247 3536.9,242.94 5012.1,252.77 5100.9,229 5122.2,223.32 5143.7,211.41 \ +5160.3,200.63", style=solid]; object [height=0.5, - pos="5994.9,91", + pos="5776.9,91", width=1.0832]; "genotype as a model of disease association" -> object [color=blue, label=object, - lp="5529.9,178", - pos="e,5956.2,94.237 3584.9,251.65 3610.9,249.78 3637.7,248.11 3662.9,247 3711.9,244.85 5381.5,244.74 5427.9,229 5451.1,221.15 5453.5,\ -212.02 5471.9,196 5489,181.17 5487.7,170.09 5507.9,160 5584.3,121.97 5838.2,101.88 5945.9,94.891", + lp="5311.9,178", + pos="e,5738.2,94.237 3366.9,251.65 3392.9,249.78 3419.7,248.11 3444.9,247 3493.9,244.85 5163.5,244.74 5209.9,229 5233.1,221.15 5235.5,\ +212.02 5253.9,196 5271,181.17 5269.7,170.09 5289.9,160 5366.3,121.97 5620.2,101.88 5727.9,94.891", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="5645.9,178", + pos="5427.9,178", width=2.3651]; "genotype as a model of disease association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="5633.9,221.5", - pos="e,5613.8,194.73 3584.9,251.64 3610.9,249.77 3637.7,248.1 3662.9,247 3765.6,242.52 5411.9,247.87 5512.9,229 5544.7,223.08 5578.7,\ -210.15 5604.4,198.93", + lp="5415.9,221.5", + pos="e,5395.8,194.73 3366.9,251.64 3392.9,249.77 3419.7,248.1 3444.9,247 3547.6,242.52 5193.9,247.87 5294.9,229 5326.7,223.08 5360.7,\ +210.15 5386.4,198.93", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="5824.9,178", + pos="5606.9,178", width=2.1123]; "genotype as a model of disease association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="5814.9,221.5", - pos="e,5796.1,194.86 3584.9,251.62 3610.9,249.75 3637.7,248.09 3662.9,247 3776.3,242.1 5594.8,251.92 5705.9,229 5734.3,223.15 5764.3,\ -210.47 5787.1,199.35", + lp="5596.9,221.5", + pos="e,5578.1,194.86 3366.9,251.62 3392.9,249.75 3419.7,248.09 3444.9,247 3558.3,242.1 5376.8,251.92 5487.9,229 5516.3,223.15 5546.3,\ +210.47 5569.1,199.35", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="5954.9,178", + pos="5736.9,178", width=1.011]; "genotype as a model of disease association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="5962.4,221.5", - pos="e,5938.3,194.31 3584.6,251.63 3610.6,249.75 3637.6,248.08 3662.9,247 3724.5,244.37 5821.1,247.09 5879.9,229 5898.4,223.33 5916.5,\ -211.51 5930.3,200.79", + lp="5744.4,221.5", + pos="e,5720.3,194.31 3366.6,251.63 3392.6,249.75 3419.6,248.08 3444.9,247 3506.5,244.37 5603.1,247.09 5661.9,229 5680.4,223.33 5698.5,\ +211.51 5712.3,200.79", style=solid]; subject [height=0.5, - pos="6065.9,178", + pos="5847.9,178", width=1.2277]; "genotype as a model of disease association" -> subject [color=blue, label=subject, - lp="6064.9,221.5", - pos="e,6055.2,195.89 3584.6,251.62 3610.6,249.74 3637.6,248.08 3662.9,247 3728.3,244.22 5957.9,254.88 6017.9,229 6030.2,223.72 6040.8,\ -213.63 6049,203.88", + lp="5846.9,221.5", + pos="e,5837.2,195.89 3366.6,251.62 3392.6,249.74 3419.6,248.08 3444.9,247 3510.3,244.22 5739.9,254.88 5799.9,229 5812.2,223.72 5822.8,\ +213.63 5831,203.88", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3709.9,265", + pos="3491.9,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3840.9,265", + pos="3622.9,265", width=2.0762]; "genotype to disease association_predicate" [color=blue, height=0.5, label="predicate type", - pos="4011.9,265", + pos="3793.9,265", width=2.1665]; relation [height=0.5, - pos="6029.9,18", + pos="5811.9,18", width=1.2999]; - object -> relation [pos="e,6021.5,36.198 6003.2,73.174 6007.3,64.896 6012.3,54.723 6016.9,45.438", + object -> relation [pos="e,5803.5,36.198 5785.2,73.174 5789.3,64.896 5794.3,54.723 5798.9,45.438", style=dotted]; "genotype to disease association_object" [color=blue, height=0.5, label="named thing", - pos="4177.9,265", + pos="3959.9,265", width=1.9318]; subject -> object [label=relation, - lp="6023.9,134.5", - pos="e,5991.1,109.01 6029.6,167.42 6016.7,162.12 6003.6,154.06 5995.9,142 5991.7,135.26 5990.3,126.93 5990.4,119.01"]; - subject -> relation [pos="e,6034.1,36.005 6062.3,160.05 6057.8,139.44 6050,103.63 6042.9,73 6040.9,64.183 6038.6,54.574 6036.5,45.938", + lp="5805.9,134.5", + pos="e,5773.1,109.01 5811.6,167.42 5798.7,162.12 5785.6,154.06 5777.9,142 5773.7,135.26 5772.3,126.93 5772.4,119.01"]; + subject -> relation [pos="e,5816.1,36.005 5844.3,160.05 5839.8,139.44 5832,103.63 5824.9,73 5822.9,64.183 5820.6,54.574 5818.5,45.938", style=dotted]; "genotype as a model of disease association_subject" [color=blue, height=0.5, label=genotype, - pos="4318.9,265", + pos="4100.9,265", width=1.4985]; } diff --git a/graphviz/genotype_as_a_model_of_disease_association.svg b/graphviz/genotype_as_a_model_of_disease_association.svg index 7153942da0..b5b6a320ff 100644 --- a/graphviz/genotype_as_a_model_of_disease_association.svg +++ b/graphviz/genotype_as_a_model_of_disease_association.svg @@ -4,16 +4,16 @@ - + %3 - + genotype as a model of disease association - -genotype as a model of disease association + +genotype as a model of disease association @@ -24,9 +24,9 @@ genotype as a model of disease association->genotype to disease association - - -is_a + + +is_a @@ -37,9 +37,9 @@ genotype as a model of disease association->model to disease association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ genotype as a model of disease association->entity to disease association mixin - - -uses + + +uses @@ -63,9 +63,9 @@ genotype as a model of disease association->id - - -id + + +id @@ -76,9 +76,9 @@ genotype as a model of disease association->iri - - -iri + + +iri @@ -89,9 +89,9 @@ genotype as a model of disease association->name - - -name + + +name @@ -102,9 +102,9 @@ genotype as a model of disease association->description - - -description + + +description @@ -115,9 +115,9 @@ genotype as a model of disease association->has attribute - - -has attribute + + +has attribute @@ -128,9 +128,9 @@ genotype as a model of disease association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ genotype as a model of disease association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ genotype as a model of disease association->publications - - -publications + + +publications @@ -167,402 +167,402 @@ genotype as a model of disease association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string genotype as a model of disease association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string genotype as a model of disease association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string genotype as a model of disease association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type genotype as a model of disease association->timepoint - - -timepoint + + +timepoint original subject - -string + +string genotype as a model of disease association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie genotype as a model of disease association->original predicate - - -original predicate + + +original predicate original object - -string + +string genotype as a model of disease association->original object - - -original object + + +original object subject category - -ontology class + +ontology class genotype as a model of disease association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class genotype as a model of disease association->object category - - -object category + + +object category subject closure - -string + +string genotype as a model of disease association->subject closure - - -subject closure + + +subject closure object closure - -string + +string genotype as a model of disease association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class genotype as a model of disease association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class genotype as a model of disease association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string genotype as a model of disease association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string genotype as a model of disease association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string genotype as a model of disease association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string genotype as a model of disease association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source genotype as a model of disease association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type genotype as a model of disease association->type - - -type + + +type category - -category + +category genotype as a model of disease association->category - - -category + + +category predicate - -predicate + +predicate genotype as a model of disease association->predicate - - -predicate + + +predicate object - -object + +object genotype as a model of disease association->object - - -object + + +object frequency qualifier - -frequency value + +frequency value genotype as a model of disease association->frequency qualifier - - -frequency qualifier + + +frequency qualifier severity qualifier - -severity value + +severity value genotype as a model of disease association->severity qualifier - - -severity qualifier + + +severity qualifier onset qualifier - -onset + +onset genotype as a model of disease association->onset qualifier - - -onset qualifier + + +onset qualifier subject - -subject + +subject genotype as a model of disease association->subject - - -subject + + +subject association_type - -string + +string association_category - -category type + +category type genotype to disease association_predicate - -predicate type + +predicate type relation - -relation + +relation object->relation - - + + genotype to disease association_object - -named thing + +named thing subject->object - - -relation + + +relation subject->relation - - + + genotype as a model of disease association_subject - -genotype + +genotype diff --git a/graphviz/genotype_to_disease_association.gv b/graphviz/genotype_to_disease_association.gv index 77a41a4b55..5d9ef3fc6f 100644 --- a/graphviz/genotype_to_disease_association.gv +++ b/graphviz/genotype_to_disease_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,5946.4,283"]; + graph [bb="0,0,5728.4,283"]; node [label="\N"]; "genotype to disease association" [height=0.5, label="genotype to disease association", - pos="3267.4,265", + pos="3049.4,265", width=4.3871]; association [height=0.5, pos="62.394,178", width=1.7332]; "genotype to disease association" -> association [label=is_a, lp="638.39,221.5", - pos="e,106.72,190.67 3110.1,263.03 2618.1,259.84 1112.7,248.66 624.39,229 406.3,220.22 350.23,228.52 134.39,196 128.62,195.13 122.62,\ + pos="e,106.72,190.67 2891.1,264.61 2504.1,265.46 1478.9,263.92 624.39,229 406.31,220.09 350.23,228.52 134.39,196 128.62,195.13 122.62,\ 194.03 116.66,192.81"]; "genotype to entity association mixin" [height=0.5, pos="322.39,178", width=4.9829]; "genotype to disease association" -> "genotype to entity association mixin" [label=uses, - lp="858.89,221.5", - pos="e,432.51,192.21 3110.1,263.41 2645.7,261.38 1285.9,253.48 842.39,229 704.99,221.42 547.8,205.26 442.54,193.35"]; + lp="857.89,221.5", + pos="e,432.81,192.23 2891.9,263.15 2456.3,260.53 1240.8,251.37 841.39,229 704.48,221.33 547.87,205.23 442.81,193.36"]; "entity to disease association mixin" [height=0.5, pos="690.39,178", width=4.7482]; "genotype to disease association" -> "entity to disease association mixin" [label=uses, - lp="1013.9,221.5", - pos="e,764.77,194.24 3109.4,264.57 2664.8,265.69 1408.3,265.43 997.39,229 921.6,222.28 836.24,207.81 774.8,196.16"]; + lp="1012.9,221.5", + pos="e,764.84,194.27 2891.4,264.27 2476.7,264.5 1363.4,261.94 996.39,229 920.98,222.23 836.05,207.8 774.83,196.18"]; id [color=blue, height=0.5, label=string, @@ -31,9 +31,9 @@ digraph { width=1.0652]; "genotype to disease association" -> id [color=blue, label=id, - lp="1131.4,221.5", - pos="e,946.38,189.98 3110.1,263.14 2648.8,260.39 1319.5,250.64 1124.4,229 1052.7,221.04 1034.9,215.43 965.39,196 962.29,195.13 959.09,\ -194.17 955.89,193.15", + lp="1130.4,221.5", + pos="e,946.38,189.97 2892.6,262.84 2464.6,259.44 1296.6,248.48 1123.4,229 1052.1,220.98 1034.5,215.35 965.39,196 962.29,195.13 959.09,\ +194.16 955.89,193.14", style=solid]; iri [color=blue, height=0.5, @@ -42,9 +42,9 @@ digraph { width=1.2277]; "genotype to disease association" -> iri [color=blue, label=iri, - lp="1244.4,221.5", - pos="e,1051.3,190.19 3110.5,262.93 2666.3,259.65 1420.3,248.81 1236.4,229 1162,220.99 1143.8,214.78 1071.4,196 1068,195.12 1064.5,194.16 \ -1061.1,193.14", + lp="1235.4,221.5", + pos="e,1051.3,190.13 2892.6,262.69 2480.9,259 1390.1,247.6 1227.4,229 1157,220.95 1139.9,214.18 1071.4,196 1068,195.11 1064.5,194.12 \ +1061.1,193.1", style=solid]; name [color=blue, height=0.5, @@ -53,8 +53,8 @@ digraph { width=1.5707]; "genotype to disease association" -> name [color=blue, label=name, - lp="1351.4,221.5", - pos="e,1175.2,191.54 3110.1,263.27 2680,260.98 1505,252.61 1331.4,229 1280.6,222.09 1224,206.58 1185.1,194.65", + lp="1337.4,221.5", + pos="e,1173.7,191.99 2892.4,263.07 2495,260.41 1470.4,251.43 1317.4,229 1270.9,222.18 1219.4,207.07 1183.4,195.23", style=solid]; description [color=blue, height=0.5, @@ -63,8 +63,8 @@ digraph { width=2.0943]; "genotype to disease association" -> description [color=blue, label=description, - lp="1471.9,221.5", - pos="e,1321.2,194.15 3109.6,263.83 2694.7,262.98 1593.9,258 1431.4,229 1396.6,222.78 1358.8,209.42 1330.7,198.07", + lp="1448.9,221.5", + pos="e,1316.7,194.75 2891.4,263.94 2508.2,263.34 1550.6,258.81 1408.4,229 1379.7,222.98 1349.1,210.3 1325.9,199.22", style=solid]; "has attribute" [color=blue, height=0.5, @@ -73,8 +73,8 @@ digraph { width=1.4443]; "genotype to disease association" -> "has attribute" [color=blue, label="has attribute", - lp="1617.4,221.5", - pos="e,1462,192.95 3109.9,263.68 2717.8,262.46 1718.9,256.65 1570.4,229 1535.9,222.58 1498.6,208.62 1471.5,197.07", + lp="1580.4,221.5", + pos="e,1455.7,194.25 2891.4,264.23 2529.6,264.19 1662.3,260.74 1533.4,229 1509,222.98 1483.6,210.39 1464.4,199.35", style=solid]; negated [color=blue, height=0.5, @@ -83,8 +83,8 @@ digraph { width=1.2999]; "genotype to disease association" -> negated [color=blue, label=negated, - lp="1772.4,221.5", - pos="e,1583.2,190.46 3109.4,264.57 2774.8,265.1 2003.6,262.49 1743.4,229 1690.8,222.23 1632.1,205.81 1593.2,193.62", + lp="1712.4,221.5", + pos="e,1577.4,192.55 2892.4,262.9 2558.5,260.12 1799.1,251.42 1683.4,229 1649.5,222.44 1612.9,208.27 1586.6,196.69", style=solid]; qualifiers [color=blue, height=0.5, @@ -93,8 +93,8 @@ digraph { width=2.1304]; "genotype to disease association" -> qualifiers [color=blue, label=qualifiers, - lp="1910.9,221.5", - pos="e,1732.1,193.2 3109.4,264.7 2797.1,265.33 2110.7,262.65 1877.4,229 1830.7,222.26 1778.9,207.87 1741.7,196.25", + lp="1815.9,221.5", + pos="e,1713.3,195.43 2891.6,263.75 2575.6,262.66 1886.7,257.04 1782.4,229 1760.9,223.21 1738.9,211.5 1721.8,200.86", style=solid]; publications [color=blue, height=0.5, @@ -103,8 +103,8 @@ digraph { width=1.7332]; "genotype to disease association" -> publications [color=blue, label=publications, - lp="2056.4,221.5", - pos="e,1883.1,192.85 3109.5,264.82 2820.8,265.46 2218.8,262.53 2012.4,229 1971,222.28 1925.6,207.95 1892.8,196.35", + lp="1907.4,221.5", + pos="e,1848.1,196.25 2891.4,264.14 2577.9,263.75 1903.7,259.36 1863.4,229 1856.2,223.56 1852.1,214.83 1849.9,206.18", style=solid]; "has evidence" [color=blue, height=0.5, @@ -113,308 +113,309 @@ digraph { width=2.0943]; "genotype to disease association" -> "has evidence" [color=blue, label="has evidence", - lp="2214.9,221.5", - pos="e,2041.4,193.63 3109.6,264.06 2850.1,263.3 2344.6,257.98 2168.4,229 2128,222.35 2083.6,208.52 2051.1,197.09", + lp="2005.9,221.5", + pos="e,1975.3,194.88 2891.3,264.64 2596.9,265.06 1991.2,261.88 1959.4,229 1950.8,220.11 1957.1,209.91 1967.3,201.06", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2205.4,178", - width=3.015]; + label=string, + pos="2135.4,178", + width=1.0652]; "genotype to disease association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2369.9,221.5", - pos="e,2230.9,195.61 3111.7,261.95 2859.2,258.09 2381.1,248.32 2305.4,229 2282.3,223.1 2258.3,211.34 2239.6,200.71", + lp="2123.9,221.5", + pos="e,2104.9,189.23 2891.6,264.08 2619.4,263.43 2087.8,258.39 2059.4,229 2054.8,224.2 2055.8,219.61 2059.4,214 2063.9,207 2079.6,199.25 \ +2095.5,192.84", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2440.4,178", - width=3.015]; + label=string, + pos="2230.4,178", + width=1.0652]; "genotype to disease association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2541.4,221.5", - pos="e,2437.4,196.33 3110.6,262.49 2879,259.52 2470.3,251.16 2446.4,229 2440.3,223.32 2437.9,214.91 2437.3,206.59", + lp="2290.4,221.5", + pos="e,2209.8,193.24 2892.3,263.11 2652.2,260.97 2219.1,253.69 2195.4,229 2187,220.29 2193.1,209.43 2202.3,200.05", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2675.4,178", - width=3.015]; + label=string, + pos="2372.4,178", + width=1.0652]; "genotype to disease association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2749.9,221.5", - pos="e,2653.6,195.87 3113.9,260.61 2934.4,255.88 2659.4,245.91 2643.4,229 2636.2,221.43 2639.7,212.05 2646.6,203.46", + lp="2510.9,221.5", + pos="e,2378.5,196.02 2892.3,262.91 2714.9,260.52 2445.4,252.94 2404.4,229 2395.1,223.61 2388.1,214.35 2383.1,205.26", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2857.4,178", + pos="2599.4,178", width=1.5346]; "genotype to disease association" -> timepoint [color=blue, label=timepoint, - lp="2904.4,221.5", - pos="e,2856.8,196.43 3117.7,259.19 3012.9,254.42 2888.4,245.38 2869.4,229 2862.9,223.36 2859.5,214.85 2858,206.44", + lp="2673.4,221.5", + pos="e,2607.8,195.97 2891.9,263.45 2794.9,260.66 2681.3,252.25 2638.4,229 2628.1,223.43 2619.7,213.89 2613.3,204.63", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2969.4,178", + pos="2711.4,178", width=1.0652]; "genotype to disease association" -> "original subject" [color=blue, label="original subject", - lp="3002.4,221.5", - pos="e,2953.6,194.82 3124.9,257.13 3045,251.78 2958.8,242.88 2946.4,229 2939.7,221.56 2942.3,211.86 2947.8,202.98", + lp="2776.4,221.5", + pos="e,2709.7,196.27 2908.3,256.82 2825.6,251.25 2734.6,242.23 2720.4,229 2714.2,223.25 2711.4,214.83 2710.3,206.52", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3083.4,178", + pos="2836.4,178", width=1.5887]; "genotype to disease association" -> "original predicate" [color=blue, label="original predicate", - lp="3128.9,221.5", - pos="e,3069.6,195.8 3137.6,254.69 3104.8,249.53 3075.9,241.49 3065.4,229 3059.5,222.05 3060.9,213.06 3064.7,204.62", + lp="2906.9,221.5", + pos="e,2834.1,196.02 2921.1,254.47 2886.5,249.28 2855.3,241.3 2843.4,229 2837.6,222.99 2835.1,214.49 2834.3,206.2", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3197.4,178", + pos="2965.4,178", width=1.0652]; "genotype to disease association" -> "original object" [color=blue, label="original object", - lp="3252.9,221.5", - pos="e,3194.9,196.07 3221.7,247.64 3213.8,242.81 3206.5,236.69 3201.4,229 3197,222.32 3195.2,214 3194.8,206.08", + lp="3034.9,221.5", + pos="e,2968.4,196.35 3007,247.47 2998.3,242.56 2989.9,236.45 2983.4,229 2977.8,222.53 2973.9,214.18 2971.2,206.16", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3330.4,178", + pos="3098.4,178", width=2.1304]; "genotype to disease association" -> "subject category" [color=blue, label="subject category", - lp="3376.9,221.5", - pos="e,3325,196.22 3290.8,247.1 3297.1,241.81 3303.5,235.61 3308.4,229 3313.6,221.97 3317.9,213.49 3321.3,205.54", + lp="3155.9,221.5", + pos="e,3098.6,196.17 3074.8,247.12 3080.8,241.98 3086.5,235.86 3090.4,229 3094.2,222.15 3096.4,213.99 3097.5,206.26", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3501.4,178", + pos="3269.4,178", width=2.1304]; "genotype to disease association" -> "object category" [color=blue, label="object category", - lp="3519.9,221.5", - pos="e,3485.3,195.91 3371.6,251.43 3394.9,246.31 3419.1,239.12 3440.4,229 3454,222.54 3467.2,212.41 3477.8,202.94", + lp="3295.9,221.5", + pos="e,3256.8,195.95 3157,251.7 3178.5,246.56 3200.3,239.29 3219.4,229 3231,222.72 3241.8,212.86 3250.2,203.55", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3634.4,178", + pos="3402.4,178", width=1.0652]; "genotype to disease association" -> "subject closure" [color=blue, label="subject closure", - lp="3656.9,221.5", - pos="e,3621.3,195.42 3379.4,252.24 3467,242.92 3574.7,231.12 3579.4,229 3592.6,223.04 3604.7,212.72 3614.3,203", + lp="3429.9,221.5", + pos="e,3391.7,195.4 3160.6,252.17 3246.3,242.92 3350.9,231.25 3355.4,229 3367.1,223.13 3377.4,213.1 3385.4,203.55", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3733.4,178", + pos="3515.4,178", width=1.0652]; "genotype to disease association" -> "object closure" [color=blue, label="object closure", - lp="3777.4,221.5", - pos="e,3731.9,196.2 3378.3,252.12 3397,250.29 3416.2,248.5 3434.4,247 3465.6,244.42 3690.4,247.8 3715.4,229 3722.7,223.5 3727.1,214.76 \ -3729.6,206.11", + lp="3552.4,221.5", + pos="e,3510.9,195.9 3160.3,252.16 3179,250.32 3198.2,248.52 3216.4,247 3246.6,244.47 3462.9,245.37 3488.4,229 3496.9,223.52 3503,214.38 \ +3507.1,205.4", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3866.4,178", + pos="3648.4,178", width=2.1304]; "genotype to disease association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3935.9,221.5", - pos="e,3859.4,196.09 3376.9,251.96 3396.1,250.11 3415.8,248.37 3434.4,247 3478.4,243.76 3792.7,250.27 3831.4,229 3841.1,223.64 3848.8,\ -214.27 3854.4,205.07", + lp="3712.9,221.5", + pos="e,3639.1,196.16 3158.9,251.98 3178.1,250.12 3197.8,248.37 3216.4,247 3259.7,243.8 3567.5,248.22 3606.4,229 3617.3,223.61 3626.4,\ +213.97 3633.4,204.58", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="4059.4,178", + pos="3841.4,178", width=2.1304]; "genotype to disease association" -> "object category closure" [color=blue, label="object category closure", - lp="4126.9,221.5", - pos="e,4053.4,196.11 3375.5,251.86 3395.1,249.98 3415.3,248.26 3434.4,247 3467.3,244.83 3998.7,245.26 4027.4,229 4036.8,223.66 4043.9,\ -214.29 4049,205.09", + lp="3904.9,221.5", + pos="e,3833.7,196.18 3157.5,251.86 3177.1,249.99 3197.3,248.26 3216.4,247 3249,244.84 3775.4,244.15 3804.4,229 3814.5,223.69 3822.6,214.19 \ +3828.6,204.89", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4249.4,178", + pos="4031.4,178", width=1.0652]; "genotype to disease association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4299.4,221.5", - pos="e,4242.4,196.18 3375.1,251.78 3394.8,249.91 3415.2,248.2 3434.4,247 3477.7,244.3 4176.2,249.46 4214.4,229 4224.2,223.75 4231.9,214.39 \ -4237.5,205.18", + lp="4078.4,221.5", + pos="e,4023.4,195.74 3157.1,251.79 3176.8,249.91 3197.2,248.2 3216.4,247 3259.4,244.31 3953.9,248.37 3992.4,229 4003.1,223.62 4011.7,\ +213.8 4018.1,204.27", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4408.4,178", + pos="4190.4,178", width=1.0652]; "genotype to disease association" -> "object namespace" [color=blue, label="object namespace", - lp="4452.4,221.5", - pos="e,4401,195.73 3374.6,251.77 3394.5,249.88 3415,248.17 3434.4,247 3486.4,243.86 4325.1,252.88 4371.4,229 4381.7,223.67 4389.9,213.99 \ -4395.9,204.55", + lp="4232.4,221.5", + pos="e,4182.1,195.77 3156.6,251.77 3176.5,249.88 3197,248.17 3216.4,247 3268.2,243.87 4103.8,251.93 4150.4,229 4161.2,223.66 4170.1,213.84 \ +4176.7,204.3", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4559.4,178", + pos="4341.4,178", width=1.0652]; "genotype to disease association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4612.4,221.5", - pos="e,4551.4,195.77 3374.6,251.72 3394.5,249.84 3415,248.14 3434.4,247 3494.6,243.44 4466.4,255.92 4520.4,229 4531.1,223.66 4539.8,213.84 \ -4546.2,204.3", + lp="4392.4,221.5", + pos="e,4332.8,195.79 3156.6,251.72 3176.5,249.84 3197,248.14 3216.4,247 3276.5,243.45 4246.2,255.21 4300.4,229 4311.4,223.69 4320.4,213.87 \ +4327.2,204.33", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4730.4,178", + pos="4512.4,178", width=1.0652]; "genotype to disease association" -> "object label closure" [color=blue, label="object label closure", - lp="4777.9,221.5", - pos="e,4722.1,195.79 3374.2,251.73 3394.2,249.83 3414.9,248.13 3434.4,247 3469.2,244.98 4659.1,244.34 4690.4,229 4701.2,223.69 4710.1,\ -213.87 4716.7,204.33", + lp="4559.9,221.5", + pos="e,4503.5,195.81 3156.2,251.73 3176.2,249.83 3196.9,248.13 3216.4,247 3251.2,244.98 4438.9,243.94 4470.4,229 4481.5,223.71 4490.8,\ +213.9 4497.7,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4872.4,178", + pos="4654.4,178", width=2.347]; "genotype to disease association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4933.9,221.5", - pos="e,4870,196.45 3374.2,251.71 3394.2,249.81 3414.9,248.11 3434.4,247 3473.7,244.75 4818.7,251 4851.4,229 4859.2,223.72 4864.1,214.91 \ -4867.2,206.14", + lp="4715.9,221.5", + pos="e,4652,196.45 3156.2,251.71 3176.2,249.81 3196.9,248.11 3216.4,247 3255.7,244.75 4600.7,251 4633.4,229 4641.2,223.72 4646.1,214.91 \ +4649.2,206.14", style=solid]; type [height=0.5, - pos="5006.4,178", + pos="4788.4,178", width=0.86659]; "genotype to disease association" -> type [color=blue, label=type, - lp="5030.4,221.5", - pos="e,5012.3,196.12 3374.2,251.69 3394.2,249.79 3414.9,248.1 3434.4,247 3456.2,245.77 4992,244.54 5007.4,229 5013.3,223.03 5014.6,214.44 \ -5013.9,206.05", + lp="4812.4,221.5", + pos="e,4794.3,196.12 3156.2,251.69 3176.2,249.79 3196.9,248.1 3216.4,247 3238.2,245.77 4774,244.54 4789.4,229 4795.3,223.03 4796.6,214.44 \ +4795.9,206.05", style=solid]; category [height=0.5, - pos="5107.4,178", + pos="4889.4,178", width=1.4263]; "genotype to disease association" -> category [color=blue, label=category, - lp="5106.9,221.5", - pos="e,5094.4,195.45 3374.2,251.68 3394.2,249.79 3414.9,248.1 3434.4,247 3479.2,244.47 5008.5,245.05 5050.4,229 5064.5,223.6 5077.4,212.99 \ -5087.4,202.94", + lp="4888.9,221.5", + pos="e,4876.4,195.45 3156.2,251.68 3176.2,249.79 3196.9,248.1 3216.4,247 3261.2,244.47 4790.5,245.05 4832.4,229 4846.5,223.6 4859.4,212.99 \ +4869.4,202.94", style=solid]; subject [height=0.5, - pos="5221.4,178", + pos="5003.4,178", width=1.2277]; "genotype to disease association" -> subject [color=blue, label=subject, - lp="5201.4,221.5", - pos="e,5203.4,194.55 3374.2,251.67 3394.2,249.78 3414.9,248.09 3434.4,247 3529.1,241.69 5051.4,255.9 5142.4,229 5161.7,223.31 5180.7,\ -211.44 5195.3,200.69", + lp="4983.4,221.5", + pos="e,4985.4,194.55 3156.2,251.67 3176.2,249.78 3196.9,248.09 3216.4,247 3311.1,241.69 4833.4,255.9 4924.4,229 4943.7,223.31 4962.7,\ +211.44 4977.3,200.69", style=solid]; predicate [height=0.5, - pos="5338.4,178", + pos="5120.4,178", width=1.5165]; "genotype to disease association" -> predicate [color=blue, label=predicate, - lp="5308.4,221.5", - pos="e,5314,194.11 3374.2,251.66 3394.2,249.77 3414.9,248.09 3434.4,247 3534.1,241.44 5134,251.14 5231.4,229 5257.4,223.09 5284.6,210.27 \ -5305.1,199.1", + lp="5090.4,221.5", + pos="e,5096,194.11 3156.2,251.66 3176.2,249.77 3196.9,248.09 3216.4,247 3316.1,241.44 4916,251.14 5013.4,229 5039.4,223.09 5066.6,210.27 \ +5087.1,199.1", style=solid]; object [height=0.5, - pos="5288.4,91", + pos="5070.4,91", width=1.0832]; "genotype to disease association" -> object [color=blue, label=object, - lp="5430.4,178", - pos="e,5318.2,102.71 3374.2,251.65 3394.2,249.76 3414.9,248.08 3434.4,247 3540.5,241.11 5244,257.43 5346.4,229 5374.2,221.27 5388.1,221.08 \ -5402.4,196 5424.7,156.94 5368.7,124.38 5327.5,106.59", + lp="5212.4,178", + pos="e,5100.2,102.71 3156.2,251.65 3176.2,249.76 3196.9,248.08 3216.4,247 3322.5,241.11 5026,257.43 5128.4,229 5156.2,221.27 5170.1,221.08 \ +5184.4,196 5206.7,156.94 5150.7,124.38 5109.5,106.59", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="5576.4,178", + pos="5358.4,178", width=2.3651]; "genotype to disease association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="5564.4,221.5", - pos="e,5544.2,194.74 3373.7,251.69 3393.9,249.78 3414.8,248.09 3434.4,247 3545.8,240.84 5333.7,249.45 5443.4,229 5475.1,223.09 5509.1,\ -210.17 5534.8,198.94", + lp="5346.4,221.5", + pos="e,5326.2,194.74 3155.7,251.69 3175.9,249.78 3196.8,248.09 3216.4,247 3327.8,240.84 5115.7,249.45 5225.4,229 5257.1,223.09 5291.1,\ +210.17 5316.8,198.94", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="5755.4,178", + pos="5537.4,178", width=2.1123]; "genotype to disease association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="5745.4,221.5", - pos="e,5726.6,194.86 3373.7,251.68 3393.9,249.77 3414.8,248.08 3434.4,247 3556.5,240.3 5516.6,253.66 5636.4,229 5664.8,223.16 5694.8,\ -210.48 5717.6,199.35", + lp="5527.4,221.5", + pos="e,5508.6,194.86 3155.7,251.68 3175.9,249.77 3196.8,248.08 3216.4,247 3338.5,240.3 5298.6,253.66 5418.4,229 5446.8,223.16 5476.8,\ +210.48 5499.6,199.35", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="5892.4,178", + pos="5674.4,178", width=1.011]; "genotype to disease association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="5894.9,221.5", - pos="e,5874.5,193.85 3373.7,251.67 3393.9,249.76 3414.8,248.07 3434.4,247 3500.3,243.4 5746.9,247.09 5810.4,229 5830.6,223.23 5850.9,\ -211 5866.1,200.07", + lp="5676.9,221.5", + pos="e,5656.5,193.85 3155.7,251.67 3175.9,249.76 3196.8,248.07 3216.4,247 3282.3,243.4 5528.9,247.09 5592.4,229 5612.6,223.23 5632.9,\ +211 5648.1,200.07", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3481.4,265", + pos="3263.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3612.4,265", + pos="3394.4,265", width=2.0762]; subject -> object [label=relation, - lp="5287.4,134.5", - pos="e,5275.7,108.05 5234.3,160.61 5244.3,147.95 5258.3,130.24 5269.5,115.98"]; + lp="5069.4,134.5", + pos="e,5057.7,108.05 5016.3,160.61 5026.3,147.95 5040.3,130.24 5051.5,115.98"]; relation [height=0.5, - pos="5233.4,18", + pos="5015.4,18", width=1.2999]; - subject -> relation [pos="e,5232.1,36.188 5222.7,159.79 5224.8,132.48 5228.8,78.994 5231.3,46.38", + subject -> relation [pos="e,5014.1,36.188 5004.7,159.79 5006.8,132.48 5010.8,78.994 5013.3,46.38", style=dotted]; "genotype to disease association_subject" [color=blue, height=0.5, label="named thing", - pos="3774.4,265", + pos="3556.4,265", width=1.9318]; "genotype to disease association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3940.4,265", + pos="3722.4,265", width=2.1665]; - object -> relation [pos="e,5246.2,35.54 5275.9,73.889 5269,64.939 5260.2,53.617 5252.4,43.584", + object -> relation [pos="e,5028.2,35.54 5057.9,73.889 5051,64.939 5042.2,53.617 5034.4,43.584", style=dotted]; "genotype to disease association_object" [color=blue, height=0.5, label="named thing", - pos="4106.4,265", + pos="3888.4,265", width=1.9318]; } diff --git a/graphviz/genotype_to_disease_association.svg b/graphviz/genotype_to_disease_association.svg index 1600312660..bebef41d51 100644 --- a/graphviz/genotype_to_disease_association.svg +++ b/graphviz/genotype_to_disease_association.svg @@ -4,16 +4,16 @@ - + %3 - + genotype to disease association - -genotype to disease association + +genotype to disease association @@ -24,7 +24,7 @@ genotype to disease association->association - + is_a @@ -37,9 +37,9 @@ genotype to disease association->genotype to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ genotype to disease association->entity to disease association mixin - - -uses + + +uses @@ -63,9 +63,9 @@ genotype to disease association->id - - -id + + +id @@ -76,9 +76,9 @@ genotype to disease association->iri - - -iri + + +iri @@ -89,9 +89,9 @@ genotype to disease association->name - - -name + + +name @@ -102,9 +102,9 @@ genotype to disease association->description - - -description + + +description @@ -115,9 +115,9 @@ genotype to disease association->has attribute - - -has attribute + + +has attribute @@ -128,9 +128,9 @@ genotype to disease association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ genotype to disease association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ genotype to disease association->publications - - -publications + + +publications @@ -167,402 +167,402 @@ genotype to disease association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string genotype to disease association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string genotype to disease association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string genotype to disease association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type genotype to disease association->timepoint - - -timepoint + + +timepoint original subject - -string + +string genotype to disease association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie genotype to disease association->original predicate - - -original predicate + + +original predicate original object - -string + +string genotype to disease association->original object - - -original object + + +original object subject category - -ontology class + +ontology class genotype to disease association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class genotype to disease association->object category - - -object category + + +object category subject closure - -string + +string genotype to disease association->subject closure - - -subject closure + + +subject closure object closure - -string + +string genotype to disease association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class genotype to disease association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class genotype to disease association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string genotype to disease association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string genotype to disease association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string genotype to disease association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string genotype to disease association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source genotype to disease association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type genotype to disease association->type - - -type + + +type category - -category + +category genotype to disease association->category - - -category + + +category subject - -subject + +subject genotype to disease association->subject - - -subject + + +subject predicate - -predicate + +predicate genotype to disease association->predicate - - -predicate + + +predicate object - -object + +object genotype to disease association->object - - -object + + +object frequency qualifier - -frequency value + +frequency value genotype to disease association->frequency qualifier - - -frequency qualifier + + +frequency qualifier severity qualifier - -severity value + +severity value genotype to disease association->severity qualifier - - -severity qualifier + + +severity qualifier onset qualifier - -onset + +onset genotype to disease association->onset qualifier - - -onset qualifier + + +onset qualifier association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + genotype to disease association_subject - -named thing + +named thing genotype to disease association_predicate - -predicate type + +predicate type object->relation - - + + genotype to disease association_object - -named thing + +named thing diff --git a/graphviz/genotype_to_gene_association.gv b/graphviz/genotype_to_gene_association.gv index 8304b56dcf..f986b1894f 100644 --- a/graphviz/genotype_to_gene_association.gv +++ b/graphviz/genotype_to_gene_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4738.4,283"]; + graph [bb="0,0,4553.4,283"]; node [label="\N"]; "genotype to gene association" [height=0.5, label="genotype to gene association", - pos="2468.4,265", + pos="2283.4,265", width=4.0441]; association [height=0.5, pos="62.394,178", width=1.7332]; "genotype to gene association" -> association [label=is_a, lp="280.39,221.5", - pos="e,102.91,191.79 2323.2,263.58 1865.2,262 468.8,255.08 266.39,229 213.1,222.13 153.57,206.61 112.64,194.66"]; + pos="e,102.91,191.77 2138.4,263.35 1707,261.16 450.04,252.8 266.39,229 213.11,222.1 153.58,206.57 112.65,194.64"]; id [color=blue, height=0.5, label=string, @@ -18,8 +18,8 @@ digraph { width=1.0652]; "genotype to gene association" -> id [color=blue, label=id, - lp="396.39,221.5", - pos="e,210.38,189.98 2323.3,263.12 1882.8,260.25 579.73,250.04 389.39,229 317.23,221.02 299.34,215.5 229.39,196 226.29,195.13 223.09,\ + lp="395.39,221.5", + pos="e,210.38,189.98 2138.5,262.88 1725.3,259.46 560.07,248.23 388.39,229 316.67,220.97 298.9,215.43 229.39,196 226.29,195.13 223.09,\ 194.17 219.89,193.15", style=solid]; iri [color=blue, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "genotype to gene association" -> iri [color=blue, label=iri, - lp="509.39,221.5", - pos="e,315.3,190.2 2323.7,262.92 1899.9,259.54 680.48,248.24 501.39,229 426.6,220.97 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ -325.06,193.15", + lp="501.39,221.5", + pos="e,315.32,190.15 2137.6,264.65 1769.7,265.72 810.35,264.88 493.39,229 422.11,220.93 404.75,214.31 335.39,196 332.02,195.11 328.55,\ +194.13 325.07,193.11", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "genotype to gene association" -> name [color=blue, label=name, - lp="616.39,221.5", - pos="e,439.35,191.54 2323.3,263.22 1913.4,260.75 765.25,251.86 596.39,229 545.26,222.08 488.24,206.51 449.14,194.57", + lp="604.39,221.5", + pos="e,437.98,191.87 2138.5,263.06 1755.5,260.27 735.68,250.88 584.39,229 537.02,222.15 484.46,206.96 447.86,195.11", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "genotype to gene association" -> description [color=blue, label=description, - lp="736.89,221.5", - pos="e,585.45,194.14 2322.9,263.73 1927.8,262.62 854.12,257.03 696.39,229 661.33,222.77 623.33,209.4 595.03,198.06", + lp="717.89,221.5", + pos="e,581.77,194.62 2138,263.77 1769.4,262.78 817.95,257.46 677.39,229 647.36,222.92 615.28,210.09 591.01,198.95", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "genotype to gene association" -> "has attribute" [color=blue, label="has attribute", - lp="882.39,221.5", - pos="e,725.98,192.82 2323,263.57 1950.1,262.07 979.07,255.64 835.39,229 800.43,222.52 762.57,208.39 735.2,196.8", + lp="852.39,221.5", + pos="e,721.33,194.01 2137.8,263.89 1790.5,263.16 932.55,258.35 805.39,229 778.89,222.88 751.04,209.98 730.13,198.82", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "genotype to gene association" -> negated [color=blue, label=negated, - lp="1038.4,221.5", - pos="e,847.59,190.46 2322.9,264.31 2005.6,264.38 1260,260.99 1009.4,229 956.09,222.2 896.47,205.66 857.14,193.46", + lp="990.39,221.5", + pos="e,843.03,191.96 2139,262.61 1820.1,259.19 1074.6,249.15 961.39,229 923.37,222.23 881.85,207.52 852.5,195.8", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "genotype to gene association" -> qualifiers [color=blue, label=qualifiers, - lp="1178.9,221.5", - pos="e,996.68,193.07 2322.9,264.36 2027.9,264.39 1368.8,260.76 1145.4,229 1097.6,222.2 1044.5,207.74 1006.5,196.11", + lp="1101.9,221.5", + pos="e,982.4,194.93 2138.5,262.94 1838.9,260.28 1170.1,251.86 1068.4,229 1041.6,222.97 1013.3,210.59 991.57,199.66", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "genotype to gene association" -> publications [color=blue, label=publications, - lp="1326.4,221.5", - pos="e,1148.1,192.71 2322.9,264.33 2051.6,264.18 1478.5,260.04 1282.4,229 1239.3,222.18 1191.8,207.69 1157.8,196.06", + lp="1202.4,221.5", + pos="e,1121.9,195.78 2139.2,262.44 1845.6,258.86 1202.3,248.8 1158.4,229 1146.3,223.57 1135.9,213.45 1128,203.73", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,276 +100,276 @@ digraph { width=2.0943]; "genotype to gene association" -> "has evidence" [color=blue, label="has evidence", - lp="1480.9,221.5", - pos="e,1305.9,193.61 2323.1,263.68 2079.9,262.37 1600.9,256.28 1434.4,229 1393.5,222.3 1348.6,208.48 1315.7,197.06", + lp="1300.9,221.5", + pos="e,1255.9,195.88 2137.7,264.32 1861,264.2 1284.5,260.2 1254.4,229 1248.2,222.63 1248.8,213.73 1251.7,205.2", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1469.4,178", - width=3.015]; + label=string, + pos="1399.4,178", + width=1.0652]; "genotype to gene association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1635.9,221.5", - pos="e,1495.5,195.59 2325.3,261.67 2090.5,257.35 1642.2,246.89 1571.4,229 1547.9,223.07 1523.5,211.31 1504.4,200.68", + lp="1419.9,221.5", + pos="e,1375.2,192.24 2138,263.73 1883.6,262.54 1382,256.67 1355.4,229 1345.9,219.09 1354.7,207.6 1366.9,198.13", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1704.4,178", - width=3.015]; + label=string, + pos="1494.4,178", + width=1.0652]; "genotype to gene association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1807.4,221.5", - pos="e,1702.1,196.41 2324.5,261.97 2111.5,258.31 1734.8,249.03 1712.4,229 1706.1,223.34 1703.4,214.82 1702.5,206.41", + lp="1589.4,221.5", + pos="e,1489,196.04 2138.7,262.69 1917,259.95 1516.3,251.87 1494.4,229 1488.6,222.94 1487.2,214.32 1487.7,205.94", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1939.4,178", - width=3.015]; + label=string, + pos="1669.4,178", + width=1.0652]; "genotype to gene association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2015.9,221.5", - pos="e,1918.7,195.97 2328.4,259.97 2167.5,254.65 1923.6,244.13 1909.4,229 1902.4,221.54 1905.6,212.18 1912,203.58", + lp="1809.9,221.5", + pos="e,1676.1,196.02 2139.7,261.9 1980.3,258.53 1740.4,250.02 1703.4,229 1693.8,223.55 1686.4,214.16 1680.9,204.98", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2121.4,178", + pos="1895.4,178", width=1.5346]; "genotype to gene association" -> timepoint [color=blue, label=timepoint, - lp="2171.4,221.5", - pos="e,2121.9,196.47 2337.6,257.08 2251.6,251.37 2152.2,242.06 2136.4,229 2129.6,223.41 2125.9,214.91 2123.8,206.49", + lp="1972.4,221.5", + pos="e,1904.8,195.92 2142.4,260.39 2062.8,256.29 1972.5,247.56 1937.4,229 1926.7,223.32 1917.5,213.63 1910.6,204.28", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2233.4,178", + pos="2007.4,178", width=1.0652]; "genotype to gene association" -> "original subject" [color=blue, label="original subject", - lp="2270.4,221.5", - pos="e,2219.6,194.92 2327,260.54 2277.4,256.1 2230.1,247.04 2214.4,229 2208.1,221.83 2209.9,212.39 2214.3,203.65", + lp="2076.4,221.5", + pos="e,2007.3,196.33 2145,259.4 2092,254.85 2039.6,246.02 2020.4,229 2013.9,223.25 2010.5,214.72 2008.7,206.31", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2347.4,178", + pos="2133.4,178", width=1.5887]; "genotype to gene association" -> "original predicate" [color=blue, label="original predicate", - lp="2397.9,221.5", - pos="e,2336.3,195.76 2383.3,250.35 2361,244.96 2341.3,237.9 2334.4,229 2329.1,222.16 2329.6,213.39 2332.4,205.11", + lp="2207.9,221.5", + pos="e,2132.9,196.42 2198.9,250.29 2174.8,244.78 2152.8,237.66 2144.4,229 2138.6,222.99 2135.5,214.63 2134,206.47", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2461.4,178", + pos="2267.4,178", width=1.0652]; "genotype to gene association" -> "original object" [color=blue, label="original object", - lp="2516.9,221.5", - pos="e,2462.8,196.18 2467,246.8 2466,235.16 2464.7,219.55 2463.6,206.24", + lp="2327.9,221.5", + pos="e,2270.6,196.18 2280.2,246.8 2278,235.16 2275,219.55 2272.5,206.24", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2594.4,178", + pos="2400.4,178", width=2.1304]; "genotype to gene association" -> "subject category" [color=blue, label="subject category", - lp="2642.9,221.5", - pos="e,2590.6,196.4 2538.8,249.24 2551,244.31 2562.8,237.74 2572.4,229 2579.1,222.84 2583.9,214.24 2587.3,205.9", + lp="2452.9,221.5", + pos="e,2398.4,196.3 2352.5,249.14 2363.9,244.22 2374.8,237.69 2383.4,229 2389.5,222.8 2393.5,214.29 2396,206.04", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2765.4,178", + pos="2571.4,178", width=2.1304]; "genotype to gene association" -> "object category" [color=blue, label="object category", - lp="2785.9,221.5", - pos="e,2750.6,195.73 2568.4,251.91 2627.6,244.29 2693.5,234.83 2706.4,229 2720,222.83 2733,212.54 2743.3,202.9", + lp="2593.9,221.5", + pos="e,2557.8,195.72 2382.6,251.82 2440.3,244.26 2504,234.9 2516.4,229 2529.3,222.88 2541.3,212.74 2550.8,203.17", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="2898.4,178", + pos="2704.4,178", width=1.0652]; "genotype to gene association" -> "subject closure" [color=blue, label="subject closure", - lp="2921.9,221.5", - pos="e,2886,195.57 2571.7,252.25 2589,250.41 2606.7,248.59 2623.4,247 2672.7,242.3 2800.2,249.12 2845.4,229 2858.3,223.24 2870.1,212.94 \ -2879.3,203.18", + lp="2728.9,221.5", + pos="e,2692.6,195.55 2386.7,252.29 2404,250.45 2421.7,248.62 2438.4,247 2486.1,242.39 2609.8,248.97 2653.4,229 2665.9,223.27 2677.1,213.12 \ +2685.9,203.45", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="2998.4,178", + pos="2812.4,178", width=1.0652]; "genotype to gene association" -> "object closure" [color=blue, label="object closure", - lp="3042.4,221.5", - pos="e,2997,196.24 2569.6,252.03 2587.5,250.16 2606,248.39 2623.4,247 2663,243.83 2948.5,252.65 2980.4,229 2987.7,223.55 2992.1,214.82 \ -2994.7,206.17", + lp="2851.4,221.5", + pos="e,2808.5,196.4 2384.6,252.05 2402.5,250.18 2421,248.4 2438.4,247 2477.1,243.88 2754.9,250.26 2787.4,229 2795.6,223.62 2801.3,214.66 \ +2805.1,205.8", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3131.4,178", + pos="2945.4,178", width=2.1304]; "genotype to gene association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3200.9,221.5", - pos="e,3124.4,196.12 2568.8,251.94 2586.9,250.05 2605.7,248.3 2623.4,247 2675.8,243.13 3050.2,254.17 3096.4,229 3106.2,223.68 3113.8,\ -214.31 3119.4,205.11", + lp="3010.9,221.5", + pos="e,2936.8,196.18 2383.8,251.94 2401.9,250.06 2420.7,248.31 2438.4,247 2490.2,243.17 2859,252.39 2905.4,229 2916,223.63 2924.8,213.99 \ +2931.3,204.6", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3323.4,178", + pos="3138.4,178", width=2.1304]; "genotype to gene association" -> "object category closure" [color=blue, label="object category closure", - lp="3390.9,221.5", - pos="e,3317.7,196.11 2567.9,251.86 2586.3,249.96 2605.4,248.22 2623.4,247 2660.5,244.47 3260.2,247.52 3292.4,229 3301.6,223.71 3308.4,\ -214.48 3313.3,205.38", + lp="3202.9,221.5", + pos="e,3131.1,196.18 2382.9,251.86 2401.3,249.96 2420.4,248.23 2438.4,247 2475.2,244.49 3069.8,246.27 3102.4,229 3112.4,223.69 3120.3,\ +214.19 3126.1,204.89", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3513.4,178", + pos="3328.4,178", width=1.0652]; "genotype to gene association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3563.4,221.5", - pos="e,3506.4,196.19 2567.5,251.81 2586.1,249.91 2605.3,248.18 2623.4,247 2670.8,243.91 3436.5,251.38 3478.4,229 3488.2,223.76 3495.9,\ -214.41 3501.5,205.19", + lp="3375.4,221.5", + pos="e,3320.7,195.74 2382.9,251.77 2401.3,249.88 2420.4,248.17 2438.4,247 2485.6,243.92 3248.2,250.48 3290.4,229 3300.8,223.68 3309.2,\ +213.99 3315.4,204.56", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3672.4,178", + pos="3487.4,178", width=1.0652]; "genotype to gene association" -> "object namespace" [color=blue, label="object namespace", - lp="3716.4,221.5", - pos="e,3665,195.74 2567.5,251.77 2586.1,249.86 2605.3,248.15 2623.4,247 2679.5,243.43 3585.4,254.75 3635.4,229 3645.7,223.68 3653.9,214 \ -3659.9,204.56", + lp="3529.4,221.5", + pos="e,3479.1,195.77 2382.5,251.77 2401.1,249.86 2420.3,248.15 2438.4,247 2494.3,243.44 3397.1,253.74 3447.4,229 3458.2,223.67 3467.1,\ +213.85 3473.7,204.31", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3823.4,178", + pos="3638.4,178", width=1.0652]; "genotype to gene association" -> "subject label closure" [color=blue, label="subject label closure", - lp="3876.4,221.5", - pos="e,3815.4,195.77 2567.5,251.73 2586,249.83 2605.3,248.13 2623.4,247 2655.6,244.99 3755.5,243.37 3784.4,229 3795.1,223.67 3803.8,213.84 \ -3810.2,204.31", + lp="3689.4,221.5", + pos="e,3629.8,195.79 2382.5,251.73 2401,249.83 2420.3,248.13 2438.4,247 2470.5,244.99 3568.4,243 3597.4,229 3608.4,223.69 3617.4,213.88 \ +3624.2,204.34", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="3994.4,178", + pos="3809.4,178", width=1.0652]; "genotype to gene association" -> "object label closure" [color=blue, label="object label closure", - lp="4041.9,221.5", - pos="e,3986.1,195.79 2567.1,251.75 2585.8,249.83 2605.2,248.12 2623.4,247 2660.3,244.73 3921.2,245.24 3954.4,229 3965.3,223.69 3974.1,\ -213.87 3980.7,204.33", + lp="3856.9,221.5", + pos="e,3800.5,195.81 2382.1,251.75 2400.8,249.83 2420.2,248.12 2438.4,247 2475.2,244.73 3734,244.82 3767.4,229 3778.5,223.72 3787.8,213.91 \ +3794.7,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4147.4,178", + pos="3962.4,178", width=2.347]; "genotype to gene association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4200.9,221.5", - pos="e,4141.4,196.18 2567.1,251.72 2585.8,249.81 2605.2,248.11 2623.4,247 2664.8,244.49 4079.2,249.12 4115.4,229 4124.9,223.75 4131.9,\ -214.39 4137,205.18", + lp="4015.9,221.5", + pos="e,3956.4,196.18 2382.1,251.72 2400.8,249.81 2420.2,248.11 2438.4,247 2479.8,244.49 3894.2,249.12 3930.4,229 3939.9,223.75 3946.9,\ +214.39 3952,205.18", style=solid]; type [height=0.5, - pos="4281.4,178", + pos="4096.4,178", width=0.86659]; "genotype to gene association" -> type [color=blue, label=type, - lp="4299.4,221.5", - pos="e,4284.1,195.98 2567.1,251.71 2585.8,249.8 2605.2,248.1 2623.4,247 2646.3,245.62 4257.2,244.14 4274.4,229 4280.9,223.32 4283.4,214.65 \ -4284.1,206.12", + lp="4114.4,221.5", + pos="e,4099.1,195.98 2382.1,251.71 2400.8,249.8 2420.2,248.1 2438.4,247 2461.3,245.62 4072.2,244.14 4089.4,229 4095.9,223.32 4098.4,214.65 \ +4099.1,206.12", style=solid]; category [height=0.5, - pos="4382.4,178", + pos="4197.4,178", width=1.4263]; "genotype to gene association" -> category [color=blue, label=category, - lp="4377.9,221.5", - pos="e,4367.7,195.48 2567.1,251.7 2585.8,249.79 2605.2,248.09 2623.4,247 2670.4,244.18 4275,244.74 4319.4,229 4334.6,223.59 4349,212.84 \ -4360.1,202.68", + lp="4192.9,221.5", + pos="e,4182.7,195.48 2382.1,251.7 2400.8,249.79 2420.2,248.09 2438.4,247 2485.4,244.18 4090,244.74 4134.4,229 4149.6,223.59 4164,212.84 \ +4175.1,202.68", style=solid]; predicate [height=0.5, - pos="4506.4,178", + pos="4321.4,178", width=1.5165]; "genotype to gene association" -> predicate [color=blue, label=predicate, - lp="4485.4,221.5", - pos="e,4484.7,194.58 2567.1,251.69 2585.8,249.79 2605.2,248.09 2623.4,247 2722.7,241.07 4317.1,253.77 4413.4,229 4435.8,223.25 4458.7,\ -211.04 4476.1,200.13", + lp="4300.4,221.5", + pos="e,4299.7,194.58 2382.1,251.69 2400.8,249.79 2420.2,248.09 2438.4,247 2537.7,241.07 4132.1,253.77 4228.4,229 4250.8,223.25 4273.7,\ +211.04 4291.1,200.13", style=solid]; subject [height=0.5, - pos="4623.4,178", + pos="4438.4,178", width=1.2277]; "genotype to gene association" -> subject [color=blue, label=subject, - lp="4590.4,221.5", - pos="e,4601.1,193.87 2567.1,251.69 2585.8,249.78 2605.2,248.08 2623.4,247 2728.8,240.74 4420.8,253.74 4523.4,229 4547.9,223.1 4573.2,\ -210.33 4592.3,199.18", + lp="4405.4,221.5", + pos="e,4416.1,193.87 2382.1,251.69 2400.8,249.78 2420.2,248.08 2438.4,247 2543.8,240.74 4235.8,253.74 4338.4,229 4362.9,223.1 4388.2,\ +210.33 4407.3,199.18", style=solid]; object [height=0.5, - pos="4666.4,91", + pos="4481.4,91", width=1.0832]; "genotype to gene association" -> object [color=blue, label=object, - lp="4716.4,178", - pos="e,4679.8,108.09 2567.1,251.68 2585.8,249.77 2605.2,248.08 2623.4,247 2734.1,240.44 4513.5,258.67 4620.4,229 4648.2,221.27 4659.2,\ -219.22 4676.4,196 4695,170.92 4698.3,156.9 4689.4,127 4688.4,123.55 4686.9,120.13 4685.1,116.85", + lp="4531.4,178", + pos="e,4494.8,108.09 2382.1,251.68 2400.8,249.77 2420.2,248.08 2438.4,247 2549.1,240.44 4328.5,258.67 4435.4,229 4463.2,221.27 4474.2,\ +219.22 4491.4,196 4510,170.92 4513.3,156.9 4504.4,127 4503.4,123.55 4501.9,120.13 4500.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2670.4,265", + pos="2485.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2801.4,265", + pos="2616.4,265", width=2.0762]; "genotype to gene association_predicate" [color=blue, height=0.5, label="predicate type", - pos="2972.4,265", + pos="2787.4,265", width=2.1665]; subject -> object [label=relation, - lp="4661.4,134.5", - pos="e,4648.5,107.23 4624.5,159.55 4625.7,149.57 4628.2,137.07 4633.4,127 4635.6,122.68 4638.5,118.52 4641.7,114.66"]; + lp="4476.4,134.5", + pos="e,4463.5,107.23 4439.5,159.55 4440.7,149.57 4443.2,137.07 4448.4,127 4450.6,122.68 4453.5,118.52 4456.7,114.66"]; relation [height=0.5, - pos="4611.4,18", + pos="4426.4,18", width=1.2999]; - subject -> relation [pos="e,4612.7,36.188 4622.1,159.79 4620,132.48 4616,78.994 4613.5,46.38", + subject -> relation [pos="e,4427.7,36.188 4437.1,159.79 4435,132.48 4431,78.994 4428.5,46.38", style=dotted]; "genotype to gene association_subject" [color=blue, height=0.5, label=genotype, - pos="3122.4,265", + pos="2937.4,265", width=1.4985]; - object -> relation [pos="e,4624.2,35.54 4653.9,73.889 4647,64.939 4638.2,53.617 4630.4,43.584", + object -> relation [pos="e,4439.2,35.54 4468.9,73.889 4462,64.939 4453.2,53.617 4445.4,43.584", style=dotted]; "genotype to gene association_object" [color=blue, height=0.5, label=gene, - pos="3227.4,265", + pos="3042.4,265", width=0.92075]; } diff --git a/graphviz/genotype_to_gene_association.svg b/graphviz/genotype_to_gene_association.svg index 5d2ae880df..e61e3586f6 100644 --- a/graphviz/genotype_to_gene_association.svg +++ b/graphviz/genotype_to_gene_association.svg @@ -4,16 +4,16 @@ - + %3 - + genotype to gene association - -genotype to gene association + +genotype to gene association @@ -24,8 +24,8 @@ genotype to gene association->association - - + + is_a @@ -37,9 +37,9 @@ genotype to gene association->id - - -id + + +id @@ -50,9 +50,9 @@ genotype to gene association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ genotype to gene association->name - - -name + + +name @@ -76,9 +76,9 @@ genotype to gene association->description - - -description + + +description @@ -89,9 +89,9 @@ genotype to gene association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ genotype to gene association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ genotype to gene association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ genotype to gene association->publications - - -publications + + +publications @@ -141,363 +141,363 @@ genotype to gene association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string genotype to gene association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string genotype to gene association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string genotype to gene association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type genotype to gene association->timepoint - - -timepoint + + +timepoint original subject - -string + +string genotype to gene association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie genotype to gene association->original predicate - - -original predicate + + +original predicate original object - -string + +string genotype to gene association->original object - - -original object + + +original object subject category - -ontology class + +ontology class genotype to gene association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class genotype to gene association->object category - - -object category + + +object category subject closure - -string + +string genotype to gene association->subject closure - - -subject closure + + +subject closure object closure - -string + +string genotype to gene association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class genotype to gene association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class genotype to gene association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string genotype to gene association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string genotype to gene association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string genotype to gene association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string genotype to gene association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source genotype to gene association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type genotype to gene association->type - - -type + + +type category - -category + +category genotype to gene association->category - - -category + + +category predicate - -predicate + +predicate genotype to gene association->predicate - - -predicate + + +predicate subject - -subject + +subject genotype to gene association->subject - - -subject + + +subject object - -object + +object genotype to gene association->object - - -object + + +object association_type - -string + +string association_category - -category type + +category type genotype to gene association_predicate - -predicate type + +predicate type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + genotype to gene association_subject - -genotype + +genotype object->relation - - + + genotype to gene association_object - -gene + +gene diff --git a/graphviz/genotype_to_genotype_part_association.gv b/graphviz/genotype_to_genotype_part_association.gv index 19182ff911..09dc4acef7 100644 --- a/graphviz/genotype_to_genotype_part_association.gv +++ b/graphviz/genotype_to_genotype_part_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4738.4,283"]; + graph [bb="0,0,4553.4,283"]; node [label="\N"]; "genotype to genotype part association" [height=0.5, label="genotype to genotype part association", - pos="2468.4,265", + pos="2283.4,265", width=5.2356]; association [height=0.5, pos="62.394,178", width=1.7332]; "genotype to genotype part association" -> association [label=is_a, lp="280.39,221.5", - pos="e,102.91,191.79 2280.6,263.43 1784.4,261.58 462.87,254.31 266.39,229 213.1,222.13 153.57,206.61 112.64,194.66"]; + pos="e,102.91,191.77 2095.9,263.13 1630,260.63 444.34,252.06 266.39,229 213.11,222.1 153.58,206.57 112.65,194.64"]; id [color=blue, height=0.5, label=string, @@ -18,8 +18,8 @@ digraph { width=1.0652]; "genotype to genotype part association" -> id [color=blue, label=id, - lp="396.39,221.5", - pos="e,210.38,189.98 2280.9,262.84 1804.8,259.62 573.95,249.41 389.39,229 317.23,221.02 299.34,215.5 229.39,196 226.29,195.13 223.09,\ + lp="395.39,221.5", + pos="e,210.38,189.98 2096.3,262.53 1651.4,258.73 554.55,247.61 388.39,229 316.67,220.97 298.9,215.43 229.39,196 226.29,195.13 223.09,\ 194.17 219.89,193.15", style=solid]; iri [color=blue, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "genotype to genotype part association" -> iri [color=blue, label=iri, - lp="509.39,221.5", - pos="e,315.3,190.2 2281.4,262.57 1824.3,258.82 674.85,247.63 501.39,229 426.6,220.97 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ -325.06,193.15", + lp="501.39,221.5", + pos="e,315.32,190.15 2094.6,264.76 1699.9,265.62 798.67,263.56 493.39,229 422.11,220.93 404.75,214.31 335.39,196 332.02,195.11 328.55,\ +194.13 325.07,193.11", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "genotype to genotype part association" -> name [color=blue, label=name, - lp="616.39,221.5", - pos="e,439.35,191.54 2281.1,262.96 1839.9,260.16 759.77,251.12 596.39,229 545.26,222.08 488.24,206.51 449.14,194.57", + lp="604.39,221.5", + pos="e,437.98,191.87 2096,262.74 1685.3,259.6 730.39,250.12 584.39,229 537.02,222.15 484.46,206.96 447.86,195.11", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "genotype to genotype part association" -> description [color=blue, label=description, - lp="736.89,221.5", - pos="e,585.45,194.14 2280.4,263.6 1856.1,262.21 848.77,256.08 696.39,229 661.33,222.77 623.33,209.4 595.03,198.06", + lp="717.89,221.5", + pos="e,581.77,194.62 2095.4,263.65 1701.1,262.36 812.83,256.42 677.39,229 647.36,222.92 615.28,210.09 591.01,198.95", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "genotype to genotype part association" -> "has attribute" [color=blue, label="has attribute", - lp="882.39,221.5", - pos="e,725.98,192.82 2280.3,263.38 1881.1,261.58 973.89,254.68 835.39,229 800.43,222.52 762.57,208.39 735.2,196.8", + lp="852.39,221.5", + pos="e,721.33,194.01 2095.2,263.79 1725.1,262.75 927.63,257.22 805.39,229 778.89,222.88 751.04,209.98 730.13,198.82", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "genotype to genotype part association" -> negated [color=blue, label=negated, - lp="1038.4,221.5", - pos="e,847.59,190.46 2279.7,264.3 1942.5,264.03 1249.3,259.61 1009.4,229 956.09,222.2 896.47,205.66 857.14,193.46", + lp="990.39,221.5", + pos="e,843.03,191.96 2097.2,262.15 1759.3,258.34 1069.9,248.31 961.39,229 923.37,222.23 881.85,207.52 852.5,195.8", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "genotype to genotype part association" -> qualifiers [color=blue, label=qualifiers, - lp="1178.9,221.5", - pos="e,996.68,193.07 2279.8,264.34 1968,263.99 1358.4,259.29 1145.4,229 1097.6,222.2 1044.5,207.74 1006.5,196.11", + lp="1101.9,221.5", + pos="e,982.4,194.93 2096.7,262.55 1780.7,259.51 1165.6,250.85 1068.4,229 1041.6,222.97 1013.3,210.59 991.57,199.66", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "genotype to genotype part association" -> publications [color=blue, label=publications, - lp="1326.4,221.5", - pos="e,1148.1,192.71 2279.8,264.27 1995,263.69 1468.6,258.48 1282.4,229 1239.3,222.18 1191.8,207.69 1157.8,196.06", + lp="1202.4,221.5", + pos="e,1121.9,195.78 2097.5,261.92 1788.9,257.93 1200.3,247.91 1158.4,229 1146.3,223.57 1135.9,213.45 1128,203.73", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,275 +100,275 @@ digraph { width=2.0943]; "genotype to genotype part association" -> "has evidence" [color=blue, label="has evidence", - lp="1480.9,221.5", - pos="e,1305.9,193.61 2280.5,263.41 2027.7,261.63 1591.7,254.76 1434.4,229 1393.5,222.3 1348.6,208.48 1315.7,197.06", + lp="1300.9,221.5", + pos="e,1255.9,195.88 2095,264.27 1805.9,263.75 1283.1,258.67 1254.4,229 1248.2,222.63 1248.8,213.73 1251.7,205.2", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1469.4,178", - width=3.015]; + label=string, + pos="1399.4,178", + width=1.0652]; "genotype to genotype part association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1635.9,221.5", - pos="e,1495.5,195.59 2284.7,260.9 2042.3,256.18 1638.3,245.9 1571.4,229 1547.9,223.07 1523.5,211.31 1504.4,200.68", + lp="1419.9,221.5", + pos="e,1375.2,192.24 2095.4,263.5 1831.6,261.86 1380.6,255.2 1355.4,229 1345.9,219.09 1354.7,207.6 1366.9,198.13", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1704.4,178", - width=3.015]; + label=string, + pos="1494.4,178", + width=1.0652]; "genotype to genotype part association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1807.4,221.5", - pos="e,1702.1,196.41 2284,261.24 2067,257.14 1733.4,247.81 1712.4,229 1706.1,223.34 1703.4,214.82 1702.5,206.41", + lp="1589.4,221.5", + pos="e,1489,196.04 2097.3,262.14 1870.6,258.94 1515,250.5 1494.4,229 1488.6,222.94 1487.2,214.32 1487.7,205.94", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1939.4,178", - width=3.015]; + label=string, + pos="1669.4,178", + width=1.0652]; "genotype to genotype part association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2015.9,221.5", - pos="e,1918.7,195.97 2291.5,258.71 2132.7,253.07 1922.6,243.01 1909.4,229 1902.4,221.54 1905.6,212.18 1912,203.58", + lp="1809.9,221.5", + pos="e,1676.1,196.02 2099.7,260.98 1942.8,257.07 1737.4,248.32 1703.4,229 1693.8,223.55 1686.4,214.16 1680.9,204.98", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2121.4,178", + pos="1895.4,178", width=1.5346]; "genotype to genotype part association" -> timepoint [color=blue, label=timepoint, - lp="2171.4,221.5", - pos="e,2121.9,196.47 2310.3,255.17 2231.7,249.38 2150.5,240.7 2136.4,229 2129.6,223.41 2125.9,214.91 2123.8,206.49", + lp="1972.4,221.5", + pos="e,1904.8,195.92 2107.9,258.34 2038.2,253.6 1967.5,244.91 1937.4,229 1926.7,223.32 1917.5,213.63 1910.6,204.28", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2233.4,178", + pos="2007.4,178", width=1.0652]; "genotype to genotype part association" -> "original subject" [color=blue, label="original subject", - lp="2270.4,221.5", - pos="e,2219.6,194.92 2297.8,257.28 2259.8,252.11 2227,243.43 2214.4,229 2208.1,221.83 2209.9,212.39 2214.3,203.65", + lp="2076.4,221.5", + pos="e,2007.3,196.33 2116.7,256.52 2074.3,251.42 2036.2,242.96 2020.4,229 2013.9,223.25 2010.5,214.72 2008.7,206.31", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2347.4,178", + pos="2133.4,178", width=1.5887]; "genotype to genotype part association" -> "original predicate" [color=blue, label="original predicate", - lp="2397.9,221.5", - pos="e,2336.3,195.76 2378.3,249.11 2358.1,243.89 2340.8,237.23 2334.4,229 2329.1,222.16 2329.6,213.39 2332.4,205.11", + lp="2207.9,221.5", + pos="e,2132.9,196.42 2193.7,249.07 2171.7,243.75 2152.2,237.04 2144.4,229 2138.6,222.99 2135.5,214.63 2134,206.47", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2461.4,178", + pos="2267.4,178", width=1.0652]; "genotype to genotype part association" -> "original object" [color=blue, label="original object", - lp="2516.9,221.5", - pos="e,2462.8,196.18 2467,246.8 2466,235.16 2464.7,219.55 2463.6,206.24", + lp="2327.9,221.5", + pos="e,2270.6,196.18 2280.2,246.8 2278,235.16 2275,219.55 2272.5,206.24", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2594.4,178", + pos="2400.4,178", width=2.1304]; "genotype to genotype part association" -> "subject category" [color=blue, label="subject category", - lp="2642.9,221.5", - pos="e,2590.6,196.4 2541,248.35 2552.4,243.53 2563.4,237.23 2572.4,229 2579.1,222.84 2583.9,214.24 2587.3,205.9", + lp="2452.9,221.5", + pos="e,2398.4,196.3 2354.6,248.23 2365.2,243.43 2375.3,237.17 2383.4,229 2389.5,222.8 2393.5,214.29 2396,206.04", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2765.4,178", + pos="2571.4,178", width=2.1304]; "genotype to genotype part association" -> "object category" [color=blue, label="object category", - lp="2785.9,221.5", - pos="e,2750.6,195.73 2621.2,254.37 2650.3,249 2679.9,240.96 2706.4,229 2720,222.83 2733,212.54 2743.3,202.9", + lp="2593.9,221.5", + pos="e,2557.8,195.72 2435.5,254.35 2463.3,248.94 2491.4,240.89 2516.4,229 2529.3,222.88 2541.3,212.74 2550.8,203.17", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="2898.4,178", + pos="2704.4,178", width=1.0652]; "genotype to genotype part association" -> "subject closure" [color=blue, label="subject closure", - lp="2921.9,221.5", - pos="e,2886,195.51 2603.8,252.46 2709.6,243.27 2839.7,231.55 2845.4,229 2858.3,223.16 2870.1,212.86 2879.2,203.11", + lp="2728.9,221.5", + pos="e,2692.6,195.5 2417.6,252.35 2521.2,243.18 2647.9,231.55 2653.4,229 2665.9,223.2 2677.1,213.04 2685.8,203.39", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="2998.4,178", + pos="2812.4,178", width=1.0652]; "genotype to genotype part association" -> "object closure" [color=blue, label="object closure", - lp="3042.4,221.5", - pos="e,2997,196.22 2600.4,252.14 2622.4,250.31 2645.1,248.53 2666.4,247 2701.3,244.51 2952.4,249.9 2980.4,229 2987.7,223.53 2992.1,214.79 \ -2994.7,206.14", + lp="2851.4,221.5", + pos="e,2808.5,196.38 2415.7,252.14 2437.6,250.32 2460.1,248.54 2481.4,247 2515.4,244.54 2759,247.75 2787.4,229 2795.6,223.59 2801.2,214.62 \ +2805,205.77", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3131.4,178", + pos="2945.4,178", width=2.1304]; "genotype to genotype part association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3200.9,221.5", - pos="e,3124.4,196.11 2598.8,251.99 2621.3,250.14 2644.5,248.4 2666.4,247 2714.1,243.95 3054.5,251.97 3096.4,229 3106.2,223.66 3113.8,\ -214.29 3119.4,205.09", + lp="3010.9,221.5", + pos="e,2936.7,196.16 2413.8,252 2436.3,250.15 2459.5,248.4 2481.4,247 2528.5,243.98 2863.3,250.32 2905.4,229 2916,223.61 2924.8,213.97 \ +2931.3,204.58", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3323.4,178", + pos="3138.4,178", width=2.1304]; "genotype to genotype part association" -> "object category closure" [color=blue, label="object category closure", - lp="3390.9,221.5", - pos="e,3317.7,196.1 2597.5,251.85 2620.4,250 2644.1,248.28 2666.4,247 2701.1,245.01 3262.2,246.36 3292.4,229 3301.6,223.71 3308.4,214.47 \ -3313.3,205.37", + lp="3202.9,221.5", + pos="e,3131.1,196.17 2412.5,251.86 2435.4,250 2459.1,248.28 2481.4,247 2515.9,245.02 3071.9,245.18 3102.4,229 3112.4,223.68 3120.3,214.18 \ +3126.1,204.88", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3513.4,178", + pos="3328.4,178", width=1.0652]; "genotype to genotype part association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3563.4,221.5", - pos="e,3506.4,196.19 2596.7,251.79 2619.8,249.93 2643.8,248.22 2666.4,247 2711.5,244.57 3438.6,250.28 3478.4,229 3488.2,223.75 3495.9,\ -214.4 3501.5,205.19", + lp="3375.4,221.5", + pos="e,3320.7,195.73 2411.7,251.79 2434.8,249.93 2458.8,248.22 2481.4,247 2526.3,244.58 3250.3,249.42 3290.4,229 3300.8,223.67 3309.2,\ +213.99 3315.4,204.55", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3672.4,178", + pos="3487.4,178", width=1.0652]; "genotype to genotype part association" -> "object namespace" [color=blue, label="object namespace", - lp="3716.4,221.5", - pos="e,3665,195.73 2596.4,251.75 2619.7,249.88 2643.7,248.18 2666.4,247 2720.2,244.2 3587.5,253.68 3635.4,229 3645.7,223.67 3653.9,213.99 \ -3659.9,204.55", + lp="3529.4,221.5", + pos="e,3479.1,195.77 2411.4,251.75 2434.7,249.88 2458.7,248.18 2481.4,247 2535,244.2 3399.2,252.7 3447.4,229 3458.2,223.66 3467.1,213.84 \ +3473.7,204.31", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3823.4,178", + pos="3638.4,178", width=1.0652]; "genotype to genotype part association" -> "subject label closure" [color=blue, label="subject label closure", - lp="3876.4,221.5", - pos="e,3815.4,195.77 2596.1,251.72 2619.5,249.85 2643.7,248.16 2666.4,247 2697.4,245.42 3756.6,242.85 3784.4,229 3795.1,223.66 3803.8,\ -213.84 3810.2,204.31", + lp="3689.4,221.5", + pos="e,3629.8,195.79 2411.1,251.72 2434.5,249.85 2458.7,248.16 2481.4,247 2512.4,245.42 3569.5,242.49 3597.4,229 3608.4,223.69 3617.4,\ +213.87 3624.2,204.33", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="3994.4,178", + pos="3809.4,178", width=1.0652]; "genotype to genotype part association" -> "object label closure" [color=blue, label="object label closure", - lp="4041.9,221.5", - pos="e,3986.1,195.79 2595.9,251.7 2619.3,249.83 2643.6,248.14 2666.4,247 2702.1,245.22 3922.3,244.72 3954.4,229 3965.3,223.69 3974.1,\ -213.87 3980.7,204.33", + lp="3856.9,221.5", + pos="e,3800.5,195.81 2410.9,251.7 2434.3,249.83 2458.6,248.14 2481.4,247 2517.1,245.22 3735.1,244.32 3767.4,229 3778.5,223.72 3787.8,\ +213.9 3794.7,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4147.4,178", + pos="3962.4,178", width=2.347]; "genotype to genotype part association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4200.9,221.5", - pos="e,4141.4,196.18 2595.6,251.69 2619.1,249.81 2643.5,248.12 2666.4,247 2706.6,245.03 4080.2,248.54 4115.4,229 4124.9,223.75 4131.9,\ -214.39 4137,205.18", + lp="4015.9,221.5", + pos="e,3956.4,196.18 2410.6,251.69 2434.1,249.81 2458.5,248.12 2481.4,247 2521.6,245.03 3895.2,248.54 3930.4,229 3939.9,223.75 3946.9,\ +214.39 3952,205.18", style=solid]; type [height=0.5, - pos="4281.4,178", + pos="4096.4,178", width=0.86659]; "genotype to genotype part association" -> type [color=blue, label=type, - lp="4299.4,221.5", - pos="e,4284.1,195.98 2595.3,251.69 2618.9,249.8 2643.4,248.11 2666.4,247 2688.7,245.92 4257.6,243.75 4274.4,229 4280.9,223.32 4283.4,\ -214.65 4284.1,206.12", + lp="4114.4,221.5", + pos="e,4099.1,195.98 2410.3,251.69 2433.9,249.8 2458.4,248.11 2481.4,247 2503.7,245.92 4072.6,243.75 4089.4,229 4095.9,223.32 4098.4,\ +214.65 4099.1,206.12", style=solid]; category [height=0.5, - pos="4382.4,178", + pos="4197.4,178", width=1.4263]; "genotype to genotype part association" -> category [color=blue, label=category, - lp="4377.9,221.5", - pos="e,4367.7,195.48 2595.3,251.69 2618.9,249.8 2643.4,248.11 2666.4,247 2712.3,244.78 4276.1,244.35 4319.4,229 4334.6,223.59 4349,212.83 \ -4360.1,202.68", + lp="4192.9,221.5", + pos="e,4182.7,195.48 2410.3,251.69 2433.9,249.8 2458.4,248.11 2481.4,247 2527.3,244.78 4091.1,244.35 4134.4,229 4149.6,223.59 4164,212.83 \ +4175.1,202.68", style=solid]; predicate [height=0.5, - pos="4506.4,178", + pos="4321.4,178", width=1.5165]; "genotype to genotype part association" -> predicate [color=blue, label=predicate, - lp="4485.4,221.5", - pos="e,4484.7,194.58 2595.3,251.68 2618.9,249.79 2643.4,248.1 2666.4,247 2763.3,242.35 4319.4,253.18 4413.4,229 4435.8,223.24 4458.7,\ -211.04 4476.1,200.13", + lp="4300.4,221.5", + pos="e,4299.7,194.58 2410.3,251.68 2433.9,249.79 2458.4,248.1 2481.4,247 2578.3,242.35 4134.4,253.18 4228.4,229 4250.8,223.24 4273.7,\ +211.04 4291.1,200.13", style=solid]; subject [height=0.5, - pos="4623.4,178", + pos="4438.4,178", width=1.2277]; "genotype to genotype part association" -> subject [color=blue, label=subject, - lp="4590.4,221.5", - pos="e,4601.1,193.87 2595.3,251.66 2618.9,249.78 2643.4,248.1 2666.4,247 2769.4,242.08 4423.1,253.19 4523.4,229 4547.9,223.09 4573.2,\ -210.33 4592.3,199.17", + lp="4405.4,221.5", + pos="e,4416.1,193.87 2410.3,251.66 2433.9,249.78 2458.4,248.1 2481.4,247 2584.4,242.08 4238.1,253.19 4338.4,229 4362.9,223.09 4388.2,\ +210.33 4407.3,199.17", style=solid]; object [height=0.5, - pos="4666.4,91", + pos="4481.4,91", width=1.0832]; "genotype to genotype part association" -> object [color=blue, label=object, - lp="4716.4,178", - pos="e,4679.8,108.09 2595.3,251.65 2618.9,249.77 2643.4,248.09 2666.4,247 2774.8,241.85 4515.8,258.05 4620.4,229 4648.2,221.27 4659.2,\ -219.22 4676.4,196 4695,170.92 4698.3,156.9 4689.4,127 4688.4,123.55 4686.9,120.13 4685.1,116.85", + lp="4531.4,178", + pos="e,4494.8,108.09 2410.3,251.65 2433.9,249.77 2458.4,248.09 2481.4,247 2589.8,241.85 4330.8,258.05 4435.4,229 4463.2,221.27 4474.2,\ +219.22 4491.4,196 4510,170.92 4513.3,156.9 4504.4,127 4503.4,123.55 4501.9,120.13 4500.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2713.4,265", + pos="2528.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2844.4,265", + pos="2659.4,265", width=2.0762]; "genotype to genotype part association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3015.4,265", + pos="2830.4,265", width=2.1665]; subject -> object [label=relation, - lp="4661.4,134.5", - pos="e,4648.5,107.23 4624.5,159.55 4625.7,149.57 4628.2,137.07 4633.4,127 4635.6,122.68 4638.5,118.52 4641.7,114.66"]; + lp="4476.4,134.5", + pos="e,4463.5,107.23 4439.5,159.55 4440.7,149.57 4443.2,137.07 4448.4,127 4450.6,122.68 4453.5,118.52 4456.7,114.66"]; relation [height=0.5, - pos="4611.4,18", + pos="4426.4,18", width=1.2999]; - subject -> relation [pos="e,4612.7,36.188 4622.1,159.79 4620,132.48 4616,78.994 4613.5,46.38", + subject -> relation [pos="e,4427.7,36.188 4437.1,159.79 4435,132.48 4431,78.994 4428.5,46.38", style=dotted]; "genotype to genotype part association_subject" [color=blue, height=0.5, label=genotype, - pos="3165.4,265", + pos="2980.4,265", width=1.4985]; - object -> relation [pos="e,4624.2,35.54 4653.9,73.889 4647,64.939 4638.2,53.617 4630.4,43.584", + object -> relation [pos="e,4439.2,35.54 4468.9,73.889 4462,64.939 4453.2,53.617 4445.4,43.584", style=dotted]; "genotype to genotype part association_object" [color=blue, height=0.5, label=genotype, - pos="3291.4,265", + pos="3106.4,265", width=1.4985]; } diff --git a/graphviz/genotype_to_genotype_part_association.svg b/graphviz/genotype_to_genotype_part_association.svg index 3602c6511a..3e85bba569 100644 --- a/graphviz/genotype_to_genotype_part_association.svg +++ b/graphviz/genotype_to_genotype_part_association.svg @@ -4,16 +4,16 @@ - + %3 - + genotype to genotype part association - -genotype to genotype part association + +genotype to genotype part association @@ -24,8 +24,8 @@ genotype to genotype part association->association - - + + is_a @@ -37,9 +37,9 @@ genotype to genotype part association->id - - -id + + +id @@ -50,9 +50,9 @@ genotype to genotype part association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ genotype to genotype part association->name - - -name + + +name @@ -76,9 +76,9 @@ genotype to genotype part association->description - - -description + + +description @@ -89,9 +89,9 @@ genotype to genotype part association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ genotype to genotype part association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ genotype to genotype part association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ genotype to genotype part association->publications - - -publications + + +publications @@ -141,363 +141,363 @@ genotype to genotype part association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string genotype to genotype part association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string genotype to genotype part association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string genotype to genotype part association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type genotype to genotype part association->timepoint - - -timepoint + + +timepoint original subject - -string + +string genotype to genotype part association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie genotype to genotype part association->original predicate - - -original predicate + + +original predicate original object - -string + +string genotype to genotype part association->original object - - -original object + + +original object subject category - -ontology class + +ontology class genotype to genotype part association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class genotype to genotype part association->object category - - -object category + + +object category subject closure - -string + +string genotype to genotype part association->subject closure - - -subject closure + + +subject closure object closure - -string + +string genotype to genotype part association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class genotype to genotype part association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class genotype to genotype part association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string genotype to genotype part association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string genotype to genotype part association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string genotype to genotype part association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string genotype to genotype part association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source genotype to genotype part association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type genotype to genotype part association->type - - -type + + +type category - -category + +category genotype to genotype part association->category - - -category + + +category predicate - -predicate + +predicate genotype to genotype part association->predicate - - -predicate + + +predicate subject - -subject + +subject genotype to genotype part association->subject - - -subject + + +subject object - -object + +object genotype to genotype part association->object - - -object + + +object association_type - -string + +string association_category - -category type + +category type genotype to genotype part association_predicate - -predicate type + +predicate type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + genotype to genotype part association_subject - -genotype + +genotype object->relation - - + + genotype to genotype part association_object - -genotype + +genotype diff --git a/graphviz/genotype_to_phenotypic_feature_association.gv b/graphviz/genotype_to_phenotypic_feature_association.gv index e869673b2d..0c9105f0c2 100644 --- a/graphviz/genotype_to_phenotypic_feature_association.gv +++ b/graphviz/genotype_to_phenotypic_feature_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,6597.4,283"]; + graph [bb="0,0,6339.4,283"]; node [label="\N"]; "genotype to phenotypic feature association" [height=0.5, label="genotype to phenotypic feature association", - pos="3653.4,265", + pos="3395.4,265", width=5.8675]; association [height=0.5, pos="62.394,178", width=1.7332]; "genotype to phenotypic feature association" -> association [label=is_a, lp="720.39,221.5", - pos="e,106.71,190.74 3443.6,262.76 2862.5,259.12 1240,247.55 706.39,229 451.9,220.15 386.38,232.73 134.39,196 128.61,195.16 122.61,194.08 \ + pos="e,106.71,190.74 3184,264.45 2730.1,264.72 1628.8,261.59 706.39,229 451.91,220.01 386.38,232.73 134.39,196 128.61,195.16 122.61,194.08 \ 116.66,192.87"]; "entity to phenotypic feature association mixin" [height=0.5, pos="367.39,178", width=6.2286]; "genotype to phenotypic feature association" -> "entity to phenotypic feature association mixin" [label=uses, lp="960.89,221.5", - pos="e,495.26,192.8 3443.1,263.29 2894.6,261.1 1429.4,253.12 944.39,229 794,221.52 622.1,205.68 505.33,193.82"]; + pos="e,495.55,192.78 3185.3,262.95 2674.5,260.09 1377.5,250.83 944.39,229 794.12,221.43 622.38,205.62 505.62,193.8"]; "genotype to entity association mixin" [height=0.5, pos="789.39,178", width=4.9829]; "genotype to phenotypic feature association" -> "genotype to entity association mixin" [label=uses, lp="1117.9,221.5", - pos="e,865.3,194.33 3443.6,262.87 2875,259.57 1331.2,248.88 1101.4,229 1024.5,222.35 937.92,207.91 875.5,196.25"]; + pos="e,865.63,194.36 3183.9,264.66 2695.8,265.55 1501.7,263.94 1101.4,229 1024.6,222.3 938.21,207.9 875.82,196.27"]; id [color=blue, height=0.5, label=string, @@ -32,7 +32,7 @@ digraph { "genotype to phenotypic feature association" -> id [color=blue, label=id, lp="1225.4,221.5", - pos="e,1054.4,189.89 3442.8,263.5 2891.9,261.83 1435.5,254.98 1218.4,229 1152.8,221.15 1136.9,214.4 1073.4,196 1070.3,195.1 1067.1,194.11 \ + pos="e,1054.4,189.89 3185.2,263.1 2677,260.58 1409.7,252.05 1218.4,229 1152.8,221.09 1136.9,214.4 1073.4,196 1070.3,195.1 1067.1,194.11 \ 1063.9,193.08", style=solid]; iri [color=blue, @@ -43,7 +43,7 @@ digraph { "genotype to phenotypic feature association" -> iri [color=blue, label=iri, lp="1313.4,221.5", - pos="e,1158.2,190.74 3442.5,263.76 2905.3,262.74 1513.3,257.35 1305.4,229 1257.2,222.42 1203.6,206.24 1167.8,194.06", + pos="e,1158.2,190.72 3184.9,263.33 2691.4,261.36 1487.6,254.01 1305.4,229 1257.2,222.38 1203.6,206.21 1167.8,194.03", style=solid]; name [color=blue, height=0.5, @@ -53,7 +53,7 @@ digraph { "genotype to phenotypic feature association" -> name [color=blue, label=name, lp="1397.4,221.5", - pos="e,1274.7,193.47 3443.7,262.74 2899.6,259.19 1477.7,248.16 1377.4,229 1344.8,222.78 1309.9,209.18 1284.1,197.73", + pos="e,1274.7,193.45 3184,264.44 2702.2,264.86 1550.8,262.3 1377.4,229 1344.9,222.75 1309.9,209.15 1284.1,197.71", style=solid]; description [color=blue, height=0.5, @@ -63,7 +63,7 @@ digraph { "genotype to phenotypic feature association" -> description [color=blue, label=description, lp="1481.9,221.5", - pos="e,1405.5,195.84 3443.3,262.86 2899.9,259.63 1486.7,249.29 1441.4,229 1429.6,223.7 1419.4,213.75 1411.7,204.1", + pos="e,1405.9,196.32 3183.9,264.67 2694.6,265.62 1519.7,264.18 1441.4,229 1429.7,223.76 1419.7,214.01 1412,204.5", style=solid]; "has attribute" [color=blue, height=0.5, @@ -73,18 +73,18 @@ digraph { "genotype to phenotypic feature association" -> "has attribute" [color=blue, label="has attribute", lp="1578.4,221.5", - pos="e,1530.8,196.02 3442.1,264.39 2911.9,264.86 1564.6,262.74 1531.4,229 1525.3,222.85 1525.2,214.11 1527.4,205.65", + pos="e,1530.8,196.02 3184.5,263.88 2702.6,263.09 1560,258.15 1531.4,229 1525.4,222.85 1525.2,214.1 1527.4,205.64", style=solid]; object [color=blue, height=0.5, label="named thing", - pos="5388.4,91", + pos="5130.4,91", width=1.9318]; "genotype to phenotypic feature association" -> object [color=blue, label=object, lp="1659.4,178", - pos="e,5318.6,91.92 3442.8,263.42 3035.9,261.72 2155.1,255.06 1852.4,229 1752.4,220.39 1567.1,231.6 1637.4,160 1704,92.178 4770.1,91.507 \ -5308.2,91.912", + pos="e,5060.8,92.016 3184.2,264.02 2813.8,263.29 2061.9,258.11 1800.4,229 1722.2,220.3 1582.3,216.17 1637.4,160 1699.2,97.017 4535,92.35 \ +5050.5,92.022", style=solid]; negated [color=blue, height=0.5, @@ -93,8 +93,8 @@ digraph { width=1.2999]; "genotype to phenotypic feature association" -> negated [color=blue, label=negated, - lp="1960.4,221.5", - pos="e,1771.2,190.49 3444.4,262.25 3018.5,258.3 2077.5,247.61 1931.4,229 1878.8,222.3 1820.1,205.86 1781.2,193.65", + lp="1877.4,221.5", + pos="e,1762,193.53 3184.6,263.89 2791.5,263.01 1974.9,257.68 1848.4,229 1821.1,222.81 1792.3,209.65 1770.9,198.38", style=solid]; qualifiers [color=blue, height=0.5, @@ -103,8 +103,8 @@ digraph { width=2.1304]; "genotype to phenotypic feature association" -> qualifiers [color=blue, label=qualifiers, - lp="2099.9,221.5", - pos="e,1920,193.12 3444.4,262.16 3044.6,258.23 2198.9,247.81 2066.4,229 2019.3,222.31 1967.1,207.84 1929.7,196.18", + lp="1966.9,221.5", + pos="e,1891.3,195.86 3185.6,262.83 2794.9,260.13 1990.3,251.81 1933.4,229 1920,223.63 1907.8,213.38 1898.3,203.55", style=solid]; publications [color=blue, height=0.5, @@ -113,8 +113,8 @@ digraph { width=1.7332]; "genotype to phenotypic feature association" -> publications [color=blue, label=publications, - lp="2246.4,221.5", - pos="e,2071.2,192.77 3444.7,262.04 3072.4,258.09 2321.4,247.9 2202.4,229 2160.2,222.3 2113.8,207.8 2080.7,196.13", + lp="2052.4,221.5", + pos="e,2017,195.33 3186.2,262.44 2803.7,259.1 2028.6,249.76 2008.4,229 2001.2,221.65 2004.4,212 2010.6,203.15", style=solid]; "has evidence" [color=blue, height=0.5, @@ -123,347 +123,349 @@ digraph { width=2.0943]; "genotype to phenotypic feature association" -> "has evidence" [color=blue, label="has evidence", - lp="2406.9,221.5", - pos="e,2230,193.56 3442,264.94 3130.2,265.2 2562.2,261.01 2360.4,229 2318.7,222.39 2272.9,208.39 2239.5,196.89", + lp="2151.9,221.5", + pos="e,2139.8,191.14 3186.8,262.03 2826.5,258.12 2124,248.08 2105.4,229 2091.3,214.53 2108,202.85 2130.3,194.43", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2393.4,178", - width=3.015]; + label=string, + pos="2323.4,178", + width=1.0652]; "genotype to phenotypic feature association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2563.9,221.5", - pos="e,2420.6,195.66 3444.3,262.28 3136.6,259.04 2588.3,250.33 2499.4,229 2475,223.14 2449.5,211.3 2429.6,200.62", + lp="2269.9,221.5", + pos="e,2294.3,189.76 3188,261.54 2851.5,257.05 2222.3,246.36 2205.4,229 2200.8,224.22 2201.3,219.27 2205.4,214 2225.1,188.61 2244.7,205.37 \ +2275.4,196 2278.5,195.06 2281.7,194.04 2284.9,192.99", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2628.4,178", - width=3.015]; + label=string, + pos="2418.4,178", + width=1.0652]; "genotype to phenotypic feature association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2737.4,221.5", - pos="e,2628.3,196.18 3443.3,263 3156.3,260.74 2673.3,253.31 2642.4,229 2635.4,223.47 2631.7,214.72 2629.8,206.08", + lp="2436.4,221.5", + pos="e,2390,190.16 3184.1,264.41 2884.8,263.94 2370.2,258.76 2341.4,229 2336.8,224.21 2337.8,219.61 2341.4,214 2343.9,210.14 2362.3,201.68 \ +2380.6,194.05", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2863.4,178", - width=3.015]; + label=string, + pos="2513.4,178", + width=1.0652]; "genotype to phenotypic feature association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2946.9,221.5", - pos="e,2846.7,195.94 3444.8,262.12 3210.8,258.95 2861.1,250.62 2840.4,229 2833.8,222.07 2835.9,212.87 2840.9,204.26", + lp="2658.9,221.5", + pos="e,2521.4,195.66 3184.2,264.41 2952.8,263.41 2607.1,257.12 2552.4,229 2541.8,223.53 2533.1,213.68 2526.7,204.17", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="3045.4,178", + pos="2740.4,178", width=1.5346]; "genotype to phenotypic feature association" -> timepoint [color=blue, label=timepoint, - lp="3104.4,221.5", - pos="e,3049,196.35 3445.5,261.75 3290.6,258.37 3100.6,249.94 3069.4,229 3061.4,223.62 3056,214.78 3052.3,206.02", + lp="2823.4,221.5", + pos="e,2751.2,195.66 3193.5,259.65 3031.3,254.95 2824.8,245.76 2788.4,229 2776.3,223.41 2765.6,213.28 2757.5,203.59", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="3157.4,178", + pos="2852.4,178", width=1.0652]; "genotype to phenotypic feature association" -> "original subject" [color=blue, label="original subject", - lp="3204.4,221.5", - pos="e,3147.9,195.88 3443.6,262.68 3314.2,259.61 3169.1,251.17 3148.4,229 3142.5,222.7 3142.4,213.92 3144.6,205.47", + lp="2930.4,221.5", + pos="e,2855.3,196.29 3191.4,260.3 3056.8,256.15 2900.6,247.4 2874.4,229 2866.6,223.54 2861.5,214.69 2858.3,205.94", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3271.4,178", + pos="2977.4,178", width=1.5887]; "genotype to phenotypic feature association" -> "original predicate" [color=blue, label="original predicate", - lp="3333.9,221.5", - pos="e,3265.7,195.91 3460.3,257.66 3372.1,252.73 3284.2,244.07 3270.4,229 3264.8,222.87 3263.5,214.34 3264.1,206.06", + lp="3065.9,221.5", + pos="e,2981.4,196.27 3213.6,255.82 3119.5,250.16 3020.6,241.39 3002.4,229 2994.4,223.52 2988.8,214.66 2985,205.92", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3385.4,178", + pos="3106.4,178", width=1.0652]; "genotype to phenotypic feature association" -> "original object" [color=blue, label="original object", - lp="3465.9,221.5", - pos="e,3390.9,196.13 3502.6,252.37 3464.6,247.13 3430.1,239.64 3414.4,229 3406,223.3 3399.7,214.27 3395.1,205.45", + lp="3203.9,221.5", + pos="e,3117.2,195.75 3253.4,251.63 3211,246.19 3170.9,238.76 3152.4,229 3141.1,223.05 3131.1,213.18 3123.4,203.78", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3518.4,178", + pos="3239.4,178", width=2.1304]; "genotype to phenotypic feature association" -> "subject category" [color=blue, label="subject category", - lp="3587.9,221.5", - pos="e,3517.5,196.32 3556.6,248.97 3546.1,244.01 3536.3,237.51 3528.4,229 3522.7,222.88 3519.9,214.5 3518.5,206.34", + lp="3331.9,221.5", + pos="e,3246.8,196.15 3310.3,248.41 3296.9,243.58 3283.7,237.27 3272.4,229 3263.9,222.8 3257,213.71 3251.7,204.98", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3689.4,178", + pos="3410.4,178", width=2.1304]; "genotype to phenotypic feature association" -> "object category" [color=blue, label="object category", - lp="3709.9,221.5", - pos="e,3667.8,195.45 3650.6,246.67 3649.8,236.72 3650,224.22 3654.4,214 3656.1,210.09 3658.4,206.38 3661.1,202.94", + lp="3451.9,221.5", + pos="e,3402.1,196.07 3394.2,246.71 3393.9,237 3394.2,224.72 3396.4,214 3396.9,211.27 3397.7,208.48 3398.6,205.72", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3822.4,178", + pos="3543.4,178", width=1.0652]; "genotype to phenotypic feature association" -> "subject closure" [color=blue, label="subject closure", - lp="3840.9,221.5", - pos="e,3807.8,194.94 3721,247.86 3736.1,242.9 3751.7,236.68 3765.4,229 3778.1,221.88 3790.4,211.6 3800.4,202.2", + lp="3576.9,221.5", + pos="e,3534.9,196.05 3470,248.1 3483.2,243.28 3496.2,237.04 3507.4,229 3516.2,222.62 3523.8,213.38 3529.6,204.58", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3918.4,178", + pos="3656.4,178", width=1.0652]; "genotype to phenotypic feature association" -> "object closure" [color=blue, label="object closure", - lp="3959.4,221.5", - pos="e,3915.7,196.01 3813.1,253.21 3850,248.03 3882.7,240.35 3897.4,229 3904.8,223.29 3909.6,214.5 3912.7,205.87", + lp="3697.4,221.5", + pos="e,3653.7,196.01 3552.8,252.95 3588.9,247.76 3621,240.15 3635.4,229 3642.8,223.28 3647.6,214.49 3650.7,205.86", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="4051.4,178", + pos="3789.4,178", width=2.1304]; "genotype to phenotypic feature association" -> "subject category closure" [color=blue, label="subject category closure", - lp="4117.9,221.5", - pos="e,4043.3,195.91 3802.5,252.23 3897.2,244.3 4003.8,234.35 4013.4,229 4023.5,223.36 4031.8,213.81 4038,204.56", + lp="3855.9,221.5", + pos="e,3781.3,195.91 3543.6,252.13 3637.1,244.2 3741.9,234.28 3751.4,229 3761.5,223.36 3769.7,213.81 3776,204.55", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="4240.4,178", + pos="3982.4,178", width=2.1304]; "genotype to phenotypic feature association" -> "object category closure" [color=blue, label="object category closure", - lp="4307.9,221.5", - pos="e,4234.6,196.01 3801.4,252.14 3825.8,250.33 3850.8,248.54 3874.4,247 3911.6,244.57 4177.3,248 4209.4,229 4218.5,223.59 4225.4,214.34 \ -4230.2,205.25", + lp="4046.9,221.5", + pos="e,3975.3,196.06 3543.7,252.13 3568,250.32 3592.9,248.54 3616.4,247 3653.1,244.59 3915.2,246.89 3947.4,229 3957.1,223.6 3964.8,214.21 \ +3970.4,205.03", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4430.4,178", + pos="4172.4,178", width=1.0652]; "genotype to phenotypic feature association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4480.4,221.5", - pos="e,4423.4,196.14 3799,251.92 3824.1,250.09 3850,248.36 3874.4,247 3903.3,245.39 4369.9,242.82 4395.4,229 4405.2,223.69 4412.8,214.33 \ -4418.4,205.13", + lp="4219.4,221.5", + pos="e,4164.7,195.68 3541,251.93 3566.1,250.09 3592,248.36 3616.4,247 3673.9,243.79 4083.3,255.48 4134.4,229 4144.8,223.6 4153.2,213.91 \ +4159.4,204.48", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4589.4,178", + pos="4331.4,178", width=1.0652]; "genotype to phenotypic feature association" -> "object namespace" [color=blue, label="object namespace", - lp="4633.4,221.5", - pos="e,4582,195.7 3797.8,251.85 3823.3,250 3849.6,248.28 3874.4,247 3912,245.05 4519,246.4 4552.4,229 4562.7,223.63 4570.9,213.94 4576.9,\ -204.51", + lp="4373.4,221.5", + pos="e,4323.1,195.73 3539.8,251.85 3565.3,250 3591.6,248.28 3616.4,247 3653.9,245.06 4257.8,245.7 4291.4,229 4302.2,223.62 4311.1,213.79 \ +4317.7,204.26", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4740.4,178", + pos="4482.4,178", width=1.0652]; "genotype to phenotypic feature association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4793.4,221.5", - pos="e,4732.4,195.74 3797.2,251.79 3822.9,249.93 3849.4,248.23 3874.4,247 3920.3,244.74 4660.3,249.61 4701.4,229 4712.1,223.63 4720.7,\ -213.81 4727.1,204.28", + lp="4533.4,221.5", + pos="e,4473.8,195.77 3539.2,251.79 3564.9,249.94 3591.4,248.23 3616.4,247 3662.2,244.74 4400.2,249.06 4441.4,229 4452.4,223.66 4461.4,\ +213.84 4468.2,204.3", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4869.4,178", + pos="4611.4,178", width=1.0652]; "genotype to phenotypic feature association" -> "object label closure" [color=blue, label="object label closure", - lp="4947.9,221.5", - pos="e,4875.8,196.1 3796.6,251.75 3822.5,249.89 3849.2,248.19 3874.4,247 3902.1,245.69 4852,248.76 4871.4,229 4877.3,223.01 4878.4,214.41 \ -4877.6,206.03", + lp="4687.9,221.5", + pos="e,4616.8,196.11 3538.6,251.75 3564.5,249.89 3591.2,248.2 3616.4,247 3644,245.69 4592,248.72 4611.4,229 4617.3,223.01 4618.7,214.41 \ +4618.2,206.03", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="5010.4,178", + pos="4752.4,178", width=2.347]; "genotype to phenotypic feature association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="5096.9,221.5", - pos="e,5021,195.98 3796.3,251.73 3822.3,249.86 3849.1,248.17 3874.4,247 3906.2,245.53 4999,251.71 5021.4,229 5027.6,222.74 5027.3,213.86 \ -5024.7,205.32", + lp="4836.9,221.5", + pos="e,4762,196.02 3538.3,251.73 3564.3,249.86 3591.1,248.17 3616.4,247 3648.2,245.53 4739.1,251.67 4761.4,229 4767.4,222.86 4767.6,214.11 \ +4765.4,205.65", style=solid]; type [height=0.5, - pos="5144.4,178", + pos="4886.4,178", width=0.86659]; "genotype to phenotypic feature association" -> type [color=blue, label=type, - lp="5191.4,221.5", - pos="e,5160.7,193.58 3796,251.71 3822,249.84 3849,248.15 3874.4,247 3892.4,246.18 5157.8,241.82 5170.4,229 5178,221.24 5174.1,210.77 \ -5167.2,201.41", + lp="4931.4,221.5", + pos="e,4902.1,194.12 3538,251.71 3564,249.84 3591,248.15 3616.4,247 3634.3,246.19 4897.8,241.8 4910.4,229 4917.7,221.55 4914.5,211.41 \ +4908.4,202.2", style=solid]; category [height=0.5, - pos="5245.4,178", + pos="4987.4,178", width=1.4263]; "genotype to phenotypic feature association" -> category [color=blue, label=category, - lp="5258.9,221.5", - pos="e,5238.8,196.21 3796,251.7 3822,249.83 3849,248.15 3874.4,247 3911.5,245.32 5178.7,246.6 5211.4,229 5221.1,223.78 5228.6,214.43 \ -5234,205.22", + lp="4999.9,221.5", + pos="e,4980.1,196.23 3538,251.7 3564,249.83 3591,248.15 3616.4,247 3653.4,245.33 4918.5,246.13 4951.4,229 4961.5,223.76 4969.4,214.27 \ +4975.2,204.96", style=solid]; predicate [height=0.5, - pos="5369.4,178", + pos="5111.4,178", width=1.5165]; "genotype to phenotypic feature association" -> predicate [color=blue, label=predicate, - lp="5360.4,221.5", - pos="e,5351.5,195.26 3796,251.68 3822,249.82 3849,248.14 3874.4,247 3953.2,243.47 5219,252.34 5294.4,229 5312.3,223.44 5330,212.1 5343.6,\ -201.62", + lp="5101.4,221.5", + pos="e,5093.6,195.02 3538,251.68 3564,249.82 3591,248.14 3616.4,247 3695.2,243.47 4960,252.09 5035.4,229 5053.7,223.41 5071.6,211.94 \ +5085.5,201.4", style=solid]; subject [height=0.5, - pos="5486.4,178", + pos="5228.4,178", width=1.2277]; "genotype to phenotypic feature association" -> subject [color=blue, label=subject, - lp="5460.4,221.5", - pos="e,5466.4,194.32 3795.7,251.69 3821.8,249.81 3848.9,248.13 3874.4,247 3959,243.25 5316.7,251.12 5398.4,229 5419.7,223.23 5441.3,211.07 \ -5457.8,200.19", + lp="5202.4,221.5", + pos="e,5208.5,194.08 3537.7,251.69 3563.8,249.81 3590.9,248.13 3616.4,247 3700.9,243.25 5057.7,250.9 5139.4,229 5161.1,223.19 5183.1,\ +210.91 5199.8,199.97", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="5633.4,178", + pos="5375.4,178", width=2.3651]; "genotype to phenotypic feature association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="5615.4,221.5", - pos="e,5599,194.6 3795.7,251.67 3821.8,249.8 3848.9,248.12 3874.4,247 4053.8,239.11 5313.5,260.04 5490.4,229 5524.7,222.98 5561.8,209.81 \ -5589.6,198.5", + lp="5357.4,221.5", + pos="e,5341,194.6 3537.7,251.67 3563.8,249.8 3590.9,248.12 3616.4,247 3795.8,239.11 5055.5,260.04 5232.4,229 5266.7,222.98 5303.8,209.81 \ +5331.6,198.5", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="5812.4,178", + pos="5554.4,178", width=2.1123]; "genotype to phenotypic feature association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="5798.4,221.5", - pos="e,5782.5,194.61 3795.4,251.67 3821.6,249.79 3848.8,248.11 3874.4,247 3975,242.63 5588.6,248.54 5687.4,229 5717.4,223.08 5749.3,210.17 \ -5773.4,198.96", + lp="5540.4,221.5", + pos="e,5524.5,194.61 3537.4,251.67 3563.6,249.79 3590.8,248.11 3616.4,247 3717,242.63 5330.6,248.54 5429.4,229 5459.4,223.08 5491.3,210.17 \ +5515.4,198.96", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="5942.4,178", + pos="5684.4,178", width=1.011]; "genotype to phenotypic feature association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="5947.9,221.5", - pos="e,5925,194.08 3795.4,251.65 3821.6,249.77 3848.8,248.1 3874.4,247 3929.6,244.63 5810.4,244.62 5863.4,229 5882.9,223.25 5902.3,211.13 \ -5916.9,200.27", + lp="5689.9,221.5", + pos="e,5667,194.08 3537.4,251.65 3563.6,249.77 3590.8,248.1 3616.4,247 3671.6,244.63 5552.4,244.62 5605.4,229 5624.9,223.25 5644.3,211.13 \ +5658.9,200.27", style=solid]; "sex qualifier" [color=blue, height=0.5, label="biological sex", - pos="6070.4,178", + pos="5812.4,178", width=2.0401]; "genotype to phenotypic feature association" -> "sex qualifier" [color=blue, label="sex qualifier", - lp="6076.4,221.5", - pos="e,6054.3,195.75 3795.4,251.64 3821.6,249.76 3848.8,248.09 3874.4,247 3933.5,244.48 5947.3,247.87 6003.4,229 6019.4,223.62 6034.7,\ -212.82 6046.6,202.64", + lp="5818.4,221.5", + pos="e,5796.3,195.75 3537.4,251.64 3563.6,249.76 3590.8,248.09 3616.4,247 3675.5,244.48 5689.3,247.87 5745.4,229 5761.4,223.62 5776.7,\ +212.82 5788.6,202.64", style=solid]; "has count" [color=blue, height=0.5, label=integer, - pos="6206.4,178", + pos="5948.4,178", width=1.2277]; "genotype to phenotypic feature association" -> "has count" [color=blue, label="has count", - lp="6193.4,221.5", - pos="e,6187.6,194.58 3795.1,251.65 3821.4,249.77 3848.7,248.09 3874.4,247 3936.8,244.35 6064.3,246.14 6124.4,229 6144.2,223.34 6164,211.48 \ -6179.2,200.72", + lp="5935.4,221.5", + pos="e,5929.6,194.58 3537.1,251.65 3563.4,249.77 3590.7,248.09 3616.4,247 3678.8,244.35 5806.3,246.14 5866.4,229 5886.2,223.34 5906,211.48 \ +5921.2,200.72", style=solid]; "has total" [color=blue, height=0.5, label=integer, - pos="6312.4,178", + pos="6054.4,178", width=1.2277]; "genotype to phenotypic feature association" -> "has total" [color=blue, label="has total", - lp="6296.9,221.5", - pos="e,6294.1,194.57 3795.1,251.64 3821.4,249.76 3848.7,248.08 3874.4,247 3939.8,244.24 6169.5,247.3 6232.4,229 6251.9,223.34 6271.2,\ -211.47 6286,200.72", + lp="6038.9,221.5", + pos="e,6036.1,194.57 3537.1,251.64 3563.4,249.76 3590.7,248.08 3616.4,247 3681.8,244.24 5911.5,247.3 5974.4,229 5993.9,223.34 6013.2,\ +211.47 6028,200.72", style=solid]; "has quotient" [color=blue, height=0.5, label=double, - pos="6416.4,178", + pos="6158.4,178", width=1.1735]; "genotype to phenotypic feature association" -> "has quotient" [color=blue, label="has quotient", - lp="6412.4,221.5", - pos="e,6397.4,194.34 3795.1,251.63 3821.4,249.75 3848.7,248.08 3874.4,247 3942.6,244.13 6266.6,247.35 6332.4,229 6352.9,223.27 6373.6,\ -211.1 6389.2,200.21", + lp="6154.4,221.5", + pos="e,6139.4,194.34 3537.1,251.63 3563.4,249.75 3590.7,248.08 3616.4,247 3684.6,244.13 6008.6,247.35 6074.4,229 6094.9,223.27 6115.6,\ +211.1 6131.2,200.21", style=solid]; "has percentage" [color=blue, height=0.5, label=double, - pos="6523.4,178", + pos="6265.4,178", width=1.1735]; "genotype to phenotypic feature association" -> "has percentage" [color=blue, label="has percentage", - lp="6542.4,221.5", - pos="e,6509.4,195 3795.1,251.63 3821.4,249.75 3848.7,248.08 3874.4,247 3946.2,243.99 6393.7,253.16 6461.4,229 6476.7,223.54 6491,212.56 \ -6502,202.28", + lp="6284.4,221.5", + pos="e,6251.4,195 3537.1,251.63 3563.4,249.75 3590.7,248.08 3616.4,247 3688.2,243.99 6135.7,253.16 6203.4,229 6218.7,223.54 6233,212.56 \ +6244,202.28", style=solid]; relation [height=0.5, - pos="5437.4,18", + pos="5179.4,18", width=1.2999]; - object -> relation [pos="e,5425.9,35.705 5400,73.174 5406,64.509 5413.4,53.768 5420,44.141", + object -> relation [pos="e,5167.9,35.705 5142,73.174 5148,64.509 5155.4,53.768 5162,44.141", style=dotted]; association_type [color=blue, height=0.5, label=string, - pos="3921.4,265", + pos="3663.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="4052.4,265", + pos="3794.4,265", width=2.0762]; "genotype to phenotypic feature association_predicate" [color=blue, height=0.5, label="predicate type", - pos="4223.4,265", + pos="3965.4,265", width=2.1665]; subject -> object [label=relation, - lp="5444.4,134.5", - pos="e,5394.8,108.97 5453.9,165.59 5441.1,159.94 5427,152.13 5416.4,142 5409.4,135.31 5403.7,126.48 5399.3,118.1"]; - subject -> relation [pos="e,5448.6,35.828 5485,159.99 5482.9,139.02 5478,102.55 5467.4,73 5463.9,63.258 5458.8,53.189 5453.8,44.423", + lp="5186.4,134.5", + pos="e,5136.8,108.97 5195.9,165.59 5183.1,159.94 5169,152.13 5158.4,142 5151.4,135.31 5145.7,126.48 5141.3,118.1"]; + subject -> relation [pos="e,5190.6,35.828 5227,159.99 5224.9,139.02 5220,102.55 5209.4,73 5205.9,63.258 5200.8,53.189 5195.8,44.423", style=dotted]; "genotype to phenotypic feature association_subject" [color=blue, height=0.5, label=genotype, - pos="4373.4,265", + pos="4115.4,265", width=1.4985]; } diff --git a/graphviz/genotype_to_phenotypic_feature_association.svg b/graphviz/genotype_to_phenotypic_feature_association.svg index 62460622d8..537795263f 100644 --- a/graphviz/genotype_to_phenotypic_feature_association.svg +++ b/graphviz/genotype_to_phenotypic_feature_association.svg @@ -4,16 +4,16 @@ - + %3 - + genotype to phenotypic feature association - -genotype to phenotypic feature association + +genotype to phenotypic feature association @@ -24,7 +24,7 @@ genotype to phenotypic feature association->association - + is_a @@ -37,8 +37,8 @@ genotype to phenotypic feature association->entity to phenotypic feature association mixin - - + + uses @@ -50,8 +50,8 @@ genotype to phenotypic feature association->genotype to entity association mixin - - + + uses @@ -63,7 +63,7 @@ genotype to phenotypic feature association->id - + id @@ -76,8 +76,8 @@ genotype to phenotypic feature association->iri - - + + iri @@ -89,8 +89,8 @@ genotype to phenotypic feature association->name - - + + name @@ -102,8 +102,8 @@ genotype to phenotypic feature association->description - - + + description @@ -115,21 +115,21 @@ genotype to phenotypic feature association->has attribute - - + + has attribute object - -named thing + +named thing genotype to phenotypic feature association->object - - + + object @@ -141,9 +141,9 @@ genotype to phenotypic feature association->negated - - -negated + + +negated @@ -154,9 +154,9 @@ genotype to phenotypic feature association->qualifiers - - -qualifiers + + +qualifiers @@ -167,9 +167,9 @@ genotype to phenotypic feature association->publications - - -publications + + +publications @@ -180,448 +180,448 @@ genotype to phenotypic feature association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string genotype to phenotypic feature association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string genotype to phenotypic feature association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string genotype to phenotypic feature association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type genotype to phenotypic feature association->timepoint - - -timepoint + + +timepoint original subject - -string + +string genotype to phenotypic feature association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie genotype to phenotypic feature association->original predicate - - -original predicate + + +original predicate original object - -string + +string genotype to phenotypic feature association->original object - - -original object + + +original object subject category - -ontology class + +ontology class genotype to phenotypic feature association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class genotype to phenotypic feature association->object category - - -object category + + +object category subject closure - -string + +string genotype to phenotypic feature association->subject closure - - -subject closure + + +subject closure object closure - -string + +string genotype to phenotypic feature association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class genotype to phenotypic feature association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class genotype to phenotypic feature association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string genotype to phenotypic feature association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string genotype to phenotypic feature association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string genotype to phenotypic feature association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string genotype to phenotypic feature association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source genotype to phenotypic feature association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type genotype to phenotypic feature association->type - - -type + + +type category - -category + +category genotype to phenotypic feature association->category - - -category + + +category predicate - -predicate + +predicate genotype to phenotypic feature association->predicate - - -predicate + + +predicate subject - -subject + +subject genotype to phenotypic feature association->subject - - -subject + + +subject frequency qualifier - -frequency value + +frequency value genotype to phenotypic feature association->frequency qualifier - - -frequency qualifier + + +frequency qualifier severity qualifier - -severity value + +severity value genotype to phenotypic feature association->severity qualifier - - -severity qualifier + + +severity qualifier onset qualifier - -onset + +onset genotype to phenotypic feature association->onset qualifier - - -onset qualifier + + +onset qualifier sex qualifier - -biological sex + +biological sex genotype to phenotypic feature association->sex qualifier - - -sex qualifier + + +sex qualifier has count - -integer + +integer genotype to phenotypic feature association->has count - - -has count + + +has count has total - -integer + +integer genotype to phenotypic feature association->has total - - -has total + + +has total has quotient - -double + +double genotype to phenotypic feature association->has quotient - - -has quotient + + +has quotient has percentage - -double + +double genotype to phenotypic feature association->has percentage - - -has percentage + + +has percentage relation - -relation + +relation object->relation - - + + association_type - -string + +string association_category - -category type + +category type genotype to phenotypic feature association_predicate - -predicate type + +predicate type subject->object - - -relation + + +relation subject->relation - - + + genotype to phenotypic feature association_subject - -genotype + +genotype diff --git a/graphviz/genotype_to_variant_association.gv b/graphviz/genotype_to_variant_association.gv index 246fd4166f..0ae20449ac 100644 --- a/graphviz/genotype_to_variant_association.gv +++ b/graphviz/genotype_to_variant_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4738.4,283"]; + graph [bb="0,0,4553.4,283"]; node [label="\N"]; "genotype to variant association" [height=0.5, label="genotype to variant association", - pos="2468.4,265", + pos="2283.4,265", width=4.351]; association [height=0.5, pos="62.394,178", width=1.7332]; "genotype to variant association" -> association [label=is_a, lp="280.39,221.5", - pos="e,102.91,191.79 2312.2,263.54 1843.2,261.89 467.2,254.87 266.39,229 213.1,222.13 153.57,206.61 112.64,194.66"]; + pos="e,102.91,191.77 2127.1,263.29 1685.5,261.02 448.47,252.59 266.39,229 213.11,222.1 153.58,206.57 112.65,194.64"]; id [color=blue, height=0.5, label=string, @@ -18,8 +18,8 @@ digraph { width=1.0652]; "genotype to variant association" -> id [color=blue, label=id, - lp="396.39,221.5", - pos="e,210.38,189.98 2312.6,263.05 1862.2,260.09 578.21,249.88 389.39,229 317.23,221.02 299.34,215.5 229.39,196 226.29,195.13 223.09,\ + lp="395.39,221.5", + pos="e,210.38,189.98 2127.6,262.79 1705.2,259.27 558.59,248.07 388.39,229 316.67,220.97 298.9,215.43 229.39,196 226.29,195.13 223.09,\ 194.17 219.89,193.15", style=solid]; iri [color=blue, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "genotype to variant association" -> iri [color=blue, label=iri, - lp="509.39,221.5", - pos="e,315.3,190.2 2312.6,262.83 1879,259.34 678.94,248.07 501.39,229 426.6,220.97 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ -325.06,193.15", + lp="501.39,221.5", + pos="e,315.32,190.15 2126.7,264.68 1751.1,265.71 807.26,264.53 493.39,229 422.11,220.93 404.75,214.31 335.39,196 332.02,195.11 328.55,\ +194.13 325.07,193.11", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "genotype to variant association" -> name [color=blue, label=name, - lp="616.39,221.5", - pos="e,439.35,191.54 2312.5,263.16 1893.7,260.6 763.8,251.66 596.39,229 545.26,222.08 488.24,206.51 449.14,194.57", + lp="604.39,221.5", + pos="e,437.98,191.87 2127.6,262.98 1736.6,260.1 734.27,250.68 584.39,229 537.02,222.15 484.46,206.96 447.86,195.11", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "genotype to variant association" -> description [color=blue, label=description, - lp="736.89,221.5", - pos="e,585.45,194.14 2312.1,263.7 1908.6,262.52 852.7,256.78 696.39,229 661.33,222.77 623.33,209.4 595.03,198.06", + lp="717.89,221.5", + pos="e,581.77,194.62 2127.1,263.74 1751,262.68 816.58,257.18 677.39,229 647.36,222.92 615.28,210.09 591.01,198.95", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "genotype to variant association" -> "has attribute" [color=blue, label="has attribute", - lp="882.39,221.5", - pos="e,725.98,192.82 2312.3,263.52 1931.9,261.95 977.72,255.39 835.39,229 800.43,222.52 762.57,208.39 735.2,196.8", + lp="852.39,221.5", + pos="e,721.33,194.01 2126.8,263.87 1772.6,263.05 931.22,258.05 805.39,229 778.89,222.88 751.04,209.98 730.13,198.82", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "genotype to variant association" -> negated [color=blue, label=negated, - lp="1038.4,221.5", - pos="e,847.59,190.46 2311.7,264.31 1988.4,264.29 1257.1,260.62 1009.4,229 956.09,222.2 896.47,205.66 857.14,193.46", + lp="990.39,221.5", + pos="e,843.03,191.96 2128.1,262.49 1803.4,258.97 1073.3,248.92 961.39,229 923.37,222.23 881.85,207.52 852.5,195.8", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "genotype to variant association" -> qualifiers [color=blue, label=qualifiers, - lp="1178.9,221.5", - pos="e,996.68,193.07 2311.7,264.36 2011.6,264.29 1366,260.36 1145.4,229 1097.6,222.2 1044.5,207.74 1006.5,196.11", + lp="1101.9,221.5", + pos="e,982.4,194.93 2127.9,262.84 1823.3,260.08 1168.9,251.59 1068.4,229 1041.6,222.97 1013.3,210.59 991.57,199.66", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "genotype to variant association" -> publications [color=blue, label=publications, - lp="1326.4,221.5", - pos="e,1148.1,192.71 2311.6,264.32 2036.1,264.06 1475.8,259.61 1282.4,229 1239.3,222.18 1191.8,207.69 1157.8,196.06", + lp="1202.4,221.5", + pos="e,1121.9,195.78 2128.5,262.31 1830.2,258.61 1201.8,248.56 1158.4,229 1146.3,223.57 1135.9,213.45 1128,203.73", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,276 +100,276 @@ digraph { width=2.0943]; "genotype to variant association" -> "has evidence" [color=blue, label="has evidence", - lp="1480.9,221.5", - pos="e,1305.9,193.61 2311.7,263.61 2065.3,262.18 1598.4,255.86 1434.4,229 1393.5,222.3 1348.6,208.48 1315.7,197.06", + lp="1300.9,221.5", + pos="e,1255.9,195.88 2126.8,264.31 1846.3,264.1 1284.2,259.8 1254.4,229 1248.2,222.63 1248.8,213.73 1251.7,205.2", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1469.4,178", - width=3.015]; + label=string, + pos="1399.4,178", + width=1.0652]; "genotype to variant association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1635.9,221.5", - pos="e,1495.5,195.59 2314.4,261.46 2076.8,257.03 1641.1,246.61 1571.4,229 1547.9,223.07 1523.5,211.31 1504.4,200.68", + lp="1419.9,221.5", + pos="e,1375.2,192.24 2127.1,263.68 1869.5,262.37 1381.7,256.28 1355.4,229 1345.9,219.09 1354.7,207.6 1366.9,198.13", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1704.4,178", - width=3.015]; + label=string, + pos="1494.4,178", + width=1.0652]; "genotype to variant association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1807.4,221.5", - pos="e,1702.1,196.41 2313.9,261.79 2099.2,258 1734.4,248.7 1712.4,229 1706.1,223.34 1703.4,214.82 1702.5,206.41", + lp="1589.4,221.5", + pos="e,1489,196.04 2127.8,262.55 1904,259.69 1515.9,251.49 1494.4,229 1488.6,222.94 1487.2,214.32 1487.7,205.94", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1939.4,178", - width=3.015]; + label=string, + pos="1669.4,178", + width=1.0652]; "genotype to variant association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2015.9,221.5", - pos="e,1918.7,195.97 2318.8,259.65 2158,254.23 1923.3,243.83 1909.4,229 1902.4,221.54 1905.6,212.18 1912,203.58", + lp="1809.9,221.5", + pos="e,1676.1,196.02 2129.3,261.67 1970.1,258.16 1739.6,249.57 1703.4,229 1693.8,223.55 1686.4,214.16 1680.9,204.98", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2121.4,178", + pos="1895.4,178", width=1.5346]; "genotype to variant association" -> timepoint [color=blue, label=timepoint, - lp="2171.4,221.5", - pos="e,2121.9,196.47 2329.8,256.56 2245.7,250.8 2151.7,241.67 2136.4,229 2129.6,223.41 2125.9,214.91 2123.8,206.49", + lp="1972.4,221.5", + pos="e,1904.8,195.92 2132.8,259.87 2055.7,255.57 1971.1,246.82 1937.4,229 1926.7,223.32 1917.5,213.63 1910.6,204.28", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2233.4,178", + pos="2007.4,178", width=1.0652]; "genotype to variant association" -> "original subject" [color=blue, label="original subject", - lp="2270.4,221.5", - pos="e,2219.6,194.92 2318.4,259.72 2272,255.01 2229.2,245.99 2214.4,229 2208.1,221.83 2209.9,212.39 2214.3,203.65", + lp="2076.4,221.5", + pos="e,2007.3,196.33 2136.4,258.63 2086.5,253.88 2038.6,245.1 2020.4,229 2013.9,223.25 2010.5,214.72 2008.7,206.31", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2347.4,178", + pos="2133.4,178", width=1.5887]; "genotype to variant association" -> "original predicate" [color=blue, label="original predicate", - lp="2397.9,221.5", - pos="e,2336.3,195.76 2381.5,249.91 2359.9,244.58 2341.1,237.66 2334.4,229 2329.1,222.16 2329.6,213.39 2332.4,205.11", + lp="2207.9,221.5", + pos="e,2132.9,196.42 2197.4,249.95 2173.9,244.49 2152.6,237.48 2144.4,229 2138.6,222.99 2135.5,214.63 2134,206.47", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2461.4,178", + pos="2267.4,178", width=1.0652]; "genotype to variant association" -> "original object" [color=blue, label="original object", - lp="2516.9,221.5", - pos="e,2462.8,196.18 2467,246.8 2466,235.16 2464.7,219.55 2463.6,206.24", + lp="2327.9,221.5", + pos="e,2270.6,196.18 2280.2,246.8 2278,235.16 2275,219.55 2272.5,206.24", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2594.4,178", + pos="2400.4,178", width=2.1304]; "genotype to variant association" -> "subject category" [color=blue, label="subject category", - lp="2642.9,221.5", - pos="e,2590.6,196.4 2539.6,248.91 2551.5,244.01 2563,237.55 2572.4,229 2579.1,222.84 2583.9,214.24 2587.3,205.9", + lp="2452.9,221.5", + pos="e,2398.4,196.3 2353.3,248.8 2364.4,243.93 2375,237.49 2383.4,229 2389.5,222.8 2393.5,214.29 2396,206.04", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2765.4,178", + pos="2571.4,178", width=2.1304]; "genotype to variant association" -> "object category" [color=blue, label="object category", - lp="2785.9,221.5", - pos="e,2750.6,195.73 2584.9,252.92 2633.8,247.03 2684.4,238.93 2706.4,229 2720,222.83 2733,212.54 2743.3,202.9", + lp="2593.9,221.5", + pos="e,2557.8,195.72 2399.5,252.87 2446.8,247.04 2495.3,239 2516.4,229 2529.3,222.88 2541.3,212.74 2550.8,203.17", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="2898.4,178", + pos="2704.4,178", width=1.0652]; "genotype to variant association" -> "subject closure" [color=blue, label="subject closure", - lp="2921.9,221.5", - pos="e,2886,195.55 2580,252.31 2598.2,250.48 2616.8,248.65 2634.4,247 2681.2,242.6 2802.4,248.22 2845.4,229 2858.3,223.21 2870.1,212.91 \ -2879.2,203.16", + lp="2728.9,221.5", + pos="e,2692.6,195.53 2395,252.35 2413.2,250.52 2431.8,248.68 2449.4,247 2494.7,242.68 2612.1,248.04 2653.4,229 2665.9,223.24 2677.1,213.09 \ +2685.9,203.42", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="2998.4,178", + pos="2812.4,178", width=1.0652]; "genotype to variant association" -> "object closure" [color=blue, label="object closure", - lp="3042.4,221.5", - pos="e,2997,196.24 2577.7,252.02 2596.6,250.17 2616.1,248.42 2634.4,247 2672.8,244.04 2949.5,251.95 2980.4,229 2987.7,223.55 2992.1,214.81 \ -2994.7,206.16", + lp="2851.4,221.5", + pos="e,2808.5,196.4 2392.7,252.04 2411.6,250.19 2431.1,248.43 2449.4,247 2486.9,244.08 2755.9,249.62 2787.4,229 2795.6,223.61 2801.3,\ +214.65 2805.1,205.79", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3131.4,178", + pos="2945.4,178", width=2.1304]; "genotype to variant association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3200.9,221.5", - pos="e,3124.4,196.12 2576.4,251.95 2595.7,250.08 2615.6,248.33 2634.4,247 2685.6,243.38 3051.3,253.61 3096.4,229 3106.2,223.67 3113.8,\ -214.3 3119.4,205.1", + lp="3010.9,221.5", + pos="e,2936.8,196.17 2391.4,251.95 2410.7,250.08 2430.6,248.33 2449.4,247 2500,243.42 2860.1,251.86 2905.4,229 2916,223.63 2924.8,213.99 \ +2931.3,204.6", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3323.4,178", + pos="3138.4,178", width=2.1304]; "genotype to variant association" -> "object category closure" [color=blue, label="object category closure", - lp="3390.9,221.5", - pos="e,3317.7,196.11 2575.5,251.85 2595,249.96 2615.3,248.24 2634.4,247 2670.9,244.64 3260.7,247.22 3292.4,229 3301.6,223.71 3308.4,214.48 \ -3313.3,205.38", + lp="3202.9,221.5", + pos="e,3131.1,196.18 2390.5,251.85 2410,249.97 2430.3,248.24 2449.4,247 2485.6,244.65 3070.3,245.99 3102.4,229 3112.4,223.69 3120.3,214.19 \ +3126.1,204.89", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3513.4,178", + pos="3328.4,178", width=1.0652]; "genotype to variant association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3563.4,221.5", - pos="e,3506.4,196.19 2575,251.8 2594.7,249.91 2615.2,248.19 2634.4,247 2681.2,244.11 3437,251.1 3478.4,229 3488.2,223.76 3495.9,214.4 \ -3501.5,205.19", + lp="3375.4,221.5", + pos="e,3320.7,195.73 2390,251.8 2409.7,249.91 2430.2,248.19 2449.4,247 2496,244.12 3248.8,250.21 3290.4,229 3300.8,223.67 3309.2,213.99 \ +3315.4,204.56", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3672.4,178", + pos="3487.4,178", width=1.0652]; "genotype to variant association" -> "object namespace" [color=blue, label="object namespace", - lp="3716.4,221.5", - pos="e,3665,195.74 2575,251.74 2594.7,249.86 2615.2,248.16 2634.4,247 2689.9,243.66 3586,254.48 3635.4,229 3645.7,223.68 3653.9,213.99 \ -3659.9,204.56", + lp="3529.4,221.5", + pos="e,3479.1,195.77 2390,251.75 2409.7,249.86 2430.2,248.16 2449.4,247 2504.7,243.67 3397.6,253.47 3447.4,229 3458.2,223.67 3467.1,213.85 \ +3473.7,204.31", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3823.4,178", + pos="3638.4,178", width=1.0652]; "genotype to variant association" -> "subject label closure" [color=blue, label="subject label closure", - lp="3876.4,221.5", - pos="e,3815.4,195.77 2574.6,251.75 2594.4,249.85 2615,248.14 2634.4,247 2666.3,245.12 3755.8,243.24 3784.4,229 3795.1,223.66 3803.8,213.84 \ -3810.2,204.31", + lp="3689.4,221.5", + pos="e,3629.8,195.79 2389.6,251.75 2409.4,249.85 2430,248.14 2449.4,247 2481.2,245.12 3568.7,242.87 3597.4,229 3608.4,223.69 3617.4,213.88 \ +3624.2,204.34", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="3994.4,178", + pos="3809.4,178", width=1.0652]; "genotype to variant association" -> "object label closure" [color=blue, label="object label closure", - lp="4041.9,221.5", - pos="e,3986.1,195.79 2574.5,251.72 2594.4,249.82 2615,248.12 2634.4,247 2671,244.88 3921.5,245.11 3954.4,229 3965.3,223.69 3974.1,213.87 \ -3980.7,204.33", + lp="3856.9,221.5", + pos="e,3800.5,195.81 2389.5,251.72 2409.4,249.82 2430,248.12 2449.4,247 2485.9,244.88 3734.3,244.69 3767.4,229 3778.5,223.72 3787.8,213.9 \ +3794.7,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4147.4,178", + pos="3962.4,178", width=2.347]; "genotype to variant association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4200.9,221.5", - pos="e,4141.4,196.18 2574.5,251.7 2594.4,249.8 2615,248.11 2634.4,247 2675.5,244.65 4079.4,248.97 4115.4,229 4124.9,223.75 4131.9,214.39 \ -4137,205.18", + lp="4015.9,221.5", + pos="e,3956.4,196.18 2389.5,251.7 2409.4,249.8 2430,248.11 2449.4,247 2490.5,244.65 3894.4,248.97 3930.4,229 3939.9,223.75 3946.9,214.39 \ +3952,205.18", style=solid]; type [height=0.5, - pos="4281.4,178", + pos="4096.4,178", width=0.86659]; "genotype to variant association" -> type [color=blue, label=type, - lp="4299.4,221.5", - pos="e,4284.1,195.98 2574.5,251.68 2594.4,249.78 2615,248.1 2634.4,247 2657.1,245.71 4257.3,244.04 4274.4,229 4280.9,223.32 4283.4,214.65 \ -4284.1,206.12", + lp="4114.4,221.5", + pos="e,4099.1,195.98 2389.5,251.68 2409.4,249.78 2430,248.1 2449.4,247 2472.1,245.71 4072.3,244.04 4089.4,229 4095.9,223.32 4098.4,214.65 \ +4099.1,206.12", style=solid]; category [height=0.5, - pos="4382.4,178", + pos="4197.4,178", width=1.4263]; "genotype to variant association" -> category [color=blue, label=category, - lp="4377.9,221.5", - pos="e,4367.7,195.48 2574.1,251.71 2594.1,249.8 2614.9,248.1 2634.4,247 2681.1,244.36 4275.3,244.64 4319.4,229 4334.6,223.59 4349,212.84 \ -4360.1,202.68", + lp="4192.9,221.5", + pos="e,4182.7,195.48 2389.1,251.71 2409.1,249.8 2429.9,248.1 2449.4,247 2496.1,244.36 4090.3,244.64 4134.4,229 4149.6,223.59 4164,212.84 \ +4175.1,202.68", style=solid]; predicate [height=0.5, - pos="4506.4,178", + pos="4321.4,178", width=1.5165]; "genotype to variant association" -> predicate [color=blue, label=predicate, - lp="4485.4,221.5", - pos="e,4484.7,194.58 2574.1,251.71 2594.1,249.8 2614.9,248.1 2634.4,247 2733.1,241.46 4317.7,253.62 4413.4,229 4435.8,223.25 4458.7,211.04 \ -4476.1,200.13", + lp="4300.4,221.5", + pos="e,4299.7,194.58 2389.1,251.71 2409.1,249.8 2429.9,248.1 2449.4,247 2548.1,241.46 4132.7,253.62 4228.4,229 4250.8,223.25 4273.7,211.04 \ +4291.1,200.13", style=solid]; subject [height=0.5, - pos="4623.4,178", + pos="4438.4,178", width=1.2277]; "genotype to variant association" -> subject [color=blue, label=subject, - lp="4590.4,221.5", - pos="e,4601.1,193.87 2574.1,251.7 2594.1,249.79 2614.9,248.09 2634.4,247 2739.2,241.15 4421.4,253.6 4523.4,229 4547.9,223.1 4573.2,210.33 \ -4592.3,199.18", + lp="4405.4,221.5", + pos="e,4416.1,193.87 2389.1,251.7 2409.1,249.79 2429.9,248.09 2449.4,247 2554.2,241.15 4236.4,253.6 4338.4,229 4362.9,223.1 4388.2,210.33 \ +4407.3,199.18", style=solid]; object [height=0.5, - pos="4666.4,91", + pos="4481.4,91", width=1.0832]; "genotype to variant association" -> object [color=blue, label=object, - lp="4716.4,178", - pos="e,4679.8,108.09 2574.1,251.69 2594.1,249.78 2614.9,248.09 2634.4,247 2744.6,240.87 4514.1,258.51 4620.4,229 4648.2,221.27 4659.2,\ -219.22 4676.4,196 4695,170.92 4698.3,156.9 4689.4,127 4688.4,123.55 4686.9,120.13 4685.1,116.85", + lp="4531.4,178", + pos="e,4494.8,108.09 2389.1,251.69 2409.1,249.78 2429.9,248.09 2449.4,247 2559.6,240.87 4329.1,258.51 4435.4,229 4463.2,221.27 4474.2,\ +219.22 4491.4,196 4510,170.92 4513.3,156.9 4504.4,127 4503.4,123.55 4501.9,120.13 4500.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2681.4,265", + pos="2496.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2812.4,265", + pos="2627.4,265", width=2.0762]; "genotype to variant association_predicate" [color=blue, height=0.5, label="predicate type", - pos="2983.4,265", + pos="2798.4,265", width=2.1665]; subject -> object [label=relation, - lp="4661.4,134.5", - pos="e,4648.5,107.23 4624.5,159.55 4625.7,149.57 4628.2,137.07 4633.4,127 4635.6,122.68 4638.5,118.52 4641.7,114.66"]; + lp="4476.4,134.5", + pos="e,4463.5,107.23 4439.5,159.55 4440.7,149.57 4443.2,137.07 4448.4,127 4450.6,122.68 4453.5,118.52 4456.7,114.66"]; relation [height=0.5, - pos="4611.4,18", + pos="4426.4,18", width=1.2999]; - subject -> relation [pos="e,4612.7,36.188 4622.1,159.79 4620,132.48 4616,78.994 4613.5,46.38", + subject -> relation [pos="e,4427.7,36.188 4437.1,159.79 4435,132.48 4431,78.994 4428.5,46.38", style=dotted]; "genotype to variant association_subject" [color=blue, height=0.5, label=genotype, - pos="3133.4,265", + pos="2948.4,265", width=1.4985]; - object -> relation [pos="e,4624.2,35.54 4653.9,73.889 4647,64.939 4638.2,53.617 4630.4,43.584", + object -> relation [pos="e,4439.2,35.54 4468.9,73.889 4462,64.939 4453.2,53.617 4445.4,43.584", style=dotted]; "genotype to variant association_object" [color=blue, height=0.5, label="sequence variant", - pos="3295.4,265", + pos="3110.4,265", width=2.5095]; } diff --git a/graphviz/genotype_to_variant_association.svg b/graphviz/genotype_to_variant_association.svg index 75cc3cd647..2e2c27a079 100644 --- a/graphviz/genotype_to_variant_association.svg +++ b/graphviz/genotype_to_variant_association.svg @@ -4,16 +4,16 @@ - + %3 - + genotype to variant association - -genotype to variant association + +genotype to variant association @@ -24,8 +24,8 @@ genotype to variant association->association - - + + is_a @@ -37,9 +37,9 @@ genotype to variant association->id - - -id + + +id @@ -50,9 +50,9 @@ genotype to variant association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ genotype to variant association->name - - -name + + +name @@ -76,9 +76,9 @@ genotype to variant association->description - - -description + + +description @@ -89,9 +89,9 @@ genotype to variant association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ genotype to variant association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ genotype to variant association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ genotype to variant association->publications - - -publications + + +publications @@ -141,363 +141,363 @@ genotype to variant association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string genotype to variant association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string genotype to variant association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string genotype to variant association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type genotype to variant association->timepoint - - -timepoint + + +timepoint original subject - -string + +string genotype to variant association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie genotype to variant association->original predicate - - -original predicate + + +original predicate original object - -string + +string genotype to variant association->original object - - -original object + + +original object subject category - -ontology class + +ontology class genotype to variant association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class genotype to variant association->object category - - -object category + + +object category subject closure - -string + +string genotype to variant association->subject closure - - -subject closure + + +subject closure object closure - -string + +string genotype to variant association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class genotype to variant association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class genotype to variant association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string genotype to variant association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string genotype to variant association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string genotype to variant association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string genotype to variant association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source genotype to variant association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type genotype to variant association->type - - -type + + +type category - -category + +category genotype to variant association->category - - -category + + +category predicate - -predicate + +predicate genotype to variant association->predicate - - -predicate + + +predicate subject - -subject + +subject genotype to variant association->subject - - -subject + + +subject object - -object + +object genotype to variant association->object - - -object + + +object association_type - -string + +string association_category - -category type + +category type genotype to variant association_predicate - -predicate type + +predicate type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + genotype to variant association_subject - -genotype + +genotype object->relation - - + + genotype to variant association_object - -sequence variant + +sequence variant diff --git a/graphviz/information_content_entity_to_named_thing_association.gv b/graphviz/information_content_entity_to_named_thing_association.gv index b788465b3b..0e1159f2d2 100644 --- a/graphviz/information_content_entity_to_named_thing_association.gv +++ b/graphviz/information_content_entity_to_named_thing_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4748,283"]; + graph [bb="0,0,4563,283"]; node [label="\N"]; "information content entity to named thing association" [height=0.5, label="information content entity to named thing association", - pos="2468.4,265", + pos="2283.4,265", width=7.2577]; association [height=0.5, pos="62.394,178", width=1.7332]; "information content entity to named thing association" -> association [label=is_a, lp="280.39,221.5", - pos="e,102.91,191.79 2208.4,263.14 1667.2,260.89 453.98,253.17 266.39,229 213.1,222.13 153.57,206.61 112.64,194.66"]; + pos="e,102.91,191.77 2023.7,262.73 1518.1,259.77 435.77,250.95 266.39,229 213.11,222.1 153.58,206.57 112.65,194.64"]; id [color=blue, height=0.5, label=string, @@ -18,8 +18,8 @@ digraph { width=1.0652]; "information content entity to named thing association" -> id [color=blue, label=id, - lp="396.39,221.5", - pos="e,210.38,189.98 2209.8,262.35 1692.6,258.65 565.38,248.46 389.39,229 317.23,221.02 299.34,215.5 229.39,196 226.29,195.13 223.09,\ + lp="395.39,221.5", + pos="e,210.38,189.98 2025.7,261.91 1545.1,257.61 546.33,246.69 388.39,229 316.67,220.97 298.9,215.43 229.39,196 226.29,195.13 223.09,\ 194.17 219.89,193.15", style=solid]; iri [color=blue, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "information content entity to named thing association" -> iri [color=blue, label=iri, - lp="509.39,221.5", - pos="e,315.3,190.2 2210.5,261.98 1715.5,257.72 666.47,246.73 501.39,229 426.6,220.97 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ -325.06,193.15", + lp="501.39,221.5", + pos="e,315.32,190.15 2022.1,264.87 1598.7,265.27 781.2,261.58 493.39,229 422.11,220.93 404.75,214.31 335.39,196 332.02,195.11 328.55,\ +194.13 325.07,193.11", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "information content entity to named thing association" -> name [color=blue, label=name, - lp="616.39,221.5", - pos="e,439.35,191.54 2209.5,262.49 1733.1,259.21 751.51,250 596.39,229 545.26,222.08 488.24,206.51 449.14,194.57", + lp="604.39,221.5", + pos="e,437.98,191.87 2025.3,262.18 1584.9,258.55 722.54,248.98 584.39,229 537.02,222.15 484.46,206.96 447.86,195.11", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "information content entity to named thing association" -> description [color=blue, label=description, - lp="736.89,221.5", - pos="e,585.45,194.14 2208.1,263.34 1751.5,261.5 840.67,254.64 696.39,229 661.33,222.77 623.33,209.4 595.03,198.06", + lp="717.89,221.5", + pos="e,581.77,194.62 2022.9,263.38 1601.6,261.61 805.05,254.85 677.39,229 647.36,222.92 615.28,210.09 591.01,198.95", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "information content entity to named thing association" -> "has attribute" [color=blue, label="has attribute", - lp="882.39,221.5", - pos="e,725.98,192.82 2208.3,263.03 1781.3,260.75 966.09,253.24 835.39,229 800.43,222.52 762.57,208.39 735.2,196.8", + lp="852.39,221.5", + pos="e,721.33,194.01 2022.9,263.54 1630.3,261.99 920.16,255.49 805.39,229 778.89,222.88 751.04,209.98 730.13,198.82", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "information content entity to named thing association" -> negated [color=blue, label=negated, - lp="1038.4,221.5", - pos="e,847.59,190.46 2207.3,264.18 1851.5,263.32 1233.2,257.56 1009.4,229 956.09,222.2 896.47,205.66 857.14,193.46", + lp="990.39,221.5", + pos="e,843.03,191.96 2027.3,261.33 1672.4,257 1062.9,247.06 961.39,229 923.37,222.23 881.85,207.52 852.5,195.8", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "information content entity to named thing association" -> qualifiers [color=blue, label=qualifiers, - lp="1178.9,221.5", - pos="e,996.68,193.07 2207.3,264.18 1881.4,263.17 1342.9,257.09 1145.4,229 1097.6,222.2 1044.5,207.74 1006.5,196.11", + lp="1101.9,221.5", + pos="e,982.4,194.93 2026,261.82 1697,258.23 1158.8,249.32 1068.4,229 1041.6,222.97 1013.3,210.59 991.57,199.66", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "information content entity to named thing association" -> publications [color=blue, label=publications, - lp="1326.4,221.5", - pos="e,1148.1,192.71 2207.2,264.04 1913,262.71 1453.7,256.12 1282.4,229 1239.3,222.18 1191.8,207.69 1157.8,196.06", + lp="1202.4,221.5", + pos="e,1121.9,195.78 2028.5,260.98 1708.8,256.48 1197.4,246.57 1158.4,229 1146.3,223.57 1135.9,213.45 1128,203.73", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,274 +100,274 @@ digraph { width=2.0943]; "information content entity to named thing association" -> "has evidence" [color=blue, label="has evidence", - lp="1480.9,221.5", - pos="e,1305.9,193.61 2208.8,262.8 1952.2,260.25 1577.6,252.47 1434.4,229 1393.5,222.3 1348.6,208.48 1315.7,197.06", + lp="1300.9,221.5", + pos="e,1255.9,195.88 2022.3,264.05 1726.2,262.79 1280.8,256.32 1254.4,229 1248.2,222.63 1248.8,213.73 1251.7,205.2", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1469.4,178", - width=3.015]; + label=string, + pos="1399.4,178", + width=1.0652]; "information content entity to named thing association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1635.9,221.5", - pos="e,1495.5,195.59 2219.1,259.56 1975.5,254.37 1632.6,244.46 1571.4,229 1547.9,223.07 1523.5,211.31 1504.4,200.68", + lp="1419.9,221.5", + pos="e,1375.2,192.24 2023.7,262.96 1757.3,260.57 1378.5,252.95 1355.4,229 1345.9,219.09 1354.7,207.6 1366.9,198.13", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1704.4,178", - width=3.015]; + label=string, + pos="1494.4,178", + width=1.0652]; "information content entity to named thing association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1807.4,221.5", - pos="e,1702.1,196.41 2217.6,259.89 2005,255.23 1731.4,245.97 1712.4,229 1706.1,223.34 1703.4,214.82 1702.5,206.41", + lp="1589.4,221.5", + pos="e,1489,196.04 2028.2,261.06 1804.8,257.18 1513,248.42 1494.4,229 1488.6,222.94 1487.2,214.32 1487.7,205.94", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1939.4,178", - width=3.015]; + label=string, + pos="1669.4,178", + width=1.0652]; "information content entity to named thing association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2015.9,221.5", - pos="e,1918.7,195.97 2236.8,256.66 2088.3,250.77 1921.1,241.45 1909.4,229 1902.4,221.54 1905.6,212.18 1912,203.58", + lp="1809.9,221.5", + pos="e,1676.1,196.02 2035.8,259.17 1891.8,254.59 1732.9,245.78 1703.4,229 1693.8,223.55 1686.4,214.16 1680.9,204.98", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2121.4,178", + pos="1895.4,178", width=1.5346]; "information content entity to named thing association" -> timepoint [color=blue, label=timepoint, - lp="2171.4,221.5", - pos="e,2121.9,196.47 2278.2,252.64 2210.8,246.96 2148.6,239.1 2136.4,229 2129.6,223.41 2125.9,214.91 2123.8,206.49", + lp="1972.4,221.5", + pos="e,1904.8,195.92 2065.9,254.96 2011.3,249.8 1961.4,241.7 1937.4,229 1926.7,223.32 1917.5,213.63 1910.6,204.28", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2233.4,178", + pos="2007.4,178", width=1.0652]; "information content entity to named thing association" -> "original subject" [color=blue, label="original subject", - lp="2270.4,221.5", - pos="e,2219.6,194.92 2272.3,253.08 2245.6,247.76 2224,240.07 2214.4,229 2208.1,221.83 2209.9,212.39 2214.3,203.65", + lp="2076.4,221.5", + pos="e,2007.3,196.33 2090.7,252.83 2059.2,247.62 2032.9,240.03 2020.4,229 2013.9,223.25 2010.5,214.72 2008.7,206.31", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2347.4,178", + pos="2133.4,178", width=1.5887]; "information content entity to named thing association" -> "original predicate" [color=blue, label="original predicate", - lp="2397.9,221.5", - pos="e,2336.3,195.76 2374.8,248.19 2356.1,243.12 2340.4,236.75 2334.4,229 2329.1,222.16 2329.6,213.39 2332.4,205.11", + lp="2207.9,221.5", + pos="e,2132.9,196.42 2190,248.17 2169.6,243 2151.8,236.59 2144.4,229 2138.6,222.99 2135.5,214.63 2134,206.47", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2461.4,178", + pos="2267.4,178", width=1.0652]; "information content entity to named thing association" -> "original object" [color=blue, label="original object", - lp="2516.9,221.5", - pos="e,2462.8,196.18 2467,246.8 2466,235.16 2464.7,219.55 2463.6,206.24", + lp="2327.9,221.5", + pos="e,2270.6,196.18 2280.2,246.8 2278,235.16 2275,219.55 2272.5,206.24", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2594.4,178", + pos="2400.4,178", width=2.1304]; "information content entity to named thing association" -> "subject category" [color=blue, label="subject category", - lp="2642.9,221.5", - pos="e,2590.6,196.4 2542.6,247.66 2553.4,242.93 2563.8,236.84 2572.4,229 2579.1,222.84 2583.9,214.24 2587.3,205.9", + lp="2452.9,221.5", + pos="e,2398.4,196.3 2355.8,247.65 2366,242.93 2375.6,236.84 2383.4,229 2389.5,222.8 2393.5,214.29 2396,206.04", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2765.4,178", + pos="2571.4,178", width=2.1304]; "information content entity to named thing association" -> "object category" [color=blue, label="object category", - lp="2785.9,221.5", - pos="e,2750.6,195.73 2636.9,251.21 2660.9,245.98 2684.7,238.8 2706.4,229 2720,222.83 2733,212.54 2743.3,202.9", + lp="2593.9,221.5", + pos="e,2557.8,195.72 2450.6,251.15 2473.3,245.9 2495.9,238.74 2516.4,229 2529.3,222.88 2541.3,212.74 2550.8,203.17", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="2898.4,178", + pos="2704.4,178", width=1.0652]; "information content entity to named thing association" -> "subject closure" [color=blue, label="subject closure", - lp="2921.9,221.5", - pos="e,2886,195.51 2652.8,252.23 2739,245.75 2827,237.33 2845.4,229 2858.3,223.16 2870.1,212.86 2879.2,203.11", + lp="2728.9,221.5", + pos="e,2692.6,195.5 2466.2,252.13 2550.3,245.66 2635.5,237.31 2653.4,229 2665.9,223.2 2677.1,213.04 2685.8,203.39", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="2998.4,178", + pos="2812.4,178", width=1.0652]; "information content entity to named thing association" -> "object closure" [color=blue, label="object closure", - lp="3042.4,221.5", - pos="e,2996.9,196.19 2651,252.09 2797.3,242.45 2978.7,230.28 2980.4,229 2987.7,223.49 2992,214.74 2994.6,206.09", + lp="2851.4,221.5", + pos="e,2808.5,196.34 2467.9,252.23 2610.4,242.98 2784,231.29 2787.4,229 2795.5,223.6 2801.1,214.76 2804.9,206", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3131.4,178", + pos="2945.4,178", width=2.1304]; "information content entity to named thing association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3200.9,221.5", - pos="e,3124.3,196.07 2652.1,252.17 2681.3,250.38 2711.2,248.6 2739.4,247 2779,244.76 3061.6,248.22 3096.4,229 3106.1,223.62 3113.8,214.24 \ -3119.4,205.05", + lp="3010.9,221.5", + pos="e,2936.7,196.12 2467.1,252.19 2496.3,250.4 2526.2,248.61 2554.4,247 2593.4,244.78 2870.6,246.81 2905.4,229 2916,223.56 2924.7,213.92 \ +2931.3,204.53", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3323.4,178", + pos="3138.4,178", width=2.1304]; "information content entity to named thing association" -> "object category closure" [color=blue, label="object category closure", - lp="3390.9,221.5", - pos="e,3317.7,196.09 2648.4,251.95 2678.8,250.13 2710,248.4 2739.4,247 2770.1,245.54 3265.8,244.38 3292.4,229 3301.6,223.69 3308.4,214.45 \ -3313.3,205.35", + lp="3202.9,221.5", + pos="e,3131.1,196.16 2463.7,251.93 2494,250.13 2525.1,248.4 2554.4,247 2584.8,245.55 3075.5,243.33 3102.4,229 3112.4,223.66 3120.3,214.16 \ +3126.1,204.86", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3513.4,178", + pos="3328.4,178", width=1.0652]; "information content entity to named thing association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3563.4,221.5", - pos="e,3506.4,196.18 2646.9,251.83 2677.7,250 2709.5,248.3 2739.4,247 2780.4,245.21 3442.2,248.41 3478.4,229 3488.2,223.74 3495.8,214.39 \ -3501.5,205.18", + lp="3375.4,221.5", + pos="e,3320.7,195.72 2461.9,251.83 2492.7,250.01 2524.5,248.3 2554.4,247 2595.3,245.22 3254,247.62 3290.4,229 3300.8,223.66 3309.2,213.97 \ +3315.4,204.54", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3672.4,178", + pos="3487.4,178", width=1.0652]; "information content entity to named thing association" -> "object namespace" [color=blue, label="object namespace", - lp="3716.4,221.5", - pos="e,3665,195.73 2645.8,251.78 2677,249.95 2709.1,248.25 2739.4,247 2789.1,244.94 3591.2,251.85 3635.4,229 3645.7,223.67 3653.9,213.98 \ -3659.9,204.55", + lp="3529.4,221.5", + pos="e,3479.1,195.76 2460.8,251.78 2492,249.95 2524.1,248.25 2554.4,247 2604,244.95 3402.9,250.94 3447.4,229 3458.2,223.66 3467.1,213.83 \ +3473.7,204.3", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3823.4,178", + pos="3638.4,178", width=1.0652]; "information content entity to named thing association" -> "subject label closure" [color=blue, label="subject label closure", - lp="3876.4,221.5", - pos="e,3815.4,195.76 2645.5,251.73 2676.7,249.9 2709,248.21 2739.4,247 2768.4,245.84 3758.4,241.96 3784.4,229 3795.1,223.66 3803.8,213.83 \ -3810.2,204.3", + lp="3689.4,221.5", + pos="e,3629.8,195.78 2460.5,251.73 2491.7,249.9 2524,248.21 2554.4,247 2612.3,244.69 3545.2,254.24 3597.4,229 3608.4,223.68 3617.4,213.87 \ +3624.2,204.33", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="3994.4,178", + pos="3809.4,178", width=1.0652]; "information content entity to named thing association" -> "object label closure" [color=blue, label="object label closure", - lp="4041.9,221.5", - pos="e,3986.1,195.78 2644.7,251.71 2676.2,249.87 2708.8,248.19 2739.4,247 2773.1,245.69 3924.1,243.85 3954.4,229 3965.2,223.68 3974.1,\ -213.87 3980.7,204.33", + lp="3856.9,221.5", + pos="e,3800.5,195.81 2459.7,251.71 2491.2,249.87 2523.8,248.19 2554.4,247 2588.1,245.69 3737,243.46 3767.4,229 3778.5,223.71 3787.8,213.9 \ +3794.7,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4147.4,178", + pos="3962.4,178", width=2.347]; "information content entity to named thing association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4200.9,221.5", - pos="e,4141.4,196.18 2644.4,251.69 2676,249.84 2708.7,248.16 2739.4,247 2777.6,245.55 4082,247.57 4115.4,229 4124.9,223.74 4131.9,214.39 \ -4137,205.18", + lp="4015.9,221.5", + pos="e,3956.4,196.18 2459.4,251.69 2491,249.84 2523.7,248.16 2554.4,247 2592.6,245.55 3897,247.57 3930.4,229 3939.9,223.74 3946.9,214.39 \ +3952,205.18", style=solid]; type [height=0.5, - pos="4281.4,178", + pos="4096.4,178", width=0.86659]; "information content entity to named thing association" -> type [color=blue, label=type, - lp="4299.4,221.5", - pos="e,4284.1,195.98 2644.4,251.66 2676,249.81 2708.7,248.14 2739.4,247 2760.7,246.21 4258.4,243.09 4274.4,229 4280.8,223.32 4283.4,214.65 \ -4284.1,206.11", + lp="4114.4,221.5", + pos="e,4099.1,195.98 2459.4,251.66 2491,249.81 2523.7,248.14 2554.4,247 2575.7,246.21 4073.4,243.09 4089.4,229 4095.8,223.32 4098.4,214.65 \ +4099.1,206.11", style=solid]; category [height=0.5, - pos="4382.4,178", + pos="4197.4,178", width=1.4263]; "information content entity to named thing association" -> category [color=blue, label=category, - lp="4377.9,221.5", - pos="e,4367.7,195.47 2644,251.67 2675.7,249.81 2708.5,248.14 2739.4,247 2783.3,245.38 4278,243.68 4319.4,229 4334.6,223.59 4349,212.83 \ -4360.1,202.68", + lp="4192.9,221.5", + pos="e,4182.7,195.47 2459,251.67 2490.7,249.81 2523.5,248.14 2554.4,247 2598.3,245.38 4093,243.68 4134.4,229 4149.6,223.59 4164,212.83 \ +4175.1,202.68", style=solid]; subject [height=0.5, - pos="4496.4,178", + pos="4311.4,178", width=1.2277]; "information content entity to named thing association" -> subject [color=blue, label=subject, - lp="4473.4,221.5", - pos="e,4477.7,194.32 2644,251.65 2675.7,249.8 2708.5,248.13 2739.4,247 2832.3,243.59 4323.9,254.39 4413.4,229 4433.6,223.28 4453.7,211.29 \ -4469.2,200.49", + lp="4288.4,221.5", + pos="e,4292.7,194.32 2459,251.65 2490.7,249.8 2523.5,248.13 2554.4,247 2647.3,243.59 4138.9,254.39 4228.4,229 4248.6,223.28 4268.7,211.29 \ +4284.2,200.49", style=solid]; object [height=0.5, - pos="4539.4,91", + pos="4354.4,91", width=1.0832]; "information content entity to named thing association" -> object [color=blue, label=object, - lp="4583.4,178", - pos="e,4552.8,108.09 2644,251.64 2675.7,249.79 2708.5,248.12 2739.4,247 2788.4,245.22 4456.8,244.24 4503.4,229 4527.3,221.17 4535.3,216.87 \ -4549.4,196 4563.2,175.52 4559.5,166.51 4562.4,142 4563.2,135.38 4564.3,133.39 4562.4,127 4561.4,123.55 4559.9,120.13 4558.1,116.85", + lp="4398.4,178", + pos="e,4367.8,108.09 2459,251.64 2490.7,249.79 2523.5,248.12 2554.4,247 2603.4,245.22 4271.8,244.24 4318.4,229 4342.3,221.17 4350.3,216.87 \ +4364.4,196 4378.2,175.52 4374.5,166.51 4377.4,142 4378.2,135.38 4379.3,133.39 4377.4,127 4376.4,123.55 4374.9,120.13 4373.1,116.85", style=solid]; predicate [height=0.5, - pos="4693.4,178", + pos="4508.4,178", width=1.5165]; "information content entity to named thing association" -> predicate [color=blue, label=predicate, - lp="4666.4,221.5", - pos="e,4669.6,194.35 2643.6,251.65 2675.5,249.79 2708.4,248.12 2739.4,247 2842.2,243.28 4490.3,252.53 4590.4,229 4615.3,223.15 4641.2,\ -210.56 4660.8,199.47", + lp="4480.4,221.5", + pos="e,4484.6,194.35 2458.6,251.65 2490.5,249.79 2523.4,248.12 2554.4,247 2657.2,243.28 4305.3,252.53 4405.4,229 4430.3,223.15 4456.2,\ +210.56 4475.8,199.47", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2786.4,265", + pos="2601.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2917.4,265", + pos="2732.4,265", width=2.0762]; subject -> object [label=relation, - lp="4534.4,134.5", - pos="e,4521.5,107.23 4497.5,159.55 4498.7,149.57 4501.2,137.07 4506.4,127 4508.6,122.68 4511.5,118.52 4514.7,114.66"]; + lp="4349.4,134.5", + pos="e,4336.5,107.23 4312.5,159.55 4313.7,149.57 4316.2,137.07 4321.4,127 4323.6,122.68 4326.5,118.52 4329.7,114.66"]; relation [height=0.5, - pos="4484.4,18", + pos="4299.4,18", width=1.2999]; - subject -> relation [pos="e,4485.7,36.188 4495.1,159.79 4493,132.48 4489,78.994 4486.5,46.38", + subject -> relation [pos="e,4300.7,36.188 4310.1,159.79 4308,132.48 4304,78.994 4301.5,46.38", style=dotted]; "information content entity to named thing association_subject" [color=blue, height=0.5, label="named thing", - pos="3079.4,265", + pos="2894.4,265", width=1.9318]; - object -> relation [pos="e,4497.2,35.54 4526.9,73.889 4520,64.939 4511.2,53.617 4503.4,43.584", + object -> relation [pos="e,4312.2,35.54 4341.9,73.889 4335,64.939 4326.2,53.617 4318.4,43.584", style=dotted]; "information content entity to named thing association_object" [color=blue, height=0.5, label="named thing", - pos="3236.4,265", + pos="3051.4,265", width=1.9318]; "information content entity to named thing association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3402.4,265", + pos="3217.4,265", width=2.1665]; } diff --git a/graphviz/information_content_entity_to_named_thing_association.svg b/graphviz/information_content_entity_to_named_thing_association.svg index 706430d3ea..7447919cd8 100644 --- a/graphviz/information_content_entity_to_named_thing_association.svg +++ b/graphviz/information_content_entity_to_named_thing_association.svg @@ -4,16 +4,16 @@ - + %3 - + information content entity to named thing association - -information content entity to named thing association + +information content entity to named thing association @@ -24,8 +24,8 @@ information content entity to named thing association->association - - + + is_a @@ -37,9 +37,9 @@ information content entity to named thing association->id - - -id + + +id @@ -50,9 +50,9 @@ information content entity to named thing association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ information content entity to named thing association->name - - -name + + +name @@ -76,9 +76,9 @@ information content entity to named thing association->description - - -description + + +description @@ -89,9 +89,9 @@ information content entity to named thing association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ information content entity to named thing association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ information content entity to named thing association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ information content entity to named thing association->publications - - -publications + + +publications @@ -141,363 +141,363 @@ information content entity to named thing association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string information content entity to named thing association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string information content entity to named thing association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string information content entity to named thing association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type information content entity to named thing association->timepoint - - -timepoint + + +timepoint original subject - -string + +string information content entity to named thing association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie information content entity to named thing association->original predicate - - -original predicate + + +original predicate original object - -string + +string information content entity to named thing association->original object - - -original object + + +original object subject category - -ontology class + +ontology class information content entity to named thing association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class information content entity to named thing association->object category - - -object category + + +object category subject closure - -string + +string information content entity to named thing association->subject closure - - -subject closure + + +subject closure object closure - -string + +string information content entity to named thing association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class information content entity to named thing association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class information content entity to named thing association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string information content entity to named thing association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string information content entity to named thing association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string information content entity to named thing association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string information content entity to named thing association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source information content entity to named thing association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type information content entity to named thing association->type - - -type + + +type category - -category + +category information content entity to named thing association->category - - -category + + +category subject - -subject + +subject information content entity to named thing association->subject - - -subject + + +subject object - -object + +object information content entity to named thing association->object - - -object + + +object predicate - -predicate + +predicate information content entity to named thing association->predicate - - -predicate + + +predicate association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + information content entity to named thing association_subject - -named thing + +named thing object->relation - - + + information content entity to named thing association_object - -named thing + +named thing information content entity to named thing association_predicate - -predicate type + +predicate type diff --git a/graphviz/log_odds_analysis_result.gv b/graphviz/log_odds_analysis_result.gv new file mode 100644 index 0000000000..61aac814a8 --- /dev/null +++ b/graphviz/log_odds_analysis_result.gv @@ -0,0 +1,153 @@ +digraph { + graph [bb="0,0,1566.1,123"]; + node [label="\N"]; + "log odds analysis result" [height=0.5, + label="log odds analysis result", + pos="851.94,105", + width=3.34]; + "study result" [height=0.5, + pos="66.944,18", + width=1.8596]; + "log odds analysis result" -> "study result" [label=is_a, + lp="289.94,61.5", + pos="e,110.54,31.78 732.45,102.79 615.51,100.19 432.63,92.322 275.94,69 222.31,61.017 162.2,45.981 120.27,34.474"]; + id [color=blue, + height=0.5, + label=string, + pos="189.94,18", + width=1.0652]; + "log odds analysis result" -> id [color=blue, + label=id, + lp="399.94,61.5", + pos="e,218.94,29.954 737.36,99.517 644.22,94.853 509.62,85.792 392.94,69 323.23,58.967 305.73,55.131 237.94,36 234.84,35.124 231.64,34.151 \ +228.45,33.129", + style=solid]; + iri [color=blue, + height=0.5, + label="iri type", + pos="290.94,18", + width=1.2277]; + "log odds analysis result" -> iri [color=blue, + label=iri, + lp="485.94,61.5", + pos="e,324.31,29.942 740.91,97.986 666.21,92.868 565.7,83.907 477.94,69 427.76,60.476 371.5,44.535 333.92,32.939", + style=solid]; + type [color=blue, + height=0.5, + label=string, + pos="391.94,18", + width=1.0652]; + "log odds analysis result" -> type [color=blue, + label=type, + lp="576.94,61.5", + pos="e,420.9,29.898 750.04,95.383 693.94,89.728 623.26,81.109 560.94,69 505.8,58.285 492.51,52.901 438.94,36 436.19,35.131 433.36,34.201 \ +430.51,33.24", + style=solid]; + name [color=blue, + height=0.5, + label="label type", + pos="504.94,18", + width=1.5707]; + "log odds analysis result" -> name [color=blue, + label=name, + lp="662.94,61.5", + pos="e,537.59,32.737 763.23,92.784 725.78,87.113 681.91,79.231 642.94,69 610.13,60.383 574.12,47.204 547.11,36.54", + style=solid]; + description [color=blue, + height=0.5, + label="narrative text", + pos="654.94,18", + width=2.0943]; + "log odds analysis result" -> description [color=blue, + label=description, + lp="747.44,61.5", + pos="e,668.24,35.782 768.99,91.897 747.93,86.728 725.91,79.392 706.94,69 695.1,62.511 684.01,52.619 675.14,43.342", + style=solid]; + "has attribute" [color=blue, + height=0.5, + label=attribute, + pos="799.94,18", + width=1.4443]; + "log odds analysis result" -> "has attribute" [color=blue, + label="has attribute", + lp="841.94,61.5", + pos="e,793.48,36.221 813.42,87.846 806.03,82.916 799.25,76.702 794.94,69 791.09,62.118 790.59,53.863 791.54,46.061", + style=solid]; + "provided by" [color=blue, + height=0.5, + label=string, + pos="907.94,18", + width=1.0652]; + "log odds analysis result" -> "provided by" [color=blue, + label="provided by", + lp="939.44,61.5", + pos="e,903.53,36.115 873.26,86.928 878.91,81.632 884.63,75.474 888.94,69 893.65,61.938 897.42,53.545 900.32,45.671", + style=solid]; + xref [color=blue, + height=0.5, + label=uriorcurie, + pos="1021.9,18", + width=1.5887]; + "log odds analysis result" -> xref [color=blue, + label=xref, + lp="1016.4,61.5", + pos="e,1013.5,36.236 934.82,91.852 952.71,86.714 970.77,79.403 985.94,69 994.94,62.829 1002.5,53.638 1008.3,44.813", + style=solid]; + category [height=0.5, + pos="1148.9,18", + width=1.4263]; + "log odds analysis result" -> category [color=blue, + label=category, + lp="1105.4,61.5", + pos="e,1121,33.349 935.81,92.028 967.29,86.479 1003.1,78.883 1034.9,69 1061.4,60.791 1089.9,48.285 1111.8,37.834", + style=solid]; + license [color=blue, + height=0.5, + label=string, + pos="1256.9,18", + width=1.0652]; + "log odds analysis result" -> license [color=blue, + label=license, + lp="1208.9,61.5", + pos="e,1232.4,32.134 938.31,92.388 952.54,90.54 967.15,88.684 980.94,87 1052,78.325 1071.8,87.362 1140.9,69 1169.7,61.368 1200.5,47.789 \ +1223.2,36.706", + style=solid]; + rights [color=blue, + height=0.5, + label=string, + pos="1351.9,18", + width=1.0652]; + "log odds analysis result" -> rights [color=blue, + label=rights, + lp="1302.4,61.5", + pos="e,1328.3,32.235 936.17,92.147 951.07,90.266 966.45,88.461 980.94,87 1094.9,75.515 1126.8,96.398 1237.9,69 1266.6,61.941 1297.1,48.195 \ +1319.3,36.899", + style=solid]; + format [color=blue, + height=0.5, + label=string, + pos="1446.9,18", + width=1.0652]; + "log odds analysis result" -> format [color=blue, + label=format, + lp="1396.4,61.5", + pos="e,1422.7,32.131 935.45,92.013 950.57,90.123 966.21,88.351 980.94,87 1134.7,72.901 1177.4,103.42 1327.9,69 1358.1,62.107 1390.3,48.118 \ +1413.6,36.685", + style=solid]; + "creation date" [color=blue, + height=0.5, + label=date, + pos="1534.9,18", + width=0.86659]; + "log odds analysis result" -> "creation date" [color=blue, + label="creation date", + lp="1515.4,61.5", + pos="e,1513.9,31.543 935.1,91.918 950.32,90.026 966.09,88.277 980.94,87 1079.3,78.54 1328.9,91.856 1424.9,69 1453.4,62.233 1483.5,48.014 \ +1505,36.463", + style=solid]; + "named thing_category" [color=blue, + height=0.5, + label="category type", + pos="1064.9,105", + width=2.0762]; +} diff --git a/graphviz/log_odds_analysis_result.svg b/graphviz/log_odds_analysis_result.svg new file mode 100644 index 0000000000..e910e2ce02 --- /dev/null +++ b/graphviz/log_odds_analysis_result.svg @@ -0,0 +1,207 @@ + + + + + + +%3 + + + +log odds analysis result + +log odds analysis result + + + +study result + +study result + + + +log odds analysis result->study result + + +is_a + + + +id + +string + + + +log odds analysis result->id + + +id + + + +iri + +iri type + + + +log odds analysis result->iri + + +iri + + + +type + +string + + + +log odds analysis result->type + + +type + + + +name + +label type + + + +log odds analysis result->name + + +name + + + +description + +narrative text + + + +log odds analysis result->description + + +description + + + +has attribute + +attribute + + + +log odds analysis result->has attribute + + +has attribute + + + +provided by + +string + + + +log odds analysis result->provided by + + +provided by + + + +xref + +uriorcurie + + + +log odds analysis result->xref + + +xref + + + +category + +category + + + +log odds analysis result->category + + +category + + + +license + +string + + + +log odds analysis result->license + + +license + + + +rights + +string + + + +log odds analysis result->rights + + +rights + + + +format + +string + + + +log odds analysis result->format + + +format + + + +creation date + +date + + + +log odds analysis result->creation date + + +creation date + + + +named thing_category + +category type + + + diff --git a/graphviz/macromolecular_machine_to_biological_process_association.gv b/graphviz/macromolecular_machine_to_biological_process_association.gv index 92e16980d8..8bc0a19f31 100644 --- a/graphviz/macromolecular_machine_to_biological_process_association.gv +++ b/graphviz/macromolecular_machine_to_biological_process_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,5410.8,283"]; + graph [bb="0,0,5192.8,283"]; node [label="\N"]; "macromolecular machine to biological process association" [height=0.5, label="macromolecular machine to biological process association", - pos="3046.8,265", + pos="2828.8,265", width=7.7813]; "functional association" [height=0.5, pos="111.79,178", width=3.1053]; "macromolecular machine to biological process association" -> "functional association" [label=is_a, - lp="727.79,221.5", - pos="e,190.45,190.88 2766.5,264.63 2328.4,264.53 1454.4,259.94 713.79,229 499.7,220.06 445.91,218.25 232.79,196 222.29,194.9 211.3,193.59 \ + lp="726.79,221.5", + pos="e,190.45,190.88 2548.8,264.01 2143.7,262.96 1370.3,257.02 712.79,229 499.15,219.9 445.47,218.22 232.79,196 222.29,194.9 211.3,193.59 \ 200.41,192.19"]; "macromolecular machine to entity association mixin" [height=0.5, pos="494.79,178", width=7.023]; "macromolecular machine to biological process association" -> "macromolecular machine to entity association mixin" [label=uses, - lp="901.29,221.5", - pos="e,592.66,194.62 2767.6,263.35 2268.5,261.54 1242.1,254.72 884.79,229 789.17,222.12 681.08,207.74 602.99,196.16"]; + lp="900.29,221.5", + pos="e,592.81,194.63 2550.6,262.76 2092.6,260.09 1198.9,252.02 883.79,229 788.58,222.05 680.98,207.71 603.11,196.17"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "macromolecular machine to biological process association" -> id [color=blue, label=id, - lp="1020.8,221.5", - pos="e,832.77,190 2770.3,262.06 2254.7,258.04 1183.3,247.56 1013.8,229 940.75,221 922.59,215.65 851.79,196 848.68,195.14 845.48,194.17 \ -842.28,193.16", + lp="1018.8,221.5", + pos="e,832.78,189.98 2548.2,264.9 2114.4,265.23 1300.6,261.28 1011.8,229 939.63,220.93 921.73,215.5 851.79,196 848.68,195.13 845.48,194.17 \ +842.29,193.15", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,9 @@ digraph { width=1.2277]; "macromolecular machine to biological process association" -> iri [color=blue, label=iri, - lp="1137.8,221.5", - pos="e,937.69,190.23 2766.5,264.78 2313.1,265.05 1438.2,261.16 1129.8,229 1052.4,220.93 1033.2,215.26 957.79,196 954.41,195.14 950.93,\ -194.18 947.45,193.17", + lp="1131.8,221.5", + pos="e,937.7,190.2 2548.8,264.22 2137.8,263.52 1391.2,258.09 1123.8,229 1049,220.86 1030.6,214.85 957.79,196 954.41,195.13 950.94,194.16 \ +947.45,193.15", style=solid]; name [color=blue, height=0.5, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "macromolecular machine to biological process association" -> name [color=blue, label=name, - lp="1249.8,221.5", - pos="e,1062.8,191.26 2770.8,261.91 2300,257.86 1377.9,247.67 1229.8,229 1175.1,222.11 1114,206.19 1072.6,194.15", + lp="1239.8,221.5", + pos="e,1061.6,191.4 2554,261.42 2129,256.91 1347.7,246.39 1219.8,229 1168.1,221.98 1110.5,206.29 1071.2,194.35", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "macromolecular machine to biological process association" -> description [color=blue, label=description, - lp="1378.3,221.5", - pos="e,1211.2,193.64 2769.3,262.49 2321.3,259.43 1474.6,250.83 1337.8,229 1297.4,222.56 1253.2,208.65 1220.8,197.13", + lp="1361.3,221.5", + pos="e,1208.3,194.11 2552.2,262.13 2149.8,258.71 1438,249.79 1320.8,229 1285.1,222.68 1246.4,209.22 1217.7,197.87", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "macromolecular machine to biological process association" -> "has attribute" [color=blue, label="has attribute", - lp="1535.8,221.5", - pos="e,1352.4,191.74 2770.9,261.74 2357.2,257.76 1611.3,248.05 1488.8,229 1444.7,222.14 1395.9,206.98 1362,195.14", + lp="1507.8,221.5", + pos="e,1349.1,192.78 2553.8,261.56 2185.1,257.58 1564.7,248.14 1460.8,229 1425.2,222.44 1386.5,208.32 1358.5,196.75", style=solid]; predicate [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=2.1665]; "macromolecular machine to biological process association" -> predicate [color=blue, label=predicate, - lp="1695.8,221.5", - pos="e,1510,193.08 2766.8,264.38 2425.1,263.53 1867.3,257.58 1661.8,229 1613,222.22 1558.9,207.75 1520,196.12", + lp="1651.8,221.5", + pos="e,1502.3,194.04 2558.1,260.33 2229.3,255.22 1707.4,244.78 1617.8,229 1581.3,222.57 1541.5,209.12 1511.9,197.79", style=solid]; negated [color=blue, height=0.5, @@ -87,8 +87,8 @@ digraph { width=1.2999]; "macromolecular machine to biological process association" -> negated [color=blue, label=negated, - lp="1840.8,221.5", - pos="e,1644.4,190.21 2769.6,262.34 2463.4,259.41 1990,251.31 1811.8,229 1756.5,222.07 1694.5,205.34 1653.9,193.13", + lp="1769.8,221.5", + pos="e,1637.3,192.62 2559.4,259.99 2263.2,254.84 1818.6,244.65 1740.8,229 1707.9,222.38 1672.4,208.39 1646.7,196.89", style=solid]; qualifiers [color=blue, height=0.5, @@ -97,8 +97,8 @@ digraph { width=2.1304]; "macromolecular machine to biological process association" -> qualifiers [color=blue, label=qualifiers, - lp="1976.3,221.5", - pos="e,1793.3,193 2769.8,262.26 2495.9,259.26 2096.2,251.12 1942.8,229 1894.8,222.07 1841.4,207.62 1803.2,196.03", + lp="1871.3,221.5", + pos="e,1772.3,195.38 2555.1,261.09 2285.6,257.13 1905,248.21 1837.8,229 1817.4,223.18 1796.8,211.62 1780.7,201.08", style=solid]; publications [color=blue, height=0.5, @@ -107,8 +107,8 @@ digraph { width=1.7332]; "macromolecular machine to biological process association" -> publications [color=blue, label=publications, - lp="2116.8,221.5", - pos="e,1943.5,192.76 2770.5,262 2530.6,258.8 2201.9,250.51 2072.8,229 2031.5,222.11 1986,207.8 1953.3,196.25", + lp="1961.8,221.5", + pos="e,1906.3,196.02 2553.4,261.63 2294.2,258.13 1942,249.61 1917.8,229 1911.2,223.37 1908.2,214.71 1907,206.17", style=solid]; "has evidence" [color=blue, height=0.5, @@ -117,261 +117,262 @@ digraph { width=2.0943]; "macromolecular machine to biological process association" -> "has evidence" [color=blue, label="has evidence", - lp="2268.3,221.5", - pos="e,2100.8,193.77 2776.5,260.2 2577.6,255.96 2324.6,247.12 2221.8,229 2183.4,222.24 2141.5,208.65 2110.4,197.35", + lp="2060.3,221.5", + pos="e,2032.4,194.37 2555,261.17 2325.6,257.41 2032.7,248.75 2013.8,229 2004.6,219.42 2012.1,209.02 2023.8,200.2", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2265.8,178", - width=3.015]; + label=string, + pos="2195.8,178", + width=1.0652]; "macromolecular machine to biological process association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2414.3,221.5", - pos="e,2287.2,195.77 2767.1,263.58 2608.2,260.67 2426.1,252.07 2349.8,229 2330.5,223.17 2311,212 2295.7,201.69", + lp="2178.3,221.5", + pos="e,2166.5,189.71 2561.9,259.43 2365.3,254.72 2129.6,245.62 2113.8,229 2109.2,224.17 2110.1,219.56 2113.8,214 2116.5,209.87 2137,201.11 \ +2156.9,193.39", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2500.8,178", - width=3.015]; + label=string, + pos="2290.8,178", + width=1.0652]; "macromolecular machine to biological process association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2581.8,221.5", - pos="e,2488.6,196.25 2802.5,256.18 2656.9,250.28 2498.2,241.12 2486.8,229 2480.8,222.6 2481.4,213.84 2484.4,205.44", + lp="2344.8,221.5", + pos="e,2267.8,192.58 2580.7,256.61 2429,250.83 2261.7,241.65 2249.8,229 2240.8,219.44 2248.6,208.17 2259.7,198.76", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2735.8,178", - width=3.015]; + label=string, + pos="2432.8,178", + width=1.0652]; "macromolecular machine to biological process association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2790.3,221.5", - pos="e,2701.7,195.1 2822,254.18 2754.2,248.9 2694.6,240.92 2683.8,229 2675,219.36 2682,209.3 2693.3,200.75", + lp="2562.3,221.5", + pos="e,2436.1,196.22 2619,253.04 2542.3,247.37 2470.5,239.41 2455.8,229 2448,223.46 2442.8,214.59 2439.3,205.85", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2917.8,178", + pos="2658.8,178", width=1.5346]; "macromolecular machine to biological process association" -> timepoint [color=blue, label=timepoint, - lp="2939.8,221.5", - pos="e,2906.7,195.8 2945.5,248.17 2926.7,243.17 2910.9,236.84 2904.8,229 2899.5,222.2 2900,213.44 2902.7,205.16", + lp="2720.8,221.5", + pos="e,2664,196.25 2721.5,248.37 2708.7,243.52 2696.4,237.2 2685.8,229 2678.1,223.04 2672.3,214.23 2668.1,205.66", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="3029.8,178", + pos="2770.8,178", width=1.0652]; "macromolecular machine to biological process association" -> "original subject" [color=blue, label="original subject", - lp="3036.8,221.5", - pos="e,3003.7,191.31 2999.3,247.11 2991.9,242.39 2985.3,236.45 2980.8,229 2973.5,216.95 2982.8,205.59 2995.2,196.74", + lp="2818.8,221.5", + pos="e,2762.8,195.83 2781.3,247.11 2773.9,242.39 2767.3,236.45 2762.8,229 2758.6,222.01 2758.5,213.51 2760.1,205.53", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3143.8,178", + pos="2896.8,178", width=1.5887]; "macromolecular machine to biological process association" -> "original predicate" [color=blue, label="original predicate", - lp="3172.3,221.5", - pos="e,3127.7,195.75 3070.6,246.75 3077.9,241.26 3085.8,235.04 3092.8,229 3102.2,220.85 3112.1,211.38 3120.6,202.9", + lp="2947.3,221.5", + pos="e,2891.6,196.38 2856.1,246.8 2862.8,241.66 2869.6,235.62 2874.8,229 2880.2,222.12 2884.6,213.69 2888,205.72", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3257.8,178", + pos="3030.8,178", width=1.0652]; "macromolecular machine to biological process association" -> "original object" [color=blue, label="original object", - lp="3302.3,221.5", - pos="e,3255.9,196.32 3182.3,249.21 3207.8,244.18 3229.7,237.58 3239.8,229 3246.6,223.24 3250.8,214.7 3253.5,206.3", + lp="3077.3,221.5", + pos="e,3029.7,196.25 2959.6,249.07 2984.2,244.05 3005.2,237.48 3014.8,229 3021.4,223.17 3025.3,214.61 3027.6,206.21", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3390.8,178", + pos="3163.8,178", width=2.1304]; "macromolecular machine to biological process association" -> "subject category" [color=blue, label="subject category", - lp="3433.3,221.5", - pos="e,3384,196.3 3259.4,253.22 3301.9,248.03 3339.3,240.36 3357.8,229 3366.9,223.43 3374,214.32 3379.2,205.38", + lp="3207.3,221.5", + pos="e,3157.7,196.26 3038.8,253.01 3079.6,247.83 3115.1,240.2 3132.8,229 3141.6,223.4 3148.4,214.27 3153.2,205.34", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3561.8,178", + pos="3334.8,178", width=2.1304]; "macromolecular machine to biological process association" -> "object category" [color=blue, label="object category", - lp="3578.3,221.5", - pos="e,3545.6,195.85 3236.2,251.72 3353.5,243.71 3484.1,233.86 3496.8,229 3512,223.15 3526.6,212.53 3538.1,202.57", + lp="3352.3,221.5", + pos="e,3318.9,195.84 3016.4,251.59 3131.2,243.59 3258.4,233.81 3270.8,229 3285.7,223.2 3300,212.72 3311.2,202.85", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3694.8,178", + pos="3467.8,178", width=1.0652]; "macromolecular machine to biological process association" -> "subject closure" [color=blue, label="subject closure", - lp="3715.3,221.5", - pos="e,3681.7,195.2 3245.5,252.28 3417,242.15 3637.5,229.12 3637.8,229 3651.8,223.26 3664.7,212.62 3674.6,202.63", + lp="3489.3,221.5", + pos="e,3455,195.2 3027.3,252.27 3195.8,242.29 3410.7,229.47 3411.8,229 3425.6,223.25 3438.3,212.61 3448.1,202.62", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3794.8,178", + pos="3575.8,178", width=1.0652]; "macromolecular machine to biological process association" -> "object closure" [color=blue, label="object closure", - lp="3835.8,221.5", - pos="e,3792.3,196.35 3241.9,252.05 3273.3,250.27 3305.4,248.52 3335.8,247 3360.1,245.78 3753.8,242.89 3773.8,229 3781.5,223.61 3786.4,\ -214.78 3789.5,206.02", + lp="3611.8,221.5", + pos="e,3571.1,196 3023.9,252.07 3055.3,250.28 3087.4,248.53 3117.8,247 3165.5,244.6 3507,254.04 3547.8,229 3556.6,223.59 3562.9,214.33 \ +3567.2,205.24", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3927.8,178", + pos="3708.8,178", width=2.1304]; "macromolecular machine to biological process association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3994.3,221.5", - pos="e,3919.8,196.18 3239.9,251.93 3271.9,250.14 3304.8,248.42 3335.8,247 3366.6,245.6 3862.4,243.13 3889.8,229 3900.1,223.69 3908.4,\ -214.2 3914.5,204.9", + lp="3772.3,221.5", + pos="e,3699.2,196.23 3021.9,251.94 3053.9,250.15 3086.8,248.42 3117.8,247 3148.2,245.61 3638.3,242.16 3665.8,229 3676.9,223.7 3686.2,\ +214.07 3693.3,204.67", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="4119.8,178", + pos="3901.8,178", width=2.1304]; "macromolecular machine to biological process association" -> "object category closure" [color=blue, label="object category closure", - lp="4185.3,221.5", - pos="e,4113.1,196.16 3238,251.82 3270.6,250 3304.2,248.31 3335.8,247 3377.4,245.28 4049.2,248.94 4085.8,229 4095.5,223.73 4102.9,214.37 \ -4108.4,205.16", + lp="3964.3,221.5", + pos="e,3893.8,196.22 3020,251.82 3052.6,250.01 3086.2,248.31 3117.8,247 3159.2,245.28 3826.9,247.87 3863.8,229 3874.1,223.74 3882.4,214.25 \ +3888.6,204.94", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4309.8,178", + pos="4091.8,178", width=1.0652]; "macromolecular machine to biological process association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4357.8,221.5", - pos="e,4302.4,195.73 3236.8,251.75 3269.8,249.93 3303.8,248.25 3335.8,247 3387.8,244.97 4226.5,252.88 4272.8,229 4283.1,223.67 4291.3,\ -213.99 4297.3,204.55", + lp="4137.8,221.5", + pos="e,4083.5,195.77 3018.8,251.75 3051.8,249.93 3085.8,248.25 3117.8,247 3169.6,244.98 4005.2,251.93 4051.8,229 4062.6,223.66 4071.5,\ +213.84 4078.1,204.3", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4468.8,178", + pos="4250.8,178", width=1.0652]; "macromolecular machine to biological process association" -> "object namespace" [color=blue, label="object namespace", - lp="4511.8,221.5", - pos="e,4460.8,195.77 3236,251.72 3269.2,249.89 3303.5,248.21 3335.8,247 3366.2,245.86 4402.6,242.56 4429.8,229 4440.5,223.66 4449.1,213.84 \ -4455.6,204.3", + lp="4291.8,221.5", + pos="e,4242.2,195.79 3018,251.72 3051.2,249.89 3085.5,248.21 3117.8,247 3148.1,245.86 4182.5,242.2 4209.8,229 4220.8,223.69 4229.8,213.87 \ +4236.6,204.33", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4619.8,178", + pos="4401.8,178", width=1.0652]; "macromolecular machine to biological process association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4671.8,221.5", - pos="e,4611.5,195.79 3235.6,251.69 3269,249.85 3303.4,248.19 3335.8,247 3370.3,245.73 4548.8,244.2 4579.8,229 4590.6,223.69 4599.5,213.87 \ -4606.1,204.33", + lp="4453.8,221.5", + pos="e,4392.9,195.81 3017.6,251.69 3051,249.86 3085.4,248.19 3117.8,247 3152.3,245.74 4328.6,243.8 4359.8,229 4370.9,223.71 4380.2,213.9 \ +4387.1,204.36", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4790.8,178", + pos="4572.8,178", width=1.0652]; "macromolecular machine to biological process association" -> "object label closure" [color=blue, label="object label closure", - lp="4839.3,221.5", - pos="e,4782.2,195.8 3235.2,251.66 3268.7,249.83 3303.3,248.16 3335.8,247 3375,245.6 4714.4,246.03 4749.8,229 4760.8,223.71 4769.8,213.89 \ -4776.6,204.35", + lp="4621.3,221.5", + pos="e,4564.2,195.8 3017.2,251.66 3050.7,249.83 3085.3,248.16 3117.8,247 3157,245.6 4496.4,246.03 4531.8,229 4542.8,223.71 4551.8,213.89 \ +4558.6,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4952.8,178", + pos="4734.8,178", width=2.347]; "macromolecular machine to biological process association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="5001.3,221.5", - pos="e,4944.2,196.29 3234.8,251.65 3268.4,249.81 3303.1,248.15 3335.8,247 3379.6,245.46 4873.4,248.2 4912.8,229 4923.5,223.78 4932.3,\ -214.16 4938.8,204.75", + lp="4783.3,221.5", + pos="e,4726.2,196.29 3016.8,251.65 3050.4,249.81 3085.1,248.15 3117.8,247 3161.6,245.46 4655.4,248.2 4694.8,229 4705.5,223.78 4714.3,\ +214.16 4720.8,204.75", style=solid]; type [height=0.5, - pos="5086.8,178", + pos="4868.8,178", width=0.86659]; "macromolecular machine to biological process association" -> type [color=blue, label=type, - lp="5100.8,221.5", - pos="e,5087.6,196.18 3234.8,251.62 3268.4,249.78 3303.1,248.13 3335.8,247 3359.9,246.17 5055.9,244.05 5074.8,229 5081.6,223.54 5085,214.92 \ -5086.5,206.37", + lp="4882.8,221.5", + pos="e,4869.6,196.18 3016.8,251.62 3050.4,249.78 3085.1,248.13 3117.8,247 3141.9,246.17 4837.9,244.05 4856.8,229 4863.6,223.54 4867,214.92 \ +4868.5,206.37", style=solid]; category [height=0.5, - pos="5187.8,178", + pos="4969.8,178", width=1.4263]; "macromolecular machine to biological process association" -> category [color=blue, label=category, - lp="5181.3,221.5", - pos="e,5172.2,195.25 3234.4,251.63 3268.2,249.79 3303,248.13 3335.8,247 3385.3,245.29 5073.8,244.86 5120.8,229 5137,223.53 5152.5,212.51 \ -5164.5,202.2", + lp="4963.3,221.5", + pos="e,4954.2,195.25 3016.4,251.63 3050.2,249.79 3085,248.13 3117.8,247 3167.3,245.29 4855.8,244.86 4902.8,229 4919,223.53 4934.5,212.51 \ +4946.5,202.2", style=solid]; subject [height=0.5, - pos="5301.8,178", + pos="5083.8,178", width=1.2277]; "macromolecular machine to biological process association" -> subject [color=blue, label=subject, - lp="5277.8,221.5", - pos="e,5282.5,194.33 3234.4,251.62 3268.2,249.77 3303,248.12 3335.8,247 3388,245.22 5166.4,242.97 5216.8,229 5237.5,223.25 5258.4,211.08 \ -5274.3,200.2", + lp="5059.8,221.5", + pos="e,5064.5,194.33 3016.4,251.62 3050.2,249.77 3085,248.12 3117.8,247 3170,245.22 4948.4,242.97 4998.8,229 5019.5,223.25 5040.4,211.08 \ +5056.3,200.2", style=solid]; object [height=0.5, - pos="5344.8,91", + pos="5126.8,91", width=1.0832]; "macromolecular machine to biological process association" -> object [color=blue, label=object, - lp="5388.8,178", - pos="e,5358.2,108.09 3234.4,251.6 3268.2,249.76 3303,248.11 3335.8,247 3390.5,245.14 5255.6,245.74 5307.8,229 5332.1,221.2 5340.4,217.1 \ -5354.8,196 5368.7,175.59 5364.9,166.51 5367.8,142 5368.6,135.38 5369.7,133.39 5367.8,127 5366.8,123.55 5365.3,120.13 5363.5,116.85", + lp="5170.8,178", + pos="e,5140.2,108.09 3016.4,251.6 3050.2,249.76 3085,248.11 3117.8,247 3172.5,245.14 5037.6,245.74 5089.8,229 5114.1,221.2 5122.4,217.1 \ +5136.8,196 5150.7,175.59 5146.9,166.51 5149.8,142 5150.6,135.38 5151.7,133.39 5149.8,127 5148.8,123.55 5147.3,120.13 5145.5,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3382.8,265", + pos="3164.8,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3513.8,265", + pos="3295.8,265", width=2.0762]; subject -> object [label=relation, - lp="5339.8,134.5", - pos="e,5326.9,107.23 5302.9,159.55 5304.1,149.57 5306.6,137.07 5311.8,127 5314,122.68 5316.9,118.52 5320.1,114.66"]; + lp="5121.8,134.5", + pos="e,5108.9,107.23 5084.9,159.55 5086.1,149.57 5088.6,137.07 5093.8,127 5096,122.68 5098.9,118.52 5102.1,114.66"]; relation [height=0.5, - pos="5289.8,18", + pos="5071.8,18", width=1.2999]; - subject -> relation [pos="e,5291.1,36.188 5300.5,159.79 5298.4,132.48 5294.3,78.994 5291.9,46.38", + subject -> relation [pos="e,5073.1,36.188 5082.5,159.79 5080.4,132.48 5076.3,78.994 5073.9,46.38", style=dotted]; "functional association_subject" [color=blue, height=0.5, label="macromolecular machine mixin", - pos="3762.8,265", + pos="3544.8,265", width=4.3329]; - object -> relation [pos="e,5302.6,35.54 5332.3,73.889 5325.4,64.939 5316.6,53.617 5308.8,43.584", + object -> relation [pos="e,5084.6,35.54 5114.3,73.889 5107.4,64.939 5098.6,53.617 5090.8,43.584", style=dotted]; "macromolecular machine to biological process association_object" [color=blue, height=0.5, label="biological process", - pos="4030.8,265", + pos="3812.8,265", width=2.5998]; } diff --git a/graphviz/macromolecular_machine_to_biological_process_association.svg b/graphviz/macromolecular_machine_to_biological_process_association.svg index 68c94bf9e0..32bcd59204 100644 --- a/graphviz/macromolecular_machine_to_biological_process_association.svg +++ b/graphviz/macromolecular_machine_to_biological_process_association.svg @@ -4,16 +4,16 @@ - + %3 - + macromolecular machine to biological process association - -macromolecular machine to biological process association + +macromolecular machine to biological process association @@ -24,9 +24,9 @@ macromolecular machine to biological process association->functional association - + -is_a +is_a @@ -37,9 +37,9 @@ macromolecular machine to biological process association->macromolecular machine to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ macromolecular machine to biological process association->id - - -id + + +id @@ -63,9 +63,9 @@ macromolecular machine to biological process association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ macromolecular machine to biological process association->name - - -name + + +name @@ -89,9 +89,9 @@ macromolecular machine to biological process association->description - - -description + + +description @@ -102,9 +102,9 @@ macromolecular machine to biological process association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ macromolecular machine to biological process association->predicate - - -predicate + + +predicate @@ -128,9 +128,9 @@ macromolecular machine to biological process association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ macromolecular machine to biological process association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ macromolecular machine to biological process association->publications - - -publications + + +publications @@ -167,344 +167,344 @@ macromolecular machine to biological process association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string macromolecular machine to biological process association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string macromolecular machine to biological process association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string macromolecular machine to biological process association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type macromolecular machine to biological process association->timepoint - - -timepoint + + +timepoint original subject - -string + +string macromolecular machine to biological process association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie macromolecular machine to biological process association->original predicate - - -original predicate + + +original predicate original object - -string + +string macromolecular machine to biological process association->original object - - -original object + + +original object subject category - -ontology class + +ontology class macromolecular machine to biological process association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class macromolecular machine to biological process association->object category - - -object category + + +object category subject closure - -string + +string macromolecular machine to biological process association->subject closure - - -subject closure + + +subject closure object closure - -string + +string macromolecular machine to biological process association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class macromolecular machine to biological process association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class macromolecular machine to biological process association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string macromolecular machine to biological process association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string macromolecular machine to biological process association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string macromolecular machine to biological process association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string macromolecular machine to biological process association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source macromolecular machine to biological process association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type macromolecular machine to biological process association->type - - -type + + +type category - -category + +category macromolecular machine to biological process association->category - - -category + + +category subject - -subject + +subject macromolecular machine to biological process association->subject - - -subject + + +subject object - -object + +object macromolecular machine to biological process association->object - - -object + + +object association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + functional association_subject - -macromolecular machine mixin + +macromolecular machine mixin object->relation - - + + macromolecular machine to biological process association_object - -biological process + +biological process diff --git a/graphviz/macromolecular_machine_to_cellular_component_association.gv b/graphviz/macromolecular_machine_to_cellular_component_association.gv index 4b555d2197..395b0f3d5b 100644 --- a/graphviz/macromolecular_machine_to_cellular_component_association.gv +++ b/graphviz/macromolecular_machine_to_cellular_component_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,5410.8,283"]; + graph [bb="0,0,5192.8,283"]; node [label="\N"]; "macromolecular machine to cellular component association" [height=0.5, label="macromolecular machine to cellular component association", - pos="3046.8,265", + pos="2828.8,265", width=7.9437]; "functional association" [height=0.5, pos="111.79,178", width=3.1053]; "macromolecular machine to cellular component association" -> "functional association" [label=is_a, - lp="727.79,221.5", - pos="e,190.45,190.88 2760.7,264.63 2320.6,264.49 1451.2,259.8 713.79,229 499.7,220.06 445.91,218.25 232.79,196 222.29,194.9 211.3,193.59 \ + lp="726.79,221.5", + pos="e,190.45,190.88 2542.9,263.99 2136.1,262.91 1367.1,256.88 712.79,229 499.15,219.9 445.47,218.22 232.79,196 222.29,194.9 211.3,193.59 \ 200.41,192.19"]; "macromolecular machine to entity association mixin" [height=0.5, pos="494.79,178", width=7.023]; "macromolecular machine to cellular component association" -> "macromolecular machine to entity association mixin" [label=uses, - lp="901.29,221.5", - pos="e,592.66,194.62 2761.7,263.33 2260.5,261.49 1240.7,254.62 884.79,229 789.17,222.12 681.08,207.74 602.99,196.16"]; + lp="900.29,221.5", + pos="e,592.81,194.63 2545.1,262.73 2085.4,260.02 1197.7,251.93 883.79,229 788.58,222.05 680.98,207.71 603.11,196.17"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "macromolecular machine to cellular component association" -> id [color=blue, label=id, - lp="1020.8,221.5", - pos="e,832.77,190 2764.5,262.02 2246.7,257.96 1182.6,247.49 1013.8,229 940.75,221 922.59,215.65 851.79,196 848.68,195.14 845.48,194.17 \ -842.28,193.16", + lp="1018.8,221.5", + pos="e,832.78,189.98 2542.5,264.91 2107.2,265.19 1299.3,261.14 1011.8,229 939.63,220.93 921.73,215.5 851.79,196 848.68,195.13 845.48,\ +194.17 842.29,193.15", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,9 @@ digraph { width=1.2277]; "macromolecular machine to cellular component association" -> iri [color=blue, label=iri, - lp="1137.8,221.5", - pos="e,937.69,190.23 2760.6,264.78 2305.5,265.01 1436.9,261.02 1129.8,229 1052.4,220.93 1033.2,215.26 957.79,196 954.41,195.14 950.93,\ -194.18 947.45,193.17", + lp="1131.8,221.5", + pos="e,937.7,190.2 2542.8,264.21 2130.6,263.47 1389.9,257.95 1123.8,229 1049,220.86 1030.6,214.85 957.79,196 954.41,195.13 950.94,194.16 \ +947.45,193.15", style=solid]; name [color=blue, height=0.5, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "macromolecular machine to cellular component association" -> name [color=blue, label=name, - lp="1249.8,221.5", - pos="e,1062.8,191.26 2764.7,261.86 2292.1,257.77 1377.3,247.59 1229.8,229 1175.1,222.11 1114,206.19 1072.6,194.15", + lp="1239.8,221.5", + pos="e,1061.6,191.4 2548.3,261.36 2122.1,256.82 1347.1,246.31 1219.8,229 1168.1,221.98 1110.5,206.29 1071.2,194.35", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "macromolecular machine to cellular component association" -> description [color=blue, label=description, - lp="1378.3,221.5", - pos="e,1211.2,193.64 2763.4,262.45 2313.9,259.36 1474,250.73 1337.8,229 1297.4,222.56 1253.2,208.65 1220.8,197.13", + lp="1361.3,221.5", + pos="e,1208.3,194.11 2546.4,262.08 2143,258.62 1437.5,249.69 1320.8,229 1285.1,222.68 1246.4,209.22 1217.7,197.87", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "macromolecular machine to cellular component association" -> "has attribute" [color=blue, label="has attribute", - lp="1535.8,221.5", - pos="e,1352.4,191.74 2765.4,261.69 2350.6,257.68 1610.8,247.97 1488.8,229 1444.7,222.14 1395.9,206.98 1362,195.14", + lp="1507.8,221.5", + pos="e,1349.1,192.78 2547.9,261.5 2178.6,257.48 1564.2,248.03 1460.8,229 1425.2,222.44 1386.5,208.32 1358.5,196.75", style=solid]; predicate [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=2.1665]; "macromolecular machine to cellular component association" -> predicate [color=blue, label=predicate, - lp="1695.8,221.5", - pos="e,1510,193.08 2760.9,264.36 2418.6,263.46 1866.2,257.41 1661.8,229 1613,222.22 1558.9,207.75 1520,196.12", + lp="1651.8,221.5", + pos="e,1502.3,194.04 2552.7,260.25 2223.7,255.11 1706.9,244.7 1617.8,229 1581.3,222.57 1541.5,209.12 1511.9,197.79", style=solid]; negated [color=blue, height=0.5, @@ -87,8 +87,8 @@ digraph { width=1.2999]; "macromolecular machine to cellular component association" -> negated [color=blue, label=negated, - lp="1840.8,221.5", - pos="e,1644.4,190.21 2763.8,262.29 2457.4,259.31 1988.8,251.17 1811.8,229 1756.5,222.07 1694.5,205.34 1653.9,193.13", + lp="1769.8,221.5", + pos="e,1637.3,192.62 2554.4,259.9 2258.2,254.72 1818.2,244.56 1740.8,229 1707.9,222.38 1672.4,208.39 1646.7,196.89", style=solid]; qualifiers [color=blue, height=0.5, @@ -97,8 +97,8 @@ digraph { width=2.1304]; "macromolecular machine to cellular component association" -> qualifiers [color=blue, label=qualifiers, - lp="1976.3,221.5", - pos="e,1793.3,193 2764.1,262.19 2490.4,259.15 2095.1,250.97 1942.8,229 1894.8,222.07 1841.4,207.62 1803.2,196.03", + lp="1871.3,221.5", + pos="e,1772.3,195.38 2549.8,261.01 2280.7,257.01 1904.5,248.08 1837.8,229 1817.4,223.18 1796.8,211.62 1780.7,201.08", style=solid]; publications [color=blue, height=0.5, @@ -107,8 +107,8 @@ digraph { width=1.7332]; "macromolecular machine to cellular component association" -> publications [color=blue, label=publications, - lp="2116.8,221.5", - pos="e,1943.5,192.76 2765,261.92 2525.6,258.67 2200.9,250.34 2072.8,229 2031.5,222.11 1986,207.8 1953.3,196.25", + lp="1961.8,221.5", + pos="e,1906.3,196.02 2548,261.55 2289.3,258.01 1941.8,249.46 1917.8,229 1911.2,223.37 1908.2,214.71 1907,206.17", style=solid]; "has evidence" [color=blue, height=0.5, @@ -117,262 +117,263 @@ digraph { width=2.0943]; "macromolecular machine to cellular component association" -> "has evidence" [color=blue, label="has evidence", - lp="2268.3,221.5", - pos="e,2100.8,193.77 2771.4,260.09 2573.3,255.8 2323.8,246.97 2221.8,229 2183.4,222.24 2141.5,208.65 2110.4,197.35", + lp="2060.3,221.5", + pos="e,2032.4,194.37 2549.7,261.08 2321.2,257.28 2032.6,248.6 2013.8,229 2004.6,219.42 2012.1,209.02 2023.8,200.2", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2265.8,178", - width=3.015]; + label=string, + pos="2195.8,178", + width=1.0652]; "macromolecular machine to cellular component association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2414.3,221.5", - pos="e,2287.2,195.77 2761.7,263.48 2604.1,260.47 2425.2,251.81 2349.8,229 2330.5,223.17 2311,212 2295.7,201.69", + lp="2178.3,221.5", + pos="e,2166.5,189.71 2557.4,259.33 2361.8,254.58 2129.5,245.5 2113.8,229 2109.2,224.17 2110.1,219.56 2113.8,214 2116.5,209.87 2137,201.11 \ +2156.9,193.39", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2500.8,178", - width=3.015]; + label=string, + pos="2290.8,178", + width=1.0652]; "macromolecular machine to cellular component association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2581.8,221.5", - pos="e,2488.6,196.25 2798.5,256.01 2654,250.11 2498.1,241.01 2486.8,229 2480.8,222.6 2481.4,213.84 2484.4,205.44", + lp="2344.8,221.5", + pos="e,2267.8,192.58 2576.6,256.45 2426,250.66 2261.6,241.53 2249.8,229 2240.8,219.44 2248.6,208.17 2259.7,198.76", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2735.8,178", - width=3.015]; + label=string, + pos="2432.8,178", + width=1.0652]; "macromolecular machine to cellular component association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2790.3,221.5", - pos="e,2701.7,195.1 2820,254.02 2753,248.74 2694.5,240.8 2683.8,229 2675,219.36 2682,209.3 2693.3,200.75", + lp="2562.3,221.5", + pos="e,2436.1,196.22 2616.9,252.89 2541,247.22 2470.3,239.32 2455.8,229 2448,223.46 2442.8,214.59 2439.3,205.85", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2917.8,178", + pos="2658.8,178", width=1.5346]; "macromolecular machine to cellular component association" -> timepoint [color=blue, label=timepoint, - lp="2939.8,221.5", - pos="e,2906.7,195.8 2945.2,248.07 2926.5,243.09 2910.9,236.79 2904.8,229 2899.5,222.2 2900,213.44 2902.7,205.16", + lp="2720.8,221.5", + pos="e,2664,196.25 2721.1,248.23 2708.5,243.4 2696.3,237.13 2685.8,229 2678.1,223.04 2672.3,214.23 2668.1,205.66", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="3029.8,178", + pos="2770.8,178", width=1.0652]; "macromolecular machine to cellular component association" -> "original subject" [color=blue, label="original subject", - lp="3036.8,221.5", - pos="e,3003.7,191.31 2999.3,247.11 2991.9,242.39 2985.3,236.45 2980.8,229 2973.5,216.95 2982.8,205.59 2995.2,196.74", + lp="2818.8,221.5", + pos="e,2762.8,195.83 2781.3,247.11 2773.9,242.39 2767.3,236.45 2762.8,229 2758.6,222.01 2758.5,213.51 2760.1,205.53", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3143.8,178", + pos="2896.8,178", width=1.5887]; "macromolecular machine to cellular component association" -> "original predicate" [color=blue, label="original predicate", - lp="3172.3,221.5", - pos="e,3127.7,195.75 3070.6,246.75 3077.9,241.26 3085.8,235.04 3092.8,229 3102.2,220.85 3112.1,211.38 3120.6,202.9", + lp="2947.3,221.5", + pos="e,2891.6,196.38 2856.1,246.8 2862.8,241.66 2869.6,235.62 2874.8,229 2880.2,222.12 2884.6,213.69 2888,205.72", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3257.8,178", + pos="3030.8,178", width=1.0652]; "macromolecular machine to cellular component association" -> "original object" [color=blue, label="original object", - lp="3302.3,221.5", - pos="e,3255.9,196.32 3182.7,249.11 3208.1,244.1 3229.7,237.52 3239.8,229 3246.6,223.24 3250.8,214.7 3253.5,206.3", + lp="3077.3,221.5", + pos="e,3029.7,196.25 2960.1,248.98 2984.4,243.96 3005.2,237.43 3014.8,229 3021.4,223.17 3025.3,214.61 3027.6,206.21", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3390.8,178", + pos="3163.8,178", width=2.1304]; "macromolecular machine to cellular component association" -> "subject category" [color=blue, label="subject category", - lp="3433.3,221.5", - pos="e,3384,196.3 3261,253.02 3302.9,247.84 3339.5,240.21 3357.8,229 3366.9,223.43 3374,214.32 3379.2,205.38", + lp="3207.3,221.5", + pos="e,3157.7,196.26 3040.3,252.81 3080.5,247.63 3115.3,240.06 3132.8,229 3141.6,223.4 3148.4,214.27 3153.2,205.34", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3561.8,178", + pos="3334.8,178", width=2.1304]; "macromolecular machine to cellular component association" -> "object category" [color=blue, label="object category", - lp="3578.3,221.5", - pos="e,3545.6,195.85 3238.1,251.59 3354.9,243.6 3484.2,233.84 3496.8,229 3512,223.15 3526.6,212.53 3538.1,202.57", + lp="3352.3,221.5", + pos="e,3318.9,195.84 3039,252.8 3141.8,246.32 3248.3,237.75 3270.8,229 3285.7,223.2 3300,212.72 3311.2,202.85", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3694.8,178", + pos="3467.8,178", width=1.0652]; "macromolecular machine to cellular component association" -> "subject closure" [color=blue, label="subject closure", - lp="3715.3,221.5", - pos="e,3681.7,195.2 3248.8,252.22 3419.5,242.24 3636.6,229.47 3637.8,229 3651.8,223.26 3664.7,212.62 3674.6,202.63", + lp="3489.3,221.5", + pos="e,3455,195.2 3030.8,252.25 3198.3,242.45 3409.5,229.94 3411.8,229 3425.6,223.25 3438.3,212.61 3448.1,202.62", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3794.8,178", + pos="3575.8,178", width=1.0652]; "macromolecular machine to cellular component association" -> "object closure" [color=blue, label="object closure", - lp="3835.8,221.5", - pos="e,3792.3,196.35 3246.3,252.07 3278.2,250.29 3310.9,248.53 3341.8,247 3365.8,245.81 3754.1,242.71 3773.8,229 3781.5,223.61 3786.4,\ -214.77 3789.5,206.02", + lp="3611.8,221.5", + pos="e,3571.1,196 3028.3,252.09 3060.2,250.3 3092.9,248.54 3123.8,247 3170.9,244.64 3507.6,253.7 3547.8,229 3556.6,223.58 3562.9,214.33 \ +3567.2,205.24", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3927.8,178", + pos="3708.8,178", width=2.1304]; "macromolecular machine to cellular component association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3994.3,221.5", - pos="e,3919.8,196.18 3244.3,251.94 3276.9,250.15 3310.3,248.43 3341.8,247 3372.2,245.62 3862.7,242.98 3889.8,229 3900.1,223.69 3908.4,\ -214.19 3914.5,204.89", + lp="3772.3,221.5", + pos="e,3699.2,196.23 3026.3,251.95 3058.9,250.16 3092.3,248.43 3123.8,247 3184,244.27 3611.5,255.04 3665.8,229 3676.9,223.7 3686.2,214.07 \ +3693.3,204.67", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="4119.8,178", + pos="3901.8,178", width=2.1304]; "macromolecular machine to cellular component association" -> "object category closure" [color=blue, label="object category closure", - lp="4185.3,221.5", - pos="e,4113.1,196.16 3241.9,251.83 3275.2,250.02 3309.5,248.32 3341.8,247 3383.1,245.31 4049.5,248.78 4085.8,229 4095.5,223.73 4102.9,\ -214.37 4108.4,205.16", + lp="3964.3,221.5", + pos="e,3893.8,196.21 3023.9,251.84 3057.2,250.02 3091.5,248.32 3123.8,247 3164.9,245.32 3827.2,247.72 3863.8,229 3874.1,223.73 3882.4,\ +214.25 3888.6,204.94", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4309.8,178", + pos="4091.8,178", width=1.0652]; "macromolecular machine to cellular component association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4357.8,221.5", - pos="e,4302.4,195.73 3240.7,251.76 3274.4,249.94 3309.1,248.26 3341.8,247 3393.5,245.01 4226.8,252.73 4272.8,229 4283.1,223.67 4291.3,\ -213.99 4297.3,204.55", + lp="4137.8,221.5", + pos="e,4083.5,195.76 3022.7,251.77 3056.4,249.94 3091.1,248.26 3123.8,247 3175.3,245.02 4005.5,251.79 4051.8,229 4062.6,223.66 4071.5,\ +213.84 4078.1,204.3", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4468.8,178", + pos="4250.8,178", width=1.0652]; "macromolecular machine to cellular component association" -> "object namespace" [color=blue, label="object namespace", - lp="4511.8,221.5", - pos="e,4460.8,195.77 3240.3,251.71 3274.1,249.89 3309,248.22 3341.8,247 3372,245.88 4402.7,242.49 4429.8,229 4440.5,223.66 4449.1,213.84 \ -4455.6,204.3", + lp="4291.8,221.5", + pos="e,4242.2,195.79 3022.3,251.71 3056.1,249.89 3091,248.22 3123.8,247 3153.9,245.88 4182.6,242.13 4209.8,229 4220.8,223.69 4229.8,213.87 \ +4236.6,204.33", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4619.8,178", + pos="4401.8,178", width=1.0652]; "macromolecular machine to cellular component association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4671.8,221.5", - pos="e,4611.5,195.79 3239.5,251.7 3273.6,249.86 3308.7,248.19 3341.8,247 3376.2,245.76 4548.9,244.12 4579.8,229 4590.6,223.69 4599.5,\ -213.87 4606.1,204.33", + lp="4453.8,221.5", + pos="e,4392.9,195.81 3021.5,251.7 3055.6,249.86 3090.7,248.19 3123.8,247 3158.1,245.76 4328.8,243.73 4359.8,229 4370.9,223.71 4380.2,\ +213.9 4387.1,204.36", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4790.8,178", + pos="4572.8,178", width=1.0652]; "macromolecular machine to cellular component association" -> "object label closure" [color=blue, label="object label closure", - lp="4839.3,221.5", - pos="e,4782.2,195.8 3239.1,251.67 3273.3,249.83 3308.6,248.17 3341.8,247 3380.9,245.62 4714.5,245.96 4749.8,229 4760.8,223.71 4769.8,\ -213.89 4776.6,204.35", + lp="4621.3,221.5", + pos="e,4564.2,195.8 3021.1,251.67 3055.3,249.83 3090.6,248.17 3123.8,247 3162.9,245.62 4496.5,245.96 4531.8,229 4542.8,223.71 4551.8,\ +213.89 4558.6,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4952.8,178", + pos="4734.8,178", width=2.347]; "macromolecular machine to cellular component association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="5001.3,221.5", - pos="e,4944.2,196.29 3238.7,251.65 3273,249.81 3308.5,248.15 3341.8,247 3385.4,245.49 4873.6,248.13 4912.8,229 4923.5,223.78 4932.3,214.16 \ -4938.8,204.75", + lp="4783.3,221.5", + pos="e,4726.2,196.29 3020.7,251.65 3055,249.81 3090.5,248.15 3123.8,247 3167.4,245.49 4655.6,248.13 4694.8,229 4705.5,223.78 4714.3,214.16 \ +4720.8,204.75", style=solid]; type [height=0.5, - pos="5086.8,178", + pos="4868.8,178", width=0.86659]; "macromolecular machine to cellular component association" -> type [color=blue, label=type, - lp="5100.8,221.5", - pos="e,5087.6,196.18 3238.7,251.62 3273,249.79 3308.5,248.13 3341.8,247 3365.8,246.18 5056,244 5074.8,229 5081.6,223.54 5085,214.92 5086.5,\ + lp="4882.8,221.5", + pos="e,4869.6,196.18 3020.7,251.62 3055,249.79 3090.5,248.13 3123.8,247 3147.8,246.18 4838,244 4856.8,229 4863.6,223.54 4867,214.92 4868.5,\ 206.37", style=solid]; category [height=0.5, - pos="5187.8,178", + pos="4969.8,178", width=1.4263]; "macromolecular machine to cellular component association" -> category [color=blue, label=category, - lp="5181.3,221.5", - pos="e,5172.2,195.25 3238.7,251.62 3273,249.78 3308.5,248.13 3341.8,247 3391.2,245.33 5074,244.81 5120.8,229 5137,223.53 5152.5,212.51 \ -5164.5,202.2", + lp="4963.3,221.5", + pos="e,4954.2,195.25 3020.7,251.62 3055,249.78 3090.5,248.13 3123.8,247 3173.2,245.33 4856,244.81 4902.8,229 4919,223.53 4934.5,212.51 \ +4946.5,202.2", style=solid]; subject [height=0.5, - pos="5301.8,178", + pos="5083.8,178", width=1.2277]; "macromolecular machine to cellular component association" -> subject [color=blue, label=subject, - lp="5277.8,221.5", - pos="e,5282.5,194.33 3238.3,251.62 3272.8,249.78 3308.3,248.12 3341.8,247 3393.8,245.25 5166.6,242.93 5216.8,229 5237.5,223.25 5258.4,\ -211.08 5274.3,200.2", + lp="5059.8,221.5", + pos="e,5064.5,194.33 3020.3,251.62 3054.8,249.78 3090.3,248.12 3123.8,247 3175.8,245.25 4948.6,242.93 4998.8,229 5019.5,223.25 5040.4,\ +211.08 5056.3,200.2", style=solid]; object [height=0.5, - pos="5344.8,91", + pos="5126.8,91", width=1.0832]; "macromolecular machine to cellular component association" -> object [color=blue, label=object, - lp="5388.8,178", - pos="e,5358.2,108.09 3238.3,251.61 3272.8,249.77 3308.3,248.12 3341.8,247 3396.4,245.18 5255.8,245.69 5307.8,229 5332.1,221.2 5340.4,\ -217.1 5354.8,196 5368.7,175.59 5364.9,166.51 5367.8,142 5368.6,135.38 5369.7,133.39 5367.8,127 5366.8,123.55 5365.3,120.13 5363.5,\ + lp="5170.8,178", + pos="e,5140.2,108.09 3020.3,251.61 3054.8,249.77 3090.3,248.12 3123.8,247 3178.4,245.18 5037.8,245.69 5089.8,229 5114.1,221.2 5122.4,\ +217.1 5136.8,196 5150.7,175.59 5146.9,166.51 5149.8,142 5150.6,135.38 5151.7,133.39 5149.8,127 5148.8,123.55 5147.3,120.13 5145.5,\ 116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3388.8,265", + pos="3170.8,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3519.8,265", + pos="3301.8,265", width=2.0762]; subject -> object [label=relation, - lp="5339.8,134.5", - pos="e,5326.9,107.23 5302.9,159.55 5304.1,149.57 5306.6,137.07 5311.8,127 5314,122.68 5316.9,118.52 5320.1,114.66"]; + lp="5121.8,134.5", + pos="e,5108.9,107.23 5084.9,159.55 5086.1,149.57 5088.6,137.07 5093.8,127 5096,122.68 5098.9,118.52 5102.1,114.66"]; relation [height=0.5, - pos="5289.8,18", + pos="5071.8,18", width=1.2999]; - subject -> relation [pos="e,5291.1,36.188 5300.5,159.79 5298.4,132.48 5294.3,78.994 5291.9,46.38", + subject -> relation [pos="e,5073.1,36.188 5082.5,159.79 5080.4,132.48 5076.3,78.994 5073.9,46.38", style=dotted]; "functional association_subject" [color=blue, height=0.5, label="macromolecular machine mixin", - pos="3768.8,265", + pos="3550.8,265", width=4.3329]; - object -> relation [pos="e,5302.6,35.54 5332.3,73.889 5325.4,64.939 5316.6,53.617 5308.8,43.584", + object -> relation [pos="e,5084.6,35.54 5114.3,73.889 5107.4,64.939 5098.6,53.617 5090.8,43.584", style=dotted]; "macromolecular machine to cellular component association_object" [color=blue, height=0.5, label="cellular component", - pos="4041.8,265", + pos="3823.8,265", width=2.7623]; } diff --git a/graphviz/macromolecular_machine_to_cellular_component_association.svg b/graphviz/macromolecular_machine_to_cellular_component_association.svg index dad3abac52..f925757963 100644 --- a/graphviz/macromolecular_machine_to_cellular_component_association.svg +++ b/graphviz/macromolecular_machine_to_cellular_component_association.svg @@ -4,16 +4,16 @@ - + %3 - + macromolecular machine to cellular component association - -macromolecular machine to cellular component association + +macromolecular machine to cellular component association @@ -24,9 +24,9 @@ macromolecular machine to cellular component association->functional association - + -is_a +is_a @@ -37,9 +37,9 @@ macromolecular machine to cellular component association->macromolecular machine to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ macromolecular machine to cellular component association->id - - -id + + +id @@ -63,9 +63,9 @@ macromolecular machine to cellular component association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ macromolecular machine to cellular component association->name - - -name + + +name @@ -89,9 +89,9 @@ macromolecular machine to cellular component association->description - - -description + + +description @@ -102,9 +102,9 @@ macromolecular machine to cellular component association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ macromolecular machine to cellular component association->predicate - - -predicate + + +predicate @@ -128,9 +128,9 @@ macromolecular machine to cellular component association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ macromolecular machine to cellular component association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ macromolecular machine to cellular component association->publications - - -publications + + +publications @@ -167,344 +167,344 @@ macromolecular machine to cellular component association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string macromolecular machine to cellular component association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string macromolecular machine to cellular component association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string macromolecular machine to cellular component association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type macromolecular machine to cellular component association->timepoint - - -timepoint + + +timepoint original subject - -string + +string macromolecular machine to cellular component association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie macromolecular machine to cellular component association->original predicate - - -original predicate + + +original predicate original object - -string + +string macromolecular machine to cellular component association->original object - - -original object + + +original object subject category - -ontology class + +ontology class macromolecular machine to cellular component association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class macromolecular machine to cellular component association->object category - - -object category + + +object category subject closure - -string + +string macromolecular machine to cellular component association->subject closure - - -subject closure + + +subject closure object closure - -string + +string macromolecular machine to cellular component association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class macromolecular machine to cellular component association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class macromolecular machine to cellular component association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string macromolecular machine to cellular component association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string macromolecular machine to cellular component association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string macromolecular machine to cellular component association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string macromolecular machine to cellular component association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source macromolecular machine to cellular component association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type macromolecular machine to cellular component association->type - - -type + + +type category - -category + +category macromolecular machine to cellular component association->category - - -category + + +category subject - -subject + +subject macromolecular machine to cellular component association->subject - - -subject + + +subject object - -object + +object macromolecular machine to cellular component association->object - - -object + + +object association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + functional association_subject - -macromolecular machine mixin + +macromolecular machine mixin object->relation - - + + macromolecular machine to cellular component association_object - -cellular component + +cellular component diff --git a/graphviz/macromolecular_machine_to_molecular_activity_association.gv b/graphviz/macromolecular_machine_to_molecular_activity_association.gv index 39f48f525d..11c7dfe50b 100644 --- a/graphviz/macromolecular_machine_to_molecular_activity_association.gv +++ b/graphviz/macromolecular_machine_to_molecular_activity_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,5410.8,283"]; + graph [bb="0,0,5192.8,283"]; node [label="\N"]; "macromolecular machine to molecular activity association" [height=0.5, label="macromolecular machine to molecular activity association", - pos="3046.8,265", + pos="2828.8,265", width=7.7813]; "functional association" [height=0.5, pos="111.79,178", width=3.1053]; "macromolecular machine to molecular activity association" -> "functional association" [label=is_a, - lp="727.79,221.5", - pos="e,190.45,190.88 2766.5,264.63 2328.4,264.53 1454.4,259.94 713.79,229 499.7,220.06 445.91,218.25 232.79,196 222.29,194.9 211.3,193.59 \ + lp="726.79,221.5", + pos="e,190.45,190.88 2548.8,264.01 2143.7,262.96 1370.3,257.02 712.79,229 499.15,219.9 445.47,218.22 232.79,196 222.29,194.9 211.3,193.59 \ 200.41,192.19"]; "macromolecular machine to entity association mixin" [height=0.5, pos="494.79,178", width=7.023]; "macromolecular machine to molecular activity association" -> "macromolecular machine to entity association mixin" [label=uses, - lp="901.29,221.5", - pos="e,592.66,194.62 2767.6,263.35 2268.5,261.54 1242.1,254.72 884.79,229 789.17,222.12 681.08,207.74 602.99,196.16"]; + lp="900.29,221.5", + pos="e,592.81,194.63 2550.6,262.76 2092.6,260.09 1198.9,252.02 883.79,229 788.58,222.05 680.98,207.71 603.11,196.17"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "macromolecular machine to molecular activity association" -> id [color=blue, label=id, - lp="1020.8,221.5", - pos="e,832.77,190 2770.3,262.06 2254.7,258.04 1183.3,247.56 1013.8,229 940.75,221 922.59,215.65 851.79,196 848.68,195.14 845.48,194.17 \ -842.28,193.16", + lp="1018.8,221.5", + pos="e,832.78,189.98 2548.2,264.9 2114.4,265.23 1300.6,261.28 1011.8,229 939.63,220.93 921.73,215.5 851.79,196 848.68,195.13 845.48,194.17 \ +842.29,193.15", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,9 @@ digraph { width=1.2277]; "macromolecular machine to molecular activity association" -> iri [color=blue, label=iri, - lp="1137.8,221.5", - pos="e,937.69,190.23 2766.5,264.78 2313.1,265.05 1438.2,261.16 1129.8,229 1052.4,220.93 1033.2,215.26 957.79,196 954.41,195.14 950.93,\ -194.18 947.45,193.17", + lp="1131.8,221.5", + pos="e,937.7,190.2 2548.8,264.22 2137.8,263.52 1391.2,258.09 1123.8,229 1049,220.86 1030.6,214.85 957.79,196 954.41,195.13 950.94,194.16 \ +947.45,193.15", style=solid]; name [color=blue, height=0.5, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "macromolecular machine to molecular activity association" -> name [color=blue, label=name, - lp="1249.8,221.5", - pos="e,1062.8,191.26 2770.8,261.91 2300,257.86 1377.9,247.67 1229.8,229 1175.1,222.11 1114,206.19 1072.6,194.15", + lp="1239.8,221.5", + pos="e,1061.6,191.4 2554,261.42 2129,256.91 1347.7,246.39 1219.8,229 1168.1,221.98 1110.5,206.29 1071.2,194.35", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "macromolecular machine to molecular activity association" -> description [color=blue, label=description, - lp="1378.3,221.5", - pos="e,1211.2,193.64 2769.3,262.49 2321.3,259.43 1474.6,250.83 1337.8,229 1297.4,222.56 1253.2,208.65 1220.8,197.13", + lp="1361.3,221.5", + pos="e,1208.3,194.11 2552.2,262.13 2149.8,258.71 1438,249.79 1320.8,229 1285.1,222.68 1246.4,209.22 1217.7,197.87", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "macromolecular machine to molecular activity association" -> "has attribute" [color=blue, label="has attribute", - lp="1535.8,221.5", - pos="e,1352.4,191.74 2770.9,261.74 2357.2,257.76 1611.3,248.05 1488.8,229 1444.7,222.14 1395.9,206.98 1362,195.14", + lp="1507.8,221.5", + pos="e,1349.1,192.78 2553.8,261.56 2185.1,257.58 1564.7,248.14 1460.8,229 1425.2,222.44 1386.5,208.32 1358.5,196.75", style=solid]; predicate [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=2.1665]; "macromolecular machine to molecular activity association" -> predicate [color=blue, label=predicate, - lp="1695.8,221.5", - pos="e,1510,193.08 2766.8,264.38 2425.1,263.53 1867.3,257.58 1661.8,229 1613,222.22 1558.9,207.75 1520,196.12", + lp="1651.8,221.5", + pos="e,1502.3,194.04 2558.1,260.33 2229.3,255.22 1707.4,244.78 1617.8,229 1581.3,222.57 1541.5,209.12 1511.9,197.79", style=solid]; negated [color=blue, height=0.5, @@ -87,8 +87,8 @@ digraph { width=1.2999]; "macromolecular machine to molecular activity association" -> negated [color=blue, label=negated, - lp="1840.8,221.5", - pos="e,1644.4,190.21 2769.6,262.34 2463.4,259.41 1990,251.31 1811.8,229 1756.5,222.07 1694.5,205.34 1653.9,193.13", + lp="1769.8,221.5", + pos="e,1637.3,192.62 2559.4,259.99 2263.2,254.84 1818.6,244.65 1740.8,229 1707.9,222.38 1672.4,208.39 1646.7,196.89", style=solid]; qualifiers [color=blue, height=0.5, @@ -97,8 +97,8 @@ digraph { width=2.1304]; "macromolecular machine to molecular activity association" -> qualifiers [color=blue, label=qualifiers, - lp="1976.3,221.5", - pos="e,1793.3,193 2769.8,262.26 2495.9,259.26 2096.2,251.12 1942.8,229 1894.8,222.07 1841.4,207.62 1803.2,196.03", + lp="1871.3,221.5", + pos="e,1772.3,195.38 2555.1,261.09 2285.6,257.13 1905,248.21 1837.8,229 1817.4,223.18 1796.8,211.62 1780.7,201.08", style=solid]; publications [color=blue, height=0.5, @@ -107,8 +107,8 @@ digraph { width=1.7332]; "macromolecular machine to molecular activity association" -> publications [color=blue, label=publications, - lp="2116.8,221.5", - pos="e,1943.5,192.76 2770.5,262 2530.6,258.8 2201.9,250.51 2072.8,229 2031.5,222.11 1986,207.8 1953.3,196.25", + lp="1961.8,221.5", + pos="e,1906.3,196.02 2553.4,261.63 2294.2,258.13 1942,249.61 1917.8,229 1911.2,223.37 1908.2,214.71 1907,206.17", style=solid]; "has evidence" [color=blue, height=0.5, @@ -117,261 +117,262 @@ digraph { width=2.0943]; "macromolecular machine to molecular activity association" -> "has evidence" [color=blue, label="has evidence", - lp="2268.3,221.5", - pos="e,2100.8,193.77 2776.5,260.2 2577.6,255.96 2324.6,247.12 2221.8,229 2183.4,222.24 2141.5,208.65 2110.4,197.35", + lp="2060.3,221.5", + pos="e,2032.4,194.37 2555,261.17 2325.6,257.41 2032.7,248.75 2013.8,229 2004.6,219.42 2012.1,209.02 2023.8,200.2", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2265.8,178", - width=3.015]; + label=string, + pos="2195.8,178", + width=1.0652]; "macromolecular machine to molecular activity association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2414.3,221.5", - pos="e,2287.2,195.77 2767.1,263.58 2608.2,260.67 2426.1,252.07 2349.8,229 2330.5,223.17 2311,212 2295.7,201.69", + lp="2178.3,221.5", + pos="e,2166.5,189.71 2561.9,259.43 2365.3,254.72 2129.6,245.62 2113.8,229 2109.2,224.17 2110.1,219.56 2113.8,214 2116.5,209.87 2137,201.11 \ +2156.9,193.39", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2500.8,178", - width=3.015]; + label=string, + pos="2290.8,178", + width=1.0652]; "macromolecular machine to molecular activity association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2581.8,221.5", - pos="e,2488.6,196.25 2802.5,256.18 2656.9,250.28 2498.2,241.12 2486.8,229 2480.8,222.6 2481.4,213.84 2484.4,205.44", + lp="2344.8,221.5", + pos="e,2267.8,192.58 2580.7,256.61 2429,250.83 2261.7,241.65 2249.8,229 2240.8,219.44 2248.6,208.17 2259.7,198.76", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2735.8,178", - width=3.015]; + label=string, + pos="2432.8,178", + width=1.0652]; "macromolecular machine to molecular activity association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2790.3,221.5", - pos="e,2701.7,195.1 2822,254.18 2754.2,248.9 2694.6,240.92 2683.8,229 2675,219.36 2682,209.3 2693.3,200.75", + lp="2562.3,221.5", + pos="e,2436.1,196.22 2619,253.04 2542.3,247.37 2470.5,239.41 2455.8,229 2448,223.46 2442.8,214.59 2439.3,205.85", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2917.8,178", + pos="2658.8,178", width=1.5346]; "macromolecular machine to molecular activity association" -> timepoint [color=blue, label=timepoint, - lp="2939.8,221.5", - pos="e,2906.7,195.8 2945.5,248.17 2926.7,243.17 2910.9,236.84 2904.8,229 2899.5,222.2 2900,213.44 2902.7,205.16", + lp="2720.8,221.5", + pos="e,2664,196.25 2721.5,248.37 2708.7,243.52 2696.4,237.2 2685.8,229 2678.1,223.04 2672.3,214.23 2668.1,205.66", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="3029.8,178", + pos="2770.8,178", width=1.0652]; "macromolecular machine to molecular activity association" -> "original subject" [color=blue, label="original subject", - lp="3036.8,221.5", - pos="e,3003.7,191.31 2999.3,247.11 2991.9,242.39 2985.3,236.45 2980.8,229 2973.5,216.95 2982.8,205.59 2995.2,196.74", + lp="2818.8,221.5", + pos="e,2762.8,195.83 2781.3,247.11 2773.9,242.39 2767.3,236.45 2762.8,229 2758.6,222.01 2758.5,213.51 2760.1,205.53", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3143.8,178", + pos="2896.8,178", width=1.5887]; "macromolecular machine to molecular activity association" -> "original predicate" [color=blue, label="original predicate", - lp="3172.3,221.5", - pos="e,3127.7,195.75 3070.6,246.75 3077.9,241.26 3085.8,235.04 3092.8,229 3102.2,220.85 3112.1,211.38 3120.6,202.9", + lp="2947.3,221.5", + pos="e,2891.6,196.38 2856.1,246.8 2862.8,241.66 2869.6,235.62 2874.8,229 2880.2,222.12 2884.6,213.69 2888,205.72", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3257.8,178", + pos="3030.8,178", width=1.0652]; "macromolecular machine to molecular activity association" -> "original object" [color=blue, label="original object", - lp="3302.3,221.5", - pos="e,3255.9,196.32 3182.3,249.21 3207.8,244.18 3229.7,237.58 3239.8,229 3246.6,223.24 3250.8,214.7 3253.5,206.3", + lp="3077.3,221.5", + pos="e,3029.7,196.25 2959.6,249.07 2984.2,244.05 3005.2,237.48 3014.8,229 3021.4,223.17 3025.3,214.61 3027.6,206.21", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3390.8,178", + pos="3163.8,178", width=2.1304]; "macromolecular machine to molecular activity association" -> "subject category" [color=blue, label="subject category", - lp="3433.3,221.5", - pos="e,3384,196.3 3259.4,253.22 3301.9,248.03 3339.3,240.36 3357.8,229 3366.9,223.43 3374,214.32 3379.2,205.38", + lp="3207.3,221.5", + pos="e,3157.7,196.26 3038.8,253.01 3079.6,247.83 3115.1,240.2 3132.8,229 3141.6,223.4 3148.4,214.27 3153.2,205.34", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3561.8,178", + pos="3334.8,178", width=2.1304]; "macromolecular machine to molecular activity association" -> "object category" [color=blue, label="object category", - lp="3578.3,221.5", - pos="e,3545.6,195.85 3236.2,251.72 3353.5,243.71 3484.1,233.86 3496.8,229 3512,223.15 3526.6,212.53 3538.1,202.57", + lp="3352.3,221.5", + pos="e,3318.9,195.84 3016.4,251.59 3131.2,243.59 3258.4,233.81 3270.8,229 3285.7,223.2 3300,212.72 3311.2,202.85", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3694.8,178", + pos="3467.8,178", width=1.0652]; "macromolecular machine to molecular activity association" -> "subject closure" [color=blue, label="subject closure", - lp="3715.3,221.5", - pos="e,3681.7,195.2 3245.5,252.28 3417,242.15 3637.5,229.12 3637.8,229 3651.8,223.26 3664.7,212.62 3674.6,202.63", + lp="3489.3,221.5", + pos="e,3455,195.2 3027.3,252.27 3195.8,242.29 3410.7,229.47 3411.8,229 3425.6,223.25 3438.3,212.61 3448.1,202.62", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3794.8,178", + pos="3575.8,178", width=1.0652]; "macromolecular machine to molecular activity association" -> "object closure" [color=blue, label="object closure", - lp="3835.8,221.5", - pos="e,3792.3,196.35 3241.9,252.05 3273.3,250.27 3305.4,248.52 3335.8,247 3360.1,245.78 3753.8,242.89 3773.8,229 3781.5,223.61 3786.4,\ -214.78 3789.5,206.02", + lp="3611.8,221.5", + pos="e,3571.1,196 3023.9,252.07 3055.3,250.28 3087.4,248.53 3117.8,247 3165.5,244.6 3507,254.04 3547.8,229 3556.6,223.59 3562.9,214.33 \ +3567.2,205.24", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3927.8,178", + pos="3708.8,178", width=2.1304]; "macromolecular machine to molecular activity association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3994.3,221.5", - pos="e,3919.8,196.18 3239.9,251.93 3271.9,250.14 3304.8,248.42 3335.8,247 3366.6,245.6 3862.4,243.13 3889.8,229 3900.1,223.69 3908.4,\ -214.2 3914.5,204.9", + lp="3772.3,221.5", + pos="e,3699.2,196.23 3021.9,251.94 3053.9,250.15 3086.8,248.42 3117.8,247 3148.2,245.61 3638.3,242.16 3665.8,229 3676.9,223.7 3686.2,\ +214.07 3693.3,204.67", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="4119.8,178", + pos="3901.8,178", width=2.1304]; "macromolecular machine to molecular activity association" -> "object category closure" [color=blue, label="object category closure", - lp="4185.3,221.5", - pos="e,4113.1,196.16 3238,251.82 3270.6,250 3304.2,248.31 3335.8,247 3377.4,245.28 4049.2,248.94 4085.8,229 4095.5,223.73 4102.9,214.37 \ -4108.4,205.16", + lp="3964.3,221.5", + pos="e,3893.8,196.22 3020,251.82 3052.6,250.01 3086.2,248.31 3117.8,247 3159.2,245.28 3826.9,247.87 3863.8,229 3874.1,223.74 3882.4,214.25 \ +3888.6,204.94", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4309.8,178", + pos="4091.8,178", width=1.0652]; "macromolecular machine to molecular activity association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4357.8,221.5", - pos="e,4302.4,195.73 3236.8,251.75 3269.8,249.93 3303.8,248.25 3335.8,247 3387.8,244.97 4226.5,252.88 4272.8,229 4283.1,223.67 4291.3,\ -213.99 4297.3,204.55", + lp="4137.8,221.5", + pos="e,4083.5,195.77 3018.8,251.75 3051.8,249.93 3085.8,248.25 3117.8,247 3169.6,244.98 4005.2,251.93 4051.8,229 4062.6,223.66 4071.5,\ +213.84 4078.1,204.3", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4468.8,178", + pos="4250.8,178", width=1.0652]; "macromolecular machine to molecular activity association" -> "object namespace" [color=blue, label="object namespace", - lp="4511.8,221.5", - pos="e,4460.8,195.77 3236,251.72 3269.2,249.89 3303.5,248.21 3335.8,247 3366.2,245.86 4402.6,242.56 4429.8,229 4440.5,223.66 4449.1,213.84 \ -4455.6,204.3", + lp="4291.8,221.5", + pos="e,4242.2,195.79 3018,251.72 3051.2,249.89 3085.5,248.21 3117.8,247 3148.1,245.86 4182.5,242.2 4209.8,229 4220.8,223.69 4229.8,213.87 \ +4236.6,204.33", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4619.8,178", + pos="4401.8,178", width=1.0652]; "macromolecular machine to molecular activity association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4671.8,221.5", - pos="e,4611.5,195.79 3235.6,251.69 3269,249.85 3303.4,248.19 3335.8,247 3370.3,245.73 4548.8,244.2 4579.8,229 4590.6,223.69 4599.5,213.87 \ -4606.1,204.33", + lp="4453.8,221.5", + pos="e,4392.9,195.81 3017.6,251.69 3051,249.86 3085.4,248.19 3117.8,247 3152.3,245.74 4328.6,243.8 4359.8,229 4370.9,223.71 4380.2,213.9 \ +4387.1,204.36", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4790.8,178", + pos="4572.8,178", width=1.0652]; "macromolecular machine to molecular activity association" -> "object label closure" [color=blue, label="object label closure", - lp="4839.3,221.5", - pos="e,4782.2,195.8 3235.2,251.66 3268.7,249.83 3303.3,248.16 3335.8,247 3375,245.6 4714.4,246.03 4749.8,229 4760.8,223.71 4769.8,213.89 \ -4776.6,204.35", + lp="4621.3,221.5", + pos="e,4564.2,195.8 3017.2,251.66 3050.7,249.83 3085.3,248.16 3117.8,247 3157,245.6 4496.4,246.03 4531.8,229 4542.8,223.71 4551.8,213.89 \ +4558.6,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4952.8,178", + pos="4734.8,178", width=2.347]; "macromolecular machine to molecular activity association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="5001.3,221.5", - pos="e,4944.2,196.29 3234.8,251.65 3268.4,249.81 3303.1,248.15 3335.8,247 3379.6,245.46 4873.4,248.2 4912.8,229 4923.5,223.78 4932.3,\ -214.16 4938.8,204.75", + lp="4783.3,221.5", + pos="e,4726.2,196.29 3016.8,251.65 3050.4,249.81 3085.1,248.15 3117.8,247 3161.6,245.46 4655.4,248.2 4694.8,229 4705.5,223.78 4714.3,\ +214.16 4720.8,204.75", style=solid]; type [height=0.5, - pos="5086.8,178", + pos="4868.8,178", width=0.86659]; "macromolecular machine to molecular activity association" -> type [color=blue, label=type, - lp="5100.8,221.5", - pos="e,5087.6,196.18 3234.8,251.62 3268.4,249.78 3303.1,248.13 3335.8,247 3359.9,246.17 5055.9,244.05 5074.8,229 5081.6,223.54 5085,214.92 \ -5086.5,206.37", + lp="4882.8,221.5", + pos="e,4869.6,196.18 3016.8,251.62 3050.4,249.78 3085.1,248.13 3117.8,247 3141.9,246.17 4837.9,244.05 4856.8,229 4863.6,223.54 4867,214.92 \ +4868.5,206.37", style=solid]; category [height=0.5, - pos="5187.8,178", + pos="4969.8,178", width=1.4263]; "macromolecular machine to molecular activity association" -> category [color=blue, label=category, - lp="5181.3,221.5", - pos="e,5172.2,195.25 3234.4,251.63 3268.2,249.79 3303,248.13 3335.8,247 3385.3,245.29 5073.8,244.86 5120.8,229 5137,223.53 5152.5,212.51 \ -5164.5,202.2", + lp="4963.3,221.5", + pos="e,4954.2,195.25 3016.4,251.63 3050.2,249.79 3085,248.13 3117.8,247 3167.3,245.29 4855.8,244.86 4902.8,229 4919,223.53 4934.5,212.51 \ +4946.5,202.2", style=solid]; subject [height=0.5, - pos="5301.8,178", + pos="5083.8,178", width=1.2277]; "macromolecular machine to molecular activity association" -> subject [color=blue, label=subject, - lp="5277.8,221.5", - pos="e,5282.5,194.33 3234.4,251.62 3268.2,249.77 3303,248.12 3335.8,247 3388,245.22 5166.4,242.97 5216.8,229 5237.5,223.25 5258.4,211.08 \ -5274.3,200.2", + lp="5059.8,221.5", + pos="e,5064.5,194.33 3016.4,251.62 3050.2,249.77 3085,248.12 3117.8,247 3170,245.22 4948.4,242.97 4998.8,229 5019.5,223.25 5040.4,211.08 \ +5056.3,200.2", style=solid]; object [height=0.5, - pos="5344.8,91", + pos="5126.8,91", width=1.0832]; "macromolecular machine to molecular activity association" -> object [color=blue, label=object, - lp="5388.8,178", - pos="e,5358.2,108.09 3234.4,251.6 3268.2,249.76 3303,248.11 3335.8,247 3390.5,245.14 5255.6,245.74 5307.8,229 5332.1,221.2 5340.4,217.1 \ -5354.8,196 5368.7,175.59 5364.9,166.51 5367.8,142 5368.6,135.38 5369.7,133.39 5367.8,127 5366.8,123.55 5365.3,120.13 5363.5,116.85", + lp="5170.8,178", + pos="e,5140.2,108.09 3016.4,251.6 3050.2,249.76 3085,248.11 3117.8,247 3172.5,245.14 5037.6,245.74 5089.8,229 5114.1,221.2 5122.4,217.1 \ +5136.8,196 5150.7,175.59 5146.9,166.51 5149.8,142 5150.6,135.38 5151.7,133.39 5149.8,127 5148.8,123.55 5147.3,120.13 5145.5,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3382.8,265", + pos="3164.8,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3513.8,265", + pos="3295.8,265", width=2.0762]; subject -> object [label=relation, - lp="5339.8,134.5", - pos="e,5326.9,107.23 5302.9,159.55 5304.1,149.57 5306.6,137.07 5311.8,127 5314,122.68 5316.9,118.52 5320.1,114.66"]; + lp="5121.8,134.5", + pos="e,5108.9,107.23 5084.9,159.55 5086.1,149.57 5088.6,137.07 5093.8,127 5096,122.68 5098.9,118.52 5102.1,114.66"]; relation [height=0.5, - pos="5289.8,18", + pos="5071.8,18", width=1.2999]; - subject -> relation [pos="e,5291.1,36.188 5300.5,159.79 5298.4,132.48 5294.3,78.994 5291.9,46.38", + subject -> relation [pos="e,5073.1,36.188 5082.5,159.79 5080.4,132.48 5076.3,78.994 5073.9,46.38", style=dotted]; "functional association_subject" [color=blue, height=0.5, label="macromolecular machine mixin", - pos="3762.8,265", + pos="3544.8,265", width=4.3329]; - object -> relation [pos="e,5302.6,35.54 5332.3,73.889 5325.4,64.939 5316.6,53.617 5308.8,43.584", + object -> relation [pos="e,5084.6,35.54 5114.3,73.889 5107.4,64.939 5098.6,53.617 5090.8,43.584", style=dotted]; "macromolecular machine to molecular activity association_object" [color=blue, height=0.5, label="molecular activity", - pos="4030.8,265", + pos="3812.8,265", width=2.6178]; } diff --git a/graphviz/macromolecular_machine_to_molecular_activity_association.svg b/graphviz/macromolecular_machine_to_molecular_activity_association.svg index 8193592edc..cf09411f26 100644 --- a/graphviz/macromolecular_machine_to_molecular_activity_association.svg +++ b/graphviz/macromolecular_machine_to_molecular_activity_association.svg @@ -4,16 +4,16 @@ - + %3 - + macromolecular machine to molecular activity association - -macromolecular machine to molecular activity association + +macromolecular machine to molecular activity association @@ -24,9 +24,9 @@ macromolecular machine to molecular activity association->functional association - + -is_a +is_a @@ -37,9 +37,9 @@ macromolecular machine to molecular activity association->macromolecular machine to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ macromolecular machine to molecular activity association->id - - -id + + +id @@ -63,9 +63,9 @@ macromolecular machine to molecular activity association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ macromolecular machine to molecular activity association->name - - -name + + +name @@ -89,9 +89,9 @@ macromolecular machine to molecular activity association->description - - -description + + +description @@ -102,9 +102,9 @@ macromolecular machine to molecular activity association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ macromolecular machine to molecular activity association->predicate - - -predicate + + +predicate @@ -128,9 +128,9 @@ macromolecular machine to molecular activity association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ macromolecular machine to molecular activity association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ macromolecular machine to molecular activity association->publications - - -publications + + +publications @@ -167,344 +167,344 @@ macromolecular machine to molecular activity association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string macromolecular machine to molecular activity association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string macromolecular machine to molecular activity association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string macromolecular machine to molecular activity association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type macromolecular machine to molecular activity association->timepoint - - -timepoint + + +timepoint original subject - -string + +string macromolecular machine to molecular activity association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie macromolecular machine to molecular activity association->original predicate - - -original predicate + + +original predicate original object - -string + +string macromolecular machine to molecular activity association->original object - - -original object + + +original object subject category - -ontology class + +ontology class macromolecular machine to molecular activity association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class macromolecular machine to molecular activity association->object category - - -object category + + +object category subject closure - -string + +string macromolecular machine to molecular activity association->subject closure - - -subject closure + + +subject closure object closure - -string + +string macromolecular machine to molecular activity association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class macromolecular machine to molecular activity association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class macromolecular machine to molecular activity association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string macromolecular machine to molecular activity association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string macromolecular machine to molecular activity association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string macromolecular machine to molecular activity association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string macromolecular machine to molecular activity association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source macromolecular machine to molecular activity association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type macromolecular machine to molecular activity association->type - - -type + + +type category - -category + +category macromolecular machine to molecular activity association->category - - -category + + +category subject - -subject + +subject macromolecular machine to molecular activity association->subject - - -subject + + +subject object - -object + +object macromolecular machine to molecular activity association->object - - -object + + +object association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + functional association_subject - -macromolecular machine mixin + +macromolecular machine mixin object->relation - - + + macromolecular machine to molecular activity association_object - -molecular activity + +molecular activity diff --git a/graphviz/material_sample_derivation_association.gv b/graphviz/material_sample_derivation_association.gv index 6ea69c3f36..566b40d82a 100644 --- a/graphviz/material_sample_derivation_association.gv +++ b/graphviz/material_sample_derivation_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4748,283"]; + graph [bb="0,0,4563,283"]; node [label="\N"]; "material sample derivation association" [height=0.5, label="material sample derivation association", - pos="2468.4,265", + pos="2283.4,265", width=5.2898]; association [height=0.5, pos="62.394,178", width=1.7332]; "material sample derivation association" -> association [label=is_a, lp="280.39,221.5", - pos="e,102.91,191.79 2278.4,263.42 1780.4,261.56 462.57,254.27 266.39,229 213.1,222.13 153.57,206.61 112.64,194.66"]; + pos="e,102.91,191.77 2093.8,263.12 1626.4,260.6 444.07,252.02 266.39,229 213.11,222.1 153.58,206.57 112.65,194.64"]; id [color=blue, height=0.5, label=string, @@ -18,8 +18,8 @@ digraph { width=1.0652]; "material sample derivation association" -> id [color=blue, label=id, - lp="396.39,221.5", - pos="e,210.38,189.98 2279.1,262.83 1801.8,259.59 573.73,249.38 389.39,229 317.23,221.02 299.34,215.5 229.39,196 226.29,195.13 223.09,\ + lp="395.39,221.5", + pos="e,210.38,189.98 2094.7,262.51 1648.7,258.71 554.35,247.59 388.39,229 316.67,220.97 298.9,215.43 229.39,196 226.29,195.13 223.09,\ 194.17 219.89,193.15", style=solid]; iri [color=blue, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "material sample derivation association" -> iri [color=blue, label=iri, - lp="509.39,221.5", - pos="e,315.3,190.2 2279.3,262.56 1820.8,258.78 674.59,247.61 501.39,229 426.6,220.97 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ -325.06,193.15", + lp="501.39,221.5", + pos="e,315.32,190.15 2092.7,264.76 1697,265.61 798.19,263.5 493.39,229 422.11,220.93 404.75,214.31 335.39,196 332.02,195.11 328.55,194.13 \ +325.07,193.11", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "material sample derivation association" -> name [color=blue, label=name, - lp="616.39,221.5", - pos="e,439.35,191.54 2279.1,262.95 1836.5,260.13 759.52,251.08 596.39,229 545.26,222.08 488.24,206.51 449.14,194.57", + lp="604.39,221.5", + pos="e,437.98,191.87 2094.5,262.73 1682.9,259.58 730.21,250.09 584.39,229 537.02,222.15 484.46,206.96 447.86,195.11", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "material sample derivation association" -> description [color=blue, label=description, - lp="736.89,221.5", - pos="e,585.45,194.14 2278.5,263.59 1852.9,262.2 848.53,256.04 696.39,229 661.33,222.77 623.33,209.4 595.03,198.06", + lp="717.89,221.5", + pos="e,581.77,194.62 2093.2,263.64 1697.7,262.34 812.57,256.37 677.39,229 647.36,222.92 615.28,210.09 591.01,198.95", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "material sample derivation association" -> "has attribute" [color=blue, label="has attribute", - lp="882.39,221.5", - pos="e,725.98,192.82 2278.4,263.38 1878.2,261.56 973.67,254.64 835.39,229 800.43,222.52 762.57,208.39 735.2,196.8", + lp="852.39,221.5", + pos="e,721.33,194.01 2093.1,263.78 1722.1,262.73 927.39,257.16 805.39,229 778.89,222.88 751.04,209.98 730.13,198.82", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "material sample derivation association" -> negated [color=blue, label=negated, - lp="1038.4,221.5", - pos="e,847.59,190.46 2278.1,264.3 1940.3,264.02 1248.9,259.56 1009.4,229 956.09,222.2 896.47,205.66 857.14,193.46", + lp="990.39,221.5", + pos="e,843.03,191.96 2095.2,262.13 1756.6,258.3 1069.7,248.27 961.39,229 923.37,222.23 881.85,207.52 852.5,195.8", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "material sample derivation association" -> qualifiers [color=blue, label=qualifiers, - lp="1178.9,221.5", - pos="e,996.68,193.07 2277.9,264.33 1965.6,263.97 1358,259.23 1145.4,229 1097.6,222.2 1044.5,207.74 1006.5,196.11", + lp="1101.9,221.5", + pos="e,982.4,194.93 2094.5,262.53 1777.9,259.47 1165.4,250.8 1068.4,229 1041.6,222.97 1013.3,210.59 991.57,199.66", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "material sample derivation association" -> publications [color=blue, label=publications, - lp="1326.4,221.5", - pos="e,1148.1,192.71 2278,264.27 1992.8,263.67 1468.2,258.42 1282.4,229 1239.3,222.18 1191.8,207.69 1157.8,196.06", + lp="1202.4,221.5", + pos="e,1121.9,195.78 2095.7,261.89 1786.6,257.89 1200.2,247.87 1158.4,229 1146.3,223.57 1135.9,213.45 1128,203.73", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,276 +100,276 @@ digraph { width=2.0943]; "material sample derivation association" -> "has evidence" [color=blue, label="has evidence", - lp="1480.9,221.5", - pos="e,1305.9,193.61 2278.6,263.4 2025.5,261.59 1591.3,254.7 1434.4,229 1393.5,222.3 1348.6,208.48 1315.7,197.06", + lp="1300.9,221.5", + pos="e,1255.9,195.88 2093,264.27 1803.5,263.72 1283,258.6 1254.4,229 1248.2,222.63 1248.8,213.73 1251.7,205.2", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1469.4,178", - width=3.015]; + label=string, + pos="1399.4,178", + width=1.0652]; "material sample derivation association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1635.9,221.5", - pos="e,1495.5,195.59 2282.9,260.86 2040.3,256.12 1638.2,245.86 1571.4,229 1547.9,223.07 1523.5,211.31 1504.4,200.68", + lp="1419.9,221.5", + pos="e,1375.2,192.24 2093.5,263.49 1829.4,261.82 1380.6,255.14 1355.4,229 1345.9,219.09 1354.7,207.6 1366.9,198.13", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1704.4,178", - width=3.015]; + label=string, + pos="1494.4,178", + width=1.0652]; "material sample derivation association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1807.4,221.5", - pos="e,1702.1,196.41 2282.1,261.2 2065.1,257.08 1733.4,247.75 1712.4,229 1706.1,223.34 1703.4,214.82 1702.5,206.41", + lp="1589.4,221.5", + pos="e,1489,196.04 2095.3,262.11 1868.5,258.89 1514.9,250.44 1494.4,229 1488.6,222.94 1487.2,214.32 1487.7,205.94", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1939.4,178", - width=3.015]; + label=string, + pos="1669.4,178", + width=1.0652]; "material sample derivation association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2015.9,221.5", - pos="e,1918.7,195.97 2290,258.65 2131.4,253 1922.5,242.96 1909.4,229 1902.4,221.54 1905.6,212.18 1912,203.58", + lp="1809.9,221.5", + pos="e,1676.1,196.02 2097.8,260.93 1941.2,257 1737.2,248.24 1703.4,229 1693.8,223.55 1686.4,214.16 1680.9,204.98", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2121.4,178", + pos="1895.4,178", width=1.5346]; "material sample derivation association" -> timepoint [color=blue, label=timepoint, - lp="2171.4,221.5", - pos="e,2121.9,196.47 2308.9,255.07 2230.8,249.28 2150.4,240.63 2136.4,229 2129.6,223.41 2125.9,214.91 2123.8,206.49", + lp="1972.4,221.5", + pos="e,1904.8,195.92 2106.5,258.24 2037.2,253.48 1967.3,244.81 1937.4,229 1926.7,223.32 1917.5,213.63 1910.6,204.28", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2233.4,178", + pos="2007.4,178", width=1.0652]; "material sample derivation association" -> "original subject" [color=blue, label="original subject", - lp="2270.4,221.5", - pos="e,2219.6,194.92 2296.8,257.15 2259.2,251.96 2226.9,243.3 2214.4,229 2208.1,221.83 2209.9,212.39 2214.3,203.65", + lp="2076.4,221.5", + pos="e,2007.3,196.33 2115.7,256.39 2073.7,251.28 2036,242.85 2020.4,229 2013.9,223.25 2010.5,214.72 2008.7,206.31", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2347.4,178", + pos="2133.4,178", width=1.5887]; "material sample derivation association" -> "original predicate" [color=blue, label="original predicate", - lp="2397.9,221.5", - pos="e,2336.3,195.76 2378.3,249.11 2358.1,243.89 2340.8,237.23 2334.4,229 2329.1,222.16 2329.6,213.39 2332.4,205.11", + lp="2207.9,221.5", + pos="e,2132.9,196.42 2193.7,249.07 2171.7,243.75 2152.2,237.04 2144.4,229 2138.6,222.99 2135.5,214.63 2134,206.47", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2461.4,178", + pos="2267.4,178", width=1.0652]; "material sample derivation association" -> "original object" [color=blue, label="original object", - lp="2516.9,221.5", - pos="e,2462.8,196.18 2467,246.8 2466,235.16 2464.7,219.55 2463.6,206.24", + lp="2327.9,221.5", + pos="e,2270.6,196.18 2280.2,246.8 2278,235.16 2275,219.55 2272.5,206.24", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2594.4,178", + pos="2400.4,178", width=2.1304]; "material sample derivation association" -> "subject category" [color=blue, label="subject category", - lp="2642.9,221.5", - pos="e,2590.6,196.4 2541,248.35 2552.4,243.53 2563.4,237.23 2572.4,229 2579.1,222.84 2583.9,214.24 2587.3,205.9", + lp="2452.9,221.5", + pos="e,2398.4,196.3 2354.6,248.23 2365.2,243.43 2375.3,237.17 2383.4,229 2389.5,222.8 2393.5,214.29 2396,206.04", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2765.4,178", + pos="2571.4,178", width=2.1304]; "material sample derivation association" -> "object category" [color=blue, label="object category", - lp="2785.9,221.5", - pos="e,2750.6,195.73 2621.8,254.26 2650.7,248.88 2680.1,240.87 2706.4,229 2720,222.83 2733,212.54 2743.3,202.9", + lp="2593.9,221.5", + pos="e,2557.8,195.72 2436.1,254.23 2463.7,248.82 2491.5,240.8 2516.4,229 2529.3,222.88 2541.3,212.74 2550.8,203.17", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="2898.4,178", + pos="2704.4,178", width=1.0652]; "material sample derivation association" -> "subject closure" [color=blue, label="subject closure", - lp="2921.9,221.5", - pos="e,2886,195.51 2604.6,252.39 2710.2,243.21 2839.8,231.55 2845.4,229 2858.3,223.16 2870.1,212.86 2879.2,203.11", + lp="2728.9,221.5", + pos="e,2692.6,195.5 2418.3,252.28 2521.8,243.13 2647.9,231.55 2653.4,229 2665.9,223.2 2677.1,213.04 2685.8,203.39", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="2998.4,178", + pos="2812.4,178", width=1.0652]; "material sample derivation association" -> "object closure" [color=blue, label="object closure", - lp="3042.4,221.5", - pos="e,2996.9,196.22 2602,252.13 2624.2,250.31 2646.9,248.53 2668.4,247 2703,244.53 2952.6,249.78 2980.4,229 2987.7,223.52 2992.1,214.79 \ -2994.7,206.14", + lp="2851.4,221.5", + pos="e,2808.5,196.38 2417,252.16 2439.2,250.34 2461.9,248.55 2483.4,247 2517.1,244.57 2759.1,247.63 2787.4,229 2795.6,223.58 2801.2,214.62 \ +2805,205.77", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3131.4,178", + pos="2945.4,178", width=2.1304]; "material sample derivation association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3200.9,221.5", - pos="e,3124.4,196.11 2600.1,252 2622.9,250.15 2646.3,248.4 2668.4,247 2715.9,243.98 3054.6,251.86 3096.4,229 3106.2,223.66 3113.8,214.28 \ -3119.4,205.09", + lp="3010.9,221.5", + pos="e,2936.7,196.16 2415.4,251.99 2438.1,250.15 2461.4,248.4 2483.4,247 2530.2,244.01 2863.5,250.23 2905.4,229 2916,223.61 2924.8,213.97 \ +2931.3,204.58", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3323.4,178", + pos="3138.4,178", width=2.1304]; "material sample derivation association" -> "object category closure" [color=blue, label="object category closure", - lp="3390.9,221.5", - pos="e,3317.7,196.1 2598.8,251.86 2621.9,250 2645.9,248.28 2668.4,247 2703,245.03 3262.3,246.3 3292.4,229 3301.6,223.71 3308.4,214.47 \ -3313.3,205.37", + lp="3202.9,221.5", + pos="e,3131.1,196.17 2413.8,251.86 2436.9,250.01 2460.9,248.28 2483.4,247 2517.7,245.04 3072,245.13 3102.4,229 3112.4,223.68 3120.3,214.18 \ +3126.1,204.88", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3513.4,178", + pos="3328.4,178", width=1.0652]; "material sample derivation association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3563.4,221.5", - pos="e,3506.4,196.19 2598,251.8 2621.4,249.93 2645.6,248.22 2668.4,247 2713.3,244.59 3438.7,250.23 3478.4,229 3488.2,223.75 3495.9,214.4 \ -3501.5,205.19", + lp="3375.4,221.5", + pos="e,3320.7,195.73 2413,251.8 2436.4,249.93 2460.6,248.22 2483.4,247 2528.2,244.6 3250.4,249.37 3290.4,229 3300.8,223.67 3309.2,213.99 \ +3315.4,204.55", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3672.4,178", + pos="3487.4,178", width=1.0652]; "material sample derivation association" -> "object namespace" [color=blue, label="object namespace", - lp="3716.4,221.5", - pos="e,3665,195.73 2597.7,251.75 2621.2,249.88 2645.5,248.18 2668.4,247 2722.1,244.22 3587.6,253.63 3635.4,229 3645.7,223.67 3653.9,213.99 \ -3659.9,204.55", + lp="3529.4,221.5", + pos="e,3479.1,195.77 2412.7,251.75 2436.2,249.88 2460.5,248.18 2483.4,247 2536.9,244.23 3399.3,252.65 3447.4,229 3458.2,223.66 3467.1,\ +213.84 3473.7,204.31", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3823.4,178", + pos="3638.4,178", width=1.0652]; "material sample derivation association" -> "subject label closure" [color=blue, label="subject label closure", - lp="3876.4,221.5", - pos="e,3815.4,195.77 2597.4,251.72 2621,249.85 2645.4,248.16 2668.4,247 2699.4,245.44 3756.6,242.83 3784.4,229 3795.1,223.66 3803.8,213.84 \ -3810.2,204.31", + lp="3689.4,221.5", + pos="e,3629.8,195.79 2412.4,251.72 2436,249.85 2460.4,248.16 2483.4,247 2514.3,245.44 3569.5,242.46 3597.4,229 3608.4,223.69 3617.4,213.87 \ +3624.2,204.33", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="3994.4,178", + pos="3809.4,178", width=1.0652]; "material sample derivation association" -> "object label closure" [color=blue, label="object label closure", - lp="4041.9,221.5", - pos="e,3986.1,195.79 2597.1,251.71 2620.8,249.83 2645.3,248.14 2668.4,247 2704.1,245.24 3922.3,244.7 3954.4,229 3965.3,223.69 3974.1,\ -213.87 3980.7,204.33", + lp="3856.9,221.5", + pos="e,3800.5,195.81 2412.1,251.71 2435.8,249.83 2460.3,248.14 2483.4,247 2519,245.24 3735.2,244.29 3767.4,229 3778.5,223.72 3787.8,213.9 \ +3794.7,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4147.4,178", + pos="3962.4,178", width=2.347]; "material sample derivation association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4200.9,221.5", - pos="e,4141.4,196.18 2596.9,251.7 2620.6,249.81 2645.2,248.13 2668.4,247 2708.5,245.05 4080.3,248.52 4115.4,229 4124.9,223.75 4131.9,\ -214.39 4137,205.18", + lp="4015.9,221.5", + pos="e,3956.4,196.18 2411.9,251.7 2435.6,249.81 2460.2,248.13 2483.4,247 2523.5,245.05 3895.3,248.52 3930.4,229 3939.9,223.75 3946.9,\ +214.39 3952,205.18", style=solid]; type [height=0.5, - pos="4281.4,178", + pos="4096.4,178", width=0.86659]; "material sample derivation association" -> type [color=blue, label=type, - lp="4299.4,221.5", - pos="e,4284.1,195.98 2596.9,251.67 2620.6,249.79 2645.2,248.11 2668.4,247 2690.7,245.93 4257.6,243.73 4274.4,229 4280.9,223.32 4283.4,\ -214.65 4284.1,206.12", + lp="4114.4,221.5", + pos="e,4099.1,195.98 2411.9,251.67 2435.6,249.79 2460.2,248.11 2483.4,247 2505.7,245.93 4072.6,243.73 4089.4,229 4095.9,223.32 4098.4,\ +214.65 4099.1,206.12", style=solid]; category [height=0.5, - pos="4382.4,178", + pos="4197.4,178", width=1.4263]; "material sample derivation association" -> category [color=blue, label=category, - lp="4377.9,221.5", - pos="e,4367.7,195.48 2596.6,251.69 2620.4,249.8 2645.2,248.11 2668.4,247 2714.2,244.81 4276.2,244.33 4319.4,229 4334.6,223.59 4349,212.83 \ -4360.1,202.68", + lp="4192.9,221.5", + pos="e,4182.7,195.48 2411.6,251.69 2435.4,249.8 2460.2,248.11 2483.4,247 2529.2,244.81 4091.2,244.33 4134.4,229 4149.6,223.59 4164,212.83 \ +4175.1,202.68", style=solid]; subject [height=0.5, - pos="4496.4,178", + pos="4311.4,178", width=1.2277]; "material sample derivation association" -> subject [color=blue, label=subject, - lp="4473.4,221.5", - pos="e,4477.7,194.32 2596.6,251.68 2620.4,249.79 2645.2,248.11 2668.4,247 2765.2,242.39 4320.1,255.44 4413.4,229 4433.6,223.29 4453.7,\ -211.3 4469.2,200.49", + lp="4288.4,221.5", + pos="e,4292.7,194.32 2411.6,251.68 2435.4,249.79 2460.2,248.11 2483.4,247 2580.2,242.39 4135.1,255.44 4228.4,229 4248.6,223.29 4268.7,\ +211.3 4284.2,200.49", style=solid]; object [height=0.5, - pos="4539.4,91", + pos="4354.4,91", width=1.0832]; "material sample derivation association" -> object [color=blue, label=object, - lp="4583.4,178", - pos="e,4552.8,108.09 2596.6,251.67 2620.4,249.78 2645.2,248.1 2668.4,247 2719.3,244.59 4454.9,244.84 4503.4,229 4527.3,221.18 4535.3,\ -216.87 4549.4,196 4563.2,175.52 4559.5,166.51 4562.4,142 4563.2,135.38 4564.3,133.39 4562.4,127 4561.4,123.55 4559.9,120.13 4558.1,\ + lp="4398.4,178", + pos="e,4367.8,108.09 2411.6,251.67 2435.4,249.78 2460.2,248.1 2483.4,247 2534.3,244.59 4269.9,244.84 4318.4,229 4342.3,221.18 4350.3,\ +216.87 4364.4,196 4378.2,175.52 4374.5,166.51 4377.4,142 4378.2,135.38 4379.3,133.39 4377.4,127 4376.4,123.55 4374.9,120.13 4373.1,\ 116.85", style=solid]; predicate [height=0.5, - pos="4693.4,178", + pos="4508.4,178", width=1.5165]; "material sample derivation association" -> predicate [color=blue, label=predicate, - lp="4666.4,221.5", - pos="e,4669.6,194.35 2596.6,251.66 2620.4,249.77 2645.2,248.09 2668.4,247 2775.1,241.97 4486.4,253.41 4590.4,229 4615.3,223.15 4641.2,\ -210.56 4660.8,199.47", + lp="4480.4,221.5", + pos="e,4484.6,194.35 2411.6,251.66 2435.4,249.77 2460.2,248.09 2483.4,247 2590.1,241.97 4301.4,253.41 4405.4,229 4430.3,223.15 4456.2,\ +210.56 4475.8,199.47", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2715.4,265", + pos="2530.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2846.4,265", + pos="2661.4,265", width=2.0762]; subject -> object [label=relation, - lp="4534.4,134.5", - pos="e,4521.5,107.23 4497.5,159.55 4498.7,149.57 4501.2,137.07 4506.4,127 4508.6,122.68 4511.5,118.52 4514.7,114.66"]; + lp="4349.4,134.5", + pos="e,4336.5,107.23 4312.5,159.55 4313.7,149.57 4316.2,137.07 4321.4,127 4323.6,122.68 4326.5,118.52 4329.7,114.66"]; relation [height=0.5, - pos="4484.4,18", + pos="4299.4,18", width=1.2999]; - subject -> relation [pos="e,4485.7,36.188 4495.1,159.79 4493,132.48 4489,78.994 4486.5,46.38", + subject -> relation [pos="e,4300.7,36.188 4310.1,159.79 4308,132.48 4304,78.994 4301.5,46.38", style=dotted]; "material sample derivation association_subject" [color=blue, height=0.5, label="material sample", - pos="3025.4,265", + pos="2840.4,265", width=2.3831]; - object -> relation [pos="e,4497.2,35.54 4526.9,73.889 4520,64.939 4511.2,53.617 4503.4,43.584", + object -> relation [pos="e,4312.2,35.54 4341.9,73.889 4335,64.939 4326.2,53.617 4318.4,43.584", style=dotted]; "material sample derivation association_object" [color=blue, height=0.5, label="named thing", - pos="3198.4,265", + pos="3013.4,265", width=1.9318]; "material sample derivation association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3364.4,265", + pos="3179.4,265", width=2.1665]; } diff --git a/graphviz/material_sample_derivation_association.svg b/graphviz/material_sample_derivation_association.svg index 2066aeaab8..7463a82870 100644 --- a/graphviz/material_sample_derivation_association.svg +++ b/graphviz/material_sample_derivation_association.svg @@ -4,16 +4,16 @@ - + %3 - + material sample derivation association - -material sample derivation association + +material sample derivation association @@ -24,8 +24,8 @@ material sample derivation association->association - - + + is_a @@ -37,9 +37,9 @@ material sample derivation association->id - - -id + + +id @@ -50,9 +50,9 @@ material sample derivation association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ material sample derivation association->name - - -name + + +name @@ -76,9 +76,9 @@ material sample derivation association->description - - -description + + +description @@ -89,9 +89,9 @@ material sample derivation association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ material sample derivation association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ material sample derivation association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ material sample derivation association->publications - - -publications + + +publications @@ -141,363 +141,363 @@ material sample derivation association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string material sample derivation association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string material sample derivation association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string material sample derivation association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type material sample derivation association->timepoint - - -timepoint + + +timepoint original subject - -string + +string material sample derivation association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie material sample derivation association->original predicate - - -original predicate + + +original predicate original object - -string + +string material sample derivation association->original object - - -original object + + +original object subject category - -ontology class + +ontology class material sample derivation association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class material sample derivation association->object category - - -object category + + +object category subject closure - -string + +string material sample derivation association->subject closure - - -subject closure + + +subject closure object closure - -string + +string material sample derivation association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class material sample derivation association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class material sample derivation association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string material sample derivation association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string material sample derivation association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string material sample derivation association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string material sample derivation association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source material sample derivation association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type material sample derivation association->type - - -type + + +type category - -category + +category material sample derivation association->category - - -category + + +category subject - -subject + +subject material sample derivation association->subject - - -subject + + +subject object - -object + +object material sample derivation association->object - - -object + + +object predicate - -predicate + +predicate material sample derivation association->predicate - - -predicate + + +predicate association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + material sample derivation association_subject - -material sample + +material sample object->relation - - + + material sample derivation association_object - -named thing + +named thing material sample derivation association_predicate - -predicate type + +predicate type diff --git a/graphviz/material_sample_to_disease_or_phenotypic_feature_association.gv b/graphviz/material_sample_to_disease_or_phenotypic_feature_association.gv index fd91f4da44..7bd27c732d 100644 --- a/graphviz/material_sample_to_disease_or_phenotypic_feature_association.gv +++ b/graphviz/material_sample_to_disease_or_phenotypic_feature_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,5883.7,283"]; + graph [bb="0,0,5618.7,283"]; node [label="\N"]; "material sample to disease or phenotypic feature association" [height=0.5, label="material sample to disease or phenotypic feature association", - pos="3267.4,265", + pos="3002.4,265", width=8.1604]; association [height=0.5, pos="62.394,178", width=1.7332]; "material sample to disease or phenotypic feature association" -> association [label=is_a, lp="806.39,221.5", - pos="e,106.46,190.89 2974.9,263.26 2511.7,261.32 1581.1,254.32 792.39,229 499.29,219.59 423.68,237.65 133.39,196 127.91,195.21 122.22,\ -194.2 116.56,193.06"]; + pos="e,106.46,190.89 2711,262.56 2288.1,259.74 1479.9,251.65 792.39,229 499.3,219.34 423.68,237.65 133.39,196 127.91,195.21 122.22,194.2 \ +116.56,193.06"]; "material sample to entity association mixin" [height=0.5, pos="354.39,178", width=5.8856]; "material sample to disease or phenotypic feature association" -> "material sample to entity association mixin" [label=uses, lp="1101.9,221.5", - pos="e,498.51,191.25 2973.9,263.81 2554.8,262.52 1760.9,256.26 1085.4,229 885.98,220.95 656.42,203.99 508.57,192.06"]; + pos="e,498.86,191.18 2710.4,262.87 2334.4,260.46 1661,252.86 1085.4,229 886.14,220.74 656.79,203.84 508.92,191.99"]; "entity to disease or phenotypic feature association mixin" [height=0.5, pos="858.39,178", width=7.6188]; "material sample to disease or phenotypic feature association" -> "entity to disease or phenotypic feature association mixin" [label=uses, lp="1285.9,221.5", - pos="e,962.42,194.68 2976,262.61 2503.8,259.73 1591.9,251.38 1269.4,229 1168.7,222.01 1054.9,207.65 972.55,196.11"]; + pos="e,962.85,194.66 2713.3,261.7 2294.9,257.76 1541.1,248.22 1269.4,229 1168.9,221.89 1055.3,207.58 972.98,196.08"]; id [color=blue, height=0.5, label=string, @@ -32,8 +32,8 @@ digraph { "material sample to disease or phenotypic feature association" -> id [color=blue, label=id, lp="1404.4,221.5", - pos="e,1218.4,189.98 2979.1,261.53 2493.3,256.94 1549.6,245.98 1397.4,229 1325.2,220.95 1307.3,215.5 1237.4,196 1234.3,195.13 1231.1,\ -194.17 1227.9,193.15", + pos="e,1218.4,189.98 2709,263.98 2316.9,262.85 1642.7,256.74 1397.4,229 1325.2,220.84 1307.3,215.5 1237.4,196 1234.3,195.13 1231.1,194.17 \ +1227.9,193.15", style=solid]; iri [color=blue, height=0.5, @@ -43,7 +43,7 @@ digraph { "material sample to disease or phenotypic feature association" -> iri [color=blue, label=iri, lp="1511.4,221.5", - pos="e,1323.3,190.16 2973.3,264.7 2547.2,264.59 1779,259.89 1503.4,229 1431.2,220.91 1413.6,214.45 1343.4,196 1340,195.11 1336.5,194.14 \ + pos="e,1323.3,190.16 2709.6,263.42 2340.9,261.59 1728.6,254.64 1503.4,229 1431.3,220.79 1413.6,214.45 1343.4,196 1340,195.11 1336.5,194.14 \ 1333.1,193.12", style=solid]; name [color=blue, @@ -54,7 +54,7 @@ digraph { "material sample to disease or phenotypic feature association" -> name [color=blue, label=name, lp="1615.4,221.5", - pos="e,1446.3,191.75 2978.2,261.75 2535.7,257.72 1727.8,247.9 1595.4,229 1546.9,222.08 1493.1,206.72 1455.8,194.84", + pos="e,1446.3,191.7 2708.4,264.88 2360.5,264.49 1802.2,258.93 1595.4,229 1546.9,221.99 1493.1,206.64 1455.8,194.79", style=solid]; description [color=blue, height=0.5, @@ -64,7 +64,7 @@ digraph { "material sample to disease or phenotypic feature association" -> description [color=blue, label=description, lp="1731.9,221.5", - pos="e,1590.8,194.37 2975.6,262.86 2554.5,260.4 1813.3,252.71 1691.4,229 1659.7,222.84 1625.7,209.79 1600.1,198.56", + pos="e,1591.1,194.45 2714.2,261.41 2358.5,257.41 1788.5,248.12 1691.4,229 1659.8,222.79 1625.9,209.81 1600.4,198.63", style=solid]; "has attribute" [color=blue, height=0.5, @@ -74,7 +74,7 @@ digraph { "material sample to disease or phenotypic feature association" -> "has attribute" [color=blue, label="has attribute", lp="1870.4,221.5", - pos="e,1730.9,193.52 2975.7,262.73 2586.2,260.14 1932.4,252.34 1823.4,229 1794.1,222.73 1763,209.39 1739.9,198.06", + pos="e,1731.3,193.71 2715.7,260.98 2394.7,256.73 1907.9,247.35 1823.4,229 1794.3,222.69 1763.4,209.49 1740.4,198.23", style=solid]; subject [color=blue, height=0.5, @@ -84,7 +84,7 @@ digraph { "material sample to disease or phenotypic feature association" -> subject [color=blue, label=subject, lp="1997.4,221.5", - pos="e,1874.5,194.33 2979,261.5 2627.1,257.62 2067,248.47 1971.4,229 1941,222.8 1908.4,209.83 1883.9,198.66", + pos="e,1874.5,194.27 2723,259.4 2442.8,254 2043,243.85 1971.4,229 1941,222.69 1908.4,209.73 1883.9,198.59", style=solid]; predicate [color=blue, height=0.5, @@ -94,7 +94,7 @@ digraph { "material sample to disease or phenotypic feature association" -> predicate [color=blue, label=predicate, lp="2076.4,221.5", - pos="e,2016.4,196.12 2976.5,262.49 2627,259.67 2082.4,251.65 2042.4,229 2033,223.67 2025.9,214.3 2020.8,205.1", + pos="e,2016.4,196.09 2719.7,260.06 2447.2,255.29 2071.7,245.72 2042.4,229 2033,223.63 2025.9,214.26 2020.9,205.06", style=solid]; object [color=blue, height=0.5, @@ -104,8 +104,8 @@ digraph { "material sample to disease or phenotypic feature association" -> object [color=blue, label=object, lp="2155.4,178", - pos="e,1984,105.47 2991,258.86 2679.9,251.27 2207.9,233.7 2133.4,196 2113.2,185.78 2116.1,172.77 2097.4,160 2065.3,138.07 2025,120.64 \ -1993.5,108.92", + pos="e,1984,105.47 2716.6,260.73 2585.1,256.48 2427.4,247.52 2286.4,229 2217.4,219.94 2194.5,229.28 2133.4,196 2113.5,185.17 2116.1,172.77 \ +2097.4,160 2065.3,138.07 2025,120.64 1993.5,108.92", style=solid]; negated [color=blue, height=0.5, @@ -114,8 +114,8 @@ digraph { width=1.2999]; "material sample to disease or phenotypic feature association" -> negated [color=blue, label=negated, - lp="2457.4,221.5", - pos="e,2267.8,190.38 2995.2,258.22 2792.8,252.87 2534,243.52 2428.4,229 2375.7,221.75 2316.7,205.44 2277.5,193.41", + lp="2353.4,221.5", + pos="e,2254.6,194.29 2712.9,261.85 2562.8,258.19 2396.2,249.41 2324.4,229 2302.5,222.79 2280.2,210.57 2263,199.77", style=solid]; qualifiers [color=blue, height=0.5, @@ -124,8 +124,8 @@ digraph { width=2.1304]; "material sample to disease or phenotypic feature association" -> qualifiers [color=blue, label=qualifiers, - lp="2588.9,221.5", - pos="e,2415.9,193.28 3003.6,257.08 2837.5,251.54 2639.2,242.46 2555.4,229 2510.8,221.84 2461.5,207.79 2425.6,196.41", + lp="2432.9,221.5", + pos="e,2378.3,196.38 2719,260.26 2576.1,256.09 2427.2,247.34 2399.4,229 2391.2,223.59 2385.6,214.63 2381.8,205.77", style=solid]; publications [color=blue, height=0.5, @@ -134,8 +134,8 @@ digraph { width=1.7332]; "material sample to disease or phenotypic feature association" -> publications [color=blue, label=publications, - lp="2723.4,221.5", - pos="e,2565.1,193.26 3016.2,255.66 2886.6,250.04 2742.8,241.36 2679.4,229 2643.2,221.93 2603.6,208.25 2574.5,196.98", + lp="2518.4,221.5", + pos="e,2497.1,193.26 2714.4,261.38 2600.6,257.29 2492.4,248.26 2474.4,229 2464.2,218.15 2474.1,207.15 2488.3,198.24", style=solid]; "has evidence" [color=blue, height=0.5, @@ -144,218 +144,220 @@ digraph { width=2.0943]; "material sample to disease or phenotypic feature association" -> "has evidence" [color=blue, label="has evidence", - lp="2864.9,221.5", - pos="e,2719.7,194.32 3008.2,256.5 2945.5,251.21 2879.1,242.66 2818.4,229 2787.5,222.06 2754.3,209.29 2729,198.39", + lp="2615.9,221.5", + pos="e,2629,189.51 2739.8,256.88 2656.6,251.89 2582.7,243.41 2569.4,229 2564.9,224.1 2565.4,219.34 2569.4,214 2576,205.09 2596.8,197.64 \ +2619.1,191.93", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2889.4,178", - width=3.015]; + label=string, + pos="2819.4,178", + width=1.0652]; "material sample to disease or phenotypic feature association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2997.9,221.5", - pos="e,2899.8,196.41 3047.1,253.05 2998.6,247.87 2955.2,240.24 2933.4,229 2922.5,223.39 2913.2,213.9 2905.9,204.68", + lp="2737.9,221.5", + pos="e,2790.7,190 2791.9,252.42 2733.2,247.05 2682.8,239.46 2673.4,229 2649.5,202.39 2681,220.13 2771.4,196 2774.6,195.16 2777.8,194.2 \ +2781.1,193.18", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="3124.4,178", - width=3.015]; + label=string, + pos="2914.4,178", + width=1.0652]; "material sample to disease or phenotypic feature association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="3164.4,221.5", - pos="e,3087.8,195.17 3115.3,249.59 3094.1,244.63 3076.9,237.96 3069.4,229 3061,218.96 3067.9,209.01 3079.3,200.67", + lp="2904.4,221.5", + pos="e,2885,189.59 2854.6,249.37 2833.7,244.43 2816.8,237.82 2809.4,229 2805.1,223.88 2805.5,219.38 2809.4,214 2825.1,192.57 2841.2,204.44 \ +2866.4,196 2869.3,195.02 2872.3,193.99 2875.4,192.95", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="3359.4,178", - width=3.015]; + label=string, + pos="3009.4,178", + width=1.0652]; "material sample to disease or phenotypic feature association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="3374.9,221.5", - pos="e,3294.9,192.66 3263.2,246.77 3261.8,236.38 3261.8,223.38 3268.4,214 3273,207.37 3279.1,202 3286,197.65", + lp="3109.9,221.5", + pos="e,3006,196.02 3002.1,246.84 3002.1,237.17 3002.4,224.89 3003.4,214 3003.6,211.42 3004,208.75 3004.3,206.08", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="3541.4,178", + pos="3229.4,178", width=1.5346]; "material sample to disease or phenotypic feature association" -> timepoint [color=blue, label=timepoint, - lp="3536.4,221.5", - pos="e,3524.1,195.19 3419.2,249.53 3440.6,244.54 3462,237.88 3481.4,229 3489.1,225.48 3503.6,213.47 3516.4,202.1", + lp="3261.4,221.5", + pos="e,3229.4,196.24 3160.1,249.8 3185.4,244.8 3206.4,238.07 3216.4,229 3222.8,223.16 3226.2,214.6 3228,206.2", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="3653.4,178", + pos="3341.4,178", width=1.0652]; "material sample to disease or phenotypic feature association" -> "original subject" [color=blue, label="original subject", - lp="3653.4,221.5", - pos="e,3631.3,192.7 3445.6,250.64 3498.9,245.12 3549.7,237.91 3574.4,229 3585.9,224.86 3587.1,220.57 3597.4,214 3605.6,208.79 3614.4,\ -203.21 3622.7,198.07", + lp="3374.4,221.5", + pos="e,3332.3,195.85 3201.9,251.72 3244.1,246.57 3281.6,239.28 3300.4,229 3311,223.23 3319.9,213.52 3326.6,204.19", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3767.4,178", + pos="3466.4,178", width=1.5887]; "material sample to disease or phenotypic feature association" -> "original predicate" [color=blue, label="original predicate", - lp="3793.9,221.5", - pos="e,3750.8,195.38 3484,252.84 3584.9,246.53 3687.6,238.1 3709.4,229 3717.1,225.8 3731.1,213.8 3743.4,202.35", + lp="3513.9,221.5", + pos="e,3460.3,195.92 3201.7,251.76 3309.9,244.45 3423.8,235.38 3434.4,229 3443.6,223.48 3450.6,214.21 3455.6,205.13", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3881.4,178", + pos="3595.4,178", width=1.0652]; "material sample to disease or phenotypic feature association" -> "original object" [color=blue, label="original object", - lp="3923.9,221.5", - pos="e,3878.5,196.31 3476,252.29 3645.6,242.67 3857.4,230.41 3859.4,229 3867.2,223.57 3872.3,214.72 3875.5,205.97", + lp="3643.9,221.5", + pos="e,3595.4,196.1 3209.3,252.18 3374.8,242.62 3579.5,230.51 3581.4,229 3588.3,223.45 3591.9,214.8 3593.8,206.26", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="4014.4,178", + pos="3728.4,178", width=2.1304]; "material sample to disease or phenotypic feature association" -> "subject category" [color=blue, label="subject category", - lp="4055.9,221.5", - pos="e,4007.4,196.1 3473.2,252.12 3505.7,250.34 3539,248.57 3570.4,247 3615.8,244.73 3939.5,250.89 3979.4,229 3989.1,223.65 3996.8,214.27 \ -4002.4,205.08", + lp="3773.9,221.5", + pos="e,3723.3,196.01 3208.6,252.14 3241,250.36 3274.1,248.59 3305.4,247 3349.2,244.77 3661.9,251.74 3699.4,229 3708.3,223.59 3714.8,214.34 \ +3719.3,205.25", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="4185.4,178", + pos="3899.4,178", width=2.1304]; "material sample to disease or phenotypic feature association" -> "object category" [color=blue, label="object category", - lp="4202.9,221.5", - pos="e,4169.5,195.61 3470.3,251.96 3503.7,250.17 3538,248.44 3570.4,247 3631.4,244.29 4061.9,249.39 4119.4,229 4135.1,223.42 4150.2,212.61 \ -4161.9,202.46", + lp="3919.9,221.5", + pos="e,3884.4,195.84 3205.7,251.97 3239,250.18 3273.2,248.45 3305.4,247 3364.5,244.34 3782,249.63 3837.4,229 3852.2,223.49 3866.1,212.94 \ +3877,202.94", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="4318.4,178", + pos="4032.4,178", width=1.0652]; "material sample to disease or phenotypic feature association" -> "subject closure" [color=blue, label="subject closure", - lp="4336.9,221.5", - pos="e,4303,194.73 3468.6,251.86 3502.6,250.06 3537.5,248.35 3570.4,247 3608.8,245.42 4225.6,243 4261.4,229 4269.2,225.94 4283.4,213.52 \ -4295.6,201.83", + lp="4057.9,221.5", + pos="e,4020.5,195.35 3203.6,251.88 3237.6,250.07 3272.5,248.36 3305.4,247 3342.8,245.45 3944.8,243.29 3979.4,229 3992.7,223.52 4004.6,\ +213.05 4013.8,203.1", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="4414.4,178", + pos="4145.4,178", width=1.0652]; "material sample to disease or phenotypic feature association" -> "object closure" [color=blue, label="object closure", - lp="4456.4,221.5", - pos="e,4412,196.42 3467.4,251.81 3501.8,249.99 3537.1,248.3 3570.4,247 3593.2,246.11 4374.5,241.86 4393.4,229 4401.2,223.69 4406.1,214.87 \ -4409.2,206.1", + lp="4181.4,221.5", + pos="e,4140.4,196.09 3202.8,251.8 3237,249.99 3272.2,248.3 3305.4,247 3350.4,245.24 4077.6,251.93 4116.4,229 4125.4,223.7 4131.8,214.46 \ +4136.4,205.36", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="4547.4,178", + pos="4278.4,178", width=2.1304]; "material sample to disease or phenotypic feature association" -> "subject category closure" [color=blue, label="subject category closure", - lp="4614.9,221.5", - pos="e,4539.8,196.22 3467,251.75 3501.5,249.94 3537,248.26 3570.4,247 3622.6,245.04 4464,252.95 4510.4,229 4520.6,223.75 4528.7,214.26 \ -4534.7,204.95", + lp="4341.9,221.5", + pos="e,4268.8,196.29 3202,251.76 3236.5,249.94 3272,248.26 3305.4,247 3357,245.05 4188.6,251.01 4235.4,229 4246.5,223.77 4255.8,214.16 \ +4263,204.75", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="4736.4,178", + pos="4471.4,178", width=2.1304]; "material sample to disease or phenotypic feature association" -> "object category closure" [color=blue, label="object category closure", - lp="4804.9,221.5", - pos="e,4731.1,196.13 3465.8,251.72 3500.6,249.89 3536.6,248.22 3570.4,247 3601.9,245.87 4679.1,244.77 4706.4,229 4715.5,223.75 4722.2,\ -214.52 4726.9,205.41", + lp="4534.9,221.5", + pos="e,4463.4,196.25 3201.2,251.7 3235.9,249.88 3271.7,248.21 3305.4,247 3336.7,245.87 4405.4,243.15 4433.4,229 4443.7,223.78 4452,214.3 \ +4458.2,204.98", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4926.4,178", + pos="4661.4,178", width=1.0652]; "material sample to disease or phenotypic feature association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4976.4,221.5", - pos="e,4919.7,196.21 3465.4,251.68 3500.3,249.85 3536.4,248.18 3570.4,247 3607.1,245.72 4860.1,246.4 4892.4,229 4902.1,223.78 4909.6,\ -214.43 4915,205.21", + lp="4708.4,221.5", + pos="e,4653.4,195.78 3200.4,251.68 3235.3,249.85 3271.4,248.18 3305.4,247 3342,245.72 4589.6,245.28 4622.4,229 4633.1,223.68 4641.8,213.86 \ +4648.2,204.32", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="5085.4,178", + pos="4820.4,178", width=1.0652]; "material sample to disease or phenotypic feature association" -> "object namespace" [color=blue, label="object namespace", - lp="5129.4,221.5", - pos="e,5078,195.76 3465,251.66 3500.1,249.83 3536.3,248.16 3570.4,247 3611.4,245.6 5011.8,247.7 5048.4,229 5058.7,223.71 5066.9,214.03 \ -5072.9,204.59", + lp="4862.4,221.5", + pos="e,4812.1,195.8 3200,251.66 3235.1,249.83 3271.3,248.16 3305.4,247 3346.3,245.6 4743.6,246.98 4780.4,229 4791.3,223.7 4800.1,213.88 \ +4806.7,204.34", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="5236.4,178", + pos="4971.4,178", width=1.0652]; "material sample to disease or phenotypic feature association" -> "subject label closure" [color=blue, label="subject label closure", - lp="5289.4,221.5", - pos="e,5228.4,195.79 3464.6,251.65 3499.8,249.81 3536.2,248.15 3570.4,247 3615.6,245.48 5156.9,249.05 5197.4,229 5208.1,223.69 5216.8,\ -213.87 5223.2,204.33", + lp="5024.4,221.5", + pos="e,4962.8,195.81 3199.6,251.65 3234.8,249.81 3271.2,248.15 3305.4,247 3350.5,245.49 4889.7,248.53 4930.4,229 4941.4,223.72 4950.4,\ +213.91 4957.2,204.36", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="5407.4,178", + pos="5142.4,178", width=1.0652]; "material sample to disease or phenotypic feature association" -> "object label closure" [color=blue, label="object label closure", - lp="5455.9,221.5", - pos="e,5399.1,195.8 3464.6,251.62 3499.8,249.78 3536.2,248.13 3570.4,247 3620.3,245.35 5322.5,250.85 5367.4,229 5378.3,223.71 5387.1,\ -213.9 5393.7,204.35", + lp="5190.9,221.5", + pos="e,5134.1,195.8 3199.6,251.62 3234.8,249.78 3271.2,248.13 3305.4,247 3355.3,245.35 5057.5,250.85 5102.4,229 5113.3,223.71 5122.1,\ +213.9 5128.7,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="5569.4,178", + pos="5304.4,178", width=2.347]; "material sample to disease or phenotypic feature association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="5617.9,221.5", - pos="e,5560.8,196.3 3464.1,251.62 3499.5,249.78 3536,248.12 3570.4,247 3624.8,245.23 5480.5,252.8 5529.4,229 5540.1,223.79 5548.9,214.18 \ -5555.4,204.76", + lp="5352.9,221.5", + pos="e,5295.8,196.3 3199.1,251.62 3234.5,249.78 3271,248.12 3305.4,247 3359.8,245.23 5215.5,252.8 5264.4,229 5275.1,223.79 5283.9,214.18 \ +5290.4,204.76", style=solid]; type [height=0.5, - pos="5731.4,178", + pos="5466.4,178", width=0.86659]; "material sample to disease or phenotypic feature association" -> type [color=blue, label=type, - lp="5726.4,221.5", - pos="e,5723.1,195.81 3464.1,251.6 3499.5,249.76 3536,248.11 3570.4,247 3599.8,246.05 5664.9,241.87 5691.4,229 5702.3,223.72 5711.1,213.91 \ -5717.7,204.36", + lp="5461.4,221.5", + pos="e,5458.1,195.81 3199.1,251.6 3234.5,249.76 3271,248.11 3305.4,247 3334.8,246.05 5399.9,241.87 5426.4,229 5437.3,223.72 5446.1,213.91 \ +5452.7,204.36", style=solid]; category [height=0.5, - pos="5832.4,178", + pos="5567.4,178", width=1.4263]; "material sample to disease or phenotypic feature association" -> category [color=blue, label=category, - lp="5812.9,221.5", - pos="e,5812.2,194.83 3464.1,251.59 3499.5,249.75 3536,248.11 3570.4,247 3630.8,245.06 5688.1,244.97 5746.4,229 5767.1,223.34 5787.9,211.43 \ -5803.9,200.65", + lp="5547.9,221.5", + pos="e,5547.2,194.83 3199.1,251.59 3234.5,249.75 3271,248.11 3305.4,247 3365.8,245.06 5423.1,244.97 5481.4,229 5502.1,223.34 5522.9,211.43 \ +5538.9,200.65", style=solid]; subject -> object [label=relation, lp="1927.4,134.5", @@ -370,11 +372,11 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="3617.4,265", + pos="3352.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3748.4,265", + pos="3483.4,265", width=2.0762]; } diff --git a/graphviz/material_sample_to_disease_or_phenotypic_feature_association.svg b/graphviz/material_sample_to_disease_or_phenotypic_feature_association.svg index aa4cfbf6cf..c8f64221ec 100644 --- a/graphviz/material_sample_to_disease_or_phenotypic_feature_association.svg +++ b/graphviz/material_sample_to_disease_or_phenotypic_feature_association.svg @@ -4,16 +4,16 @@ - + %3 - + material sample to disease or phenotypic feature association - -material sample to disease or phenotypic feature association + +material sample to disease or phenotypic feature association @@ -24,7 +24,7 @@ material sample to disease or phenotypic feature association->association - + is_a @@ -37,8 +37,8 @@ material sample to disease or phenotypic feature association->material sample to entity association mixin - - + + uses @@ -50,8 +50,8 @@ material sample to disease or phenotypic feature association->entity to disease or phenotypic feature association mixin - - + + uses @@ -63,7 +63,7 @@ material sample to disease or phenotypic feature association->id - + id @@ -76,7 +76,7 @@ material sample to disease or phenotypic feature association->iri - + iri @@ -89,8 +89,8 @@ material sample to disease or phenotypic feature association->name - - + + name @@ -102,8 +102,8 @@ material sample to disease or phenotypic feature association->description - - + + description @@ -115,8 +115,8 @@ material sample to disease or phenotypic feature association->has attribute - - + + has attribute @@ -128,8 +128,8 @@ material sample to disease or phenotypic feature association->subject - - + + subject @@ -141,8 +141,8 @@ material sample to disease or phenotypic feature association->predicate - - + + predicate @@ -154,7 +154,7 @@ material sample to disease or phenotypic feature association->object - + object @@ -167,9 +167,9 @@ material sample to disease or phenotypic feature association->negated - - -negated + + +negated @@ -180,9 +180,9 @@ material sample to disease or phenotypic feature association->qualifiers - - -qualifiers + + +qualifiers @@ -193,9 +193,9 @@ material sample to disease or phenotypic feature association->publications - - -publications + + +publications @@ -206,269 +206,269 @@ material sample to disease or phenotypic feature association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string material sample to disease or phenotypic feature association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string material sample to disease or phenotypic feature association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string material sample to disease or phenotypic feature association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type material sample to disease or phenotypic feature association->timepoint - - -timepoint + + +timepoint original subject - -string + +string material sample to disease or phenotypic feature association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie material sample to disease or phenotypic feature association->original predicate - - -original predicate + + +original predicate original object - -string + +string material sample to disease or phenotypic feature association->original object - - -original object + + +original object subject category - -ontology class + +ontology class material sample to disease or phenotypic feature association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class material sample to disease or phenotypic feature association->object category - - -object category + + +object category subject closure - -string + +string material sample to disease or phenotypic feature association->subject closure - - -subject closure + + +subject closure object closure - -string + +string material sample to disease or phenotypic feature association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class material sample to disease or phenotypic feature association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class material sample to disease or phenotypic feature association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string material sample to disease or phenotypic feature association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string material sample to disease or phenotypic feature association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string material sample to disease or phenotypic feature association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string material sample to disease or phenotypic feature association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source material sample to disease or phenotypic feature association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type material sample to disease or phenotypic feature association->type - - -type + + +type category - -category + +category material sample to disease or phenotypic feature association->category - - -category + + +category @@ -498,14 +498,14 @@ association_type - -string + +string association_category - -category type + +category type diff --git a/graphviz/molecular_activity_to_chemical_entity_association.gv b/graphviz/molecular_activity_to_chemical_entity_association.gv index 0b883f073c..cbb6c19b28 100644 --- a/graphviz/molecular_activity_to_chemical_entity_association.gv +++ b/graphviz/molecular_activity_to_chemical_entity_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4788.4,283"]; + graph [bb="0,0,4570.4,283"]; node [label="\N"]; "molecular activity to chemical entity association" [height=0.5, label="molecular activity to chemical entity association", - pos="2492.4,265", + pos="2274.4,265", width=6.5355]; association [height=0.5, pos="62.394,178", width=1.7332]; "molecular activity to chemical entity association" -> association [label=is_a, - lp="281.39,221.5", - pos="e,103.12,191.79 2258.1,263.28 1726.5,261.21 460.31,253.73 267.39,229 213.85,222.14 154.03,206.61 112.9,194.67"]; + lp="280.39,221.5", + pos="e,102.91,191.77 2040.6,262.85 1548.6,260.02 437.82,251.22 266.39,229 213.11,222.09 153.58,206.57 112.65,194.64"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "molecular activity to chemical entity association" -> id [color=blue, label=id, - lp="398.39,221.5", - pos="e,210.38,190 2258.9,262.54 1750.1,259 572.49,248.78 391.39,229 318.35,221.02 300.2,215.65 229.39,196 226.29,195.14 223.09,194.17 \ -219.89,193.16", + lp="396.39,221.5", + pos="e,210.38,189.98 2042.1,262.09 1574.3,257.9 549.2,246.81 389.39,229 317.23,220.96 299.34,215.5 229.39,196 226.29,195.13 223.09,194.17 \ +219.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "molecular activity to chemical entity association" -> iri [color=blue, label=iri, - lp="515.39,221.5", - pos="e,315.29,190.23 2259.9,262.15 1773.1,257.95 677.2,246.65 507.39,229 429.97,220.95 410.81,215.26 335.39,196 332.02,195.14 328.54,\ -194.18 325.05,193.17", + lp="509.39,221.5", + pos="e,315.3,190.2 2039.2,264.51 1627.4,264.53 792.07,260.51 501.39,229 426.61,220.89 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ +325.06,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "molecular activity to chemical entity association" -> name [color=blue, label=name, - lp="627.39,221.5", - pos="e,440.01,191.15 2259.2,262.45 1790.8,258.93 766.83,249.04 607.39,229 552.58,222.11 491.21,206.11 449.83,194.05", + lp="617.39,221.5", + pos="e,439.19,191.41 2042.1,262.09 1615.1,258.14 736.31,247.83 597.39,229 545.74,222 488.1,206.31 448.78,194.36", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "molecular activity to chemical entity association" -> description [color=blue, label=description, - lp="755.89,221.5", - pos="e,588.8,193.65 2258.4,262.99 1810.5,260.52 863.43,252.56 715.39,229 675.03,222.58 630.79,208.66 598.44,197.14", + lp="739.89,221.5", + pos="e,586.19,194.12 2040.6,262.71 1634,259.89 827.43,251.51 699.39,229 663.52,222.69 624.55,209.24 595.6,197.88", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "molecular activity to chemical entity association" -> "has attribute" [color=blue, label="has attribute", - lp="913.39,221.5", - pos="e,729.98,191.75 2259.4,262.39 1842.5,259.01 999.89,249.69 866.39,229 822.26,222.16 773.51,207 739.58,195.15", + lp="887.39,221.5", + pos="e,726.83,192.67 2041.9,262.26 1665.9,258.85 954.84,249.74 840.39,229 804.17,222.43 764.8,208.24 736.39,196.65", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "molecular activity to chemical entity association" -> predicate [color=blue, label=predicate, - lp="1074.4,221.5", - pos="e,887.81,193.09 2257,264.77 1907.5,264.81 1268,260.37 1040.4,229 991.17,222.22 936.47,207.65 897.4,195.99", + lp="1031.4,221.5", + pos="e,880.43,194.06 2044,261.28 1704,256.72 1097.1,246.29 997.39,229 960.25,222.56 919.77,209.02 889.78,197.66", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "molecular activity to chemical entity association" -> negated [color=blue, label=negated, - lp="1220.4,221.5", - pos="e,1022.3,190.23 2258.2,263.06 1940.8,260.87 1390.8,253.53 1191.4,229 1135.6,222.13 1072.9,205.38 1032,193.16", + lp="1151.4,221.5", + pos="e,1015.6,192.51 2044.7,261 1734.4,256.34 1209.9,246.07 1122.4,229 1088.3,222.36 1051.5,208.2 1024.9,196.64", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "molecular activity to chemical entity association" -> qualifiers [color=blue, label=qualifiers, - lp="1356.9,221.5", - pos="e,1171.6,193.02 2258.3,263.1 1970,260.93 1497.3,253.59 1323.4,229 1274.6,222.11 1220.5,207.65 1181.6,196.05", + lp="1254.9,221.5", + pos="e,1151.6,195.39 2042.5,261.89 1756.4,258.42 1298.2,249.69 1221.4,229 1199.7,223.15 1177.4,211.43 1160.1,200.81", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "molecular activity to chemical entity association" -> publications [color=blue, label=publications, - lp="1499.4,221.5", - pos="e,1321.9,192.66 2258.5,262.94 2001.1,260.57 1604.1,252.98 1455.4,229 1412.5,222.09 1365.3,207.61 1331.5,196.01", + lp="1346.4,221.5", + pos="e,1286.4,196.26 2041.9,262.2 1763.7,259.09 1331.6,250.75 1302.4,229 1295.1,223.57 1290.9,214.84 1288.5,206.19", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,262 +110,263 @@ digraph { width=2.0943]; "molecular activity to chemical entity association" -> "has evidence" [color=blue, label="has evidence", - lp="1652.9,221.5", - pos="e,1479.4,193.55 2261.5,261.53 2041.8,257.97 1727.5,249.4 1606.4,229 1566,222.2 1521.6,208.38 1489.1,196.99", + lp="1444.9,221.5", + pos="e,1413.8,194.93 2041.2,262.59 1789.2,259.88 1420.5,252 1398.4,229 1390,220.25 1395.9,210.18 1405.7,201.37", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1643.4,178", - width=3.015]; + label=string, + pos="1573.4,178", + width=1.0652]; "molecular activity to chemical entity association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1802.9,221.5", - pos="e,1667.9,195.78 2257.2,264.2 2073,262.28 1832.7,254.63 1738.4,229 1716.6,223.09 1694.2,211.61 1676.7,201.13", + lp="1562.9,221.5", + pos="e,1543.3,189.28 2044,261.28 1822.1,257.49 1517.2,248.71 1498.4,229 1493.8,224.18 1494.8,219.62 1498.4,214 1502.8,207.12 1518,199.47 \ +1533.6,193.08", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1878.4,178", - width=3.015]; + label=string, + pos="1668.4,178", + width=1.0652]; "molecular activity to chemical entity association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1972.4,221.5", - pos="e,1872.6,196 2272.6,258.53 2101.7,253.17 1891.2,243.64 1877.4,229 1871.6,222.9 1870.4,214.27 1871,205.9", + lp="1729.4,221.5", + pos="e,1648.1,193.48 2052.3,259.02 1873.3,253.88 1649,244.4 1634.4,229 1626.3,220.46 1631.8,209.82 1640.6,200.55", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2113.4,178", - width=3.015]; + label=string, + pos="1810.4,178", + width=1.0652]; "molecular activity to chemical entity association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2180.9,221.5", - pos="e,2087.6,195.53 2273.7,258.34 2180.2,253.61 2089,244.93 2074.4,229 2066.7,220.62 2071.6,210.86 2080.1,202.2", + lp="1949.9,221.5", + pos="e,1816.9,195.93 2073.5,255.62 1971.2,249.93 1864,241.2 1843.4,229 1834,223.44 1826.8,214.03 1821.5,204.86", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2295.4,178", + pos="2037.4,178", width=1.5346]; "molecular activity to chemical entity association" -> timepoint [color=blue, label=timepoint, - lp="2332.4,221.5", - pos="e,2291.1,196.26 2349.5,250.63 2325.6,245.57 2305.8,238.6 2297.4,229 2292,222.83 2290.3,214.43 2290.3,206.27", + lp="2112.4,221.5", + pos="e,2046.6,196.08 2153.4,249.53 2121.1,244.12 2091.3,237.25 2077.4,229 2067.4,223.06 2058.9,213.63 2052.3,204.55", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2407.4,178", + pos="2149.4,178", width=1.0652]; "molecular activity to chemical entity association" -> "original subject" [color=blue, label="original subject", - lp="2430.4,221.5", - pos="e,2387.4,193.75 2397.4,248.51 2388.5,243.59 2380.5,237.22 2374.4,229 2367.7,220.01 2372.5,209.73 2380.3,200.83", + lp="2214.4,221.5", + pos="e,2148.2,196.23 2184.7,248.3 2174.8,243.46 2165.7,237.17 2158.4,229 2152.9,222.8 2150.2,214.39 2149,206.23", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2521.4,178", + pos="2274.4,178", width=1.5887]; "molecular activity to chemical entity association" -> "original predicate" [color=blue, label="original predicate", - lp="2556.9,221.5", - pos="e,2504.6,195.4 2490.1,246.84 2489.4,236.95 2489.6,224.45 2493.4,214 2494.7,210.42 2496.5,206.94 2498.6,203.64", + lp="2337.9,221.5", + pos="e,2274.4,196.18 2274.4,246.8 2274.4,235.16 2274.4,219.55 2274.4,206.24", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2635.4,178", + pos="2403.4,178", width=1.0652]; "molecular activity to chemical entity association" -> "original object" [color=blue, label="original object", - lp="2681.9,221.5", - pos="e,2634.3,196.46 2590.7,248.54 2601.6,243.65 2611.9,237.29 2620.4,229 2626.5,223.04 2630.2,214.69 2632.3,206.52", + lp="2459.9,221.5", + pos="e,2407.8,195.99 2361.7,248.26 2380.4,243.1 2396.4,236.68 2402.4,229 2407.4,222.62 2408.9,214.26 2408.7,206.21", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2768.4,178", + pos="2536.4,178", width=2.1304]; "molecular activity to chemical entity association" -> "subject category" [color=blue, label="subject category", - lp="2811.9,221.5", - pos="e,2762.2,196.16 2651.6,251.7 2688.6,246.5 2721.8,239.2 2737.4,229 2746.2,223.28 2752.9,214.13 2757.8,205.22", + lp="2586.9,221.5", + pos="e,2533.7,196.01 2438.7,252.08 2472.4,246.92 2501.8,239.55 2515.4,229 2522.8,223.28 2527.6,214.49 2530.7,205.86", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2939.4,178", + pos="2707.4,178", width=2.1304]; "molecular activity to chemical entity association" -> "object category" [color=blue, label="object category", - lp="2956.9,221.5", - pos="e,2923.4,195.77 2664.7,252.72 2756.8,245.89 2855.2,236.99 2875.4,229 2890.3,223.11 2904.5,212.62 2915.8,202.76", + lp="2728.9,221.5", + pos="e,2693.3,196.01 2447.2,252.78 2536.6,246.1 2631.1,237.32 2650.4,229 2663.9,223.19 2676.4,212.95 2686.3,203.24", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3072.4,178", + pos="2840.4,178", width=1.0652]; "molecular activity to chemical entity association" -> "subject closure" [color=blue, label="subject closure", - lp="3093.9,221.5", - pos="e,3059.6,195.17 2659.4,252.3 2685.5,250.5 2712.2,248.69 2737.4,247 2799.4,242.85 2959.1,253 3016.4,229 3030.2,223.22 3042.9,212.58 \ -3052.7,202.59", + lp="2864.9,221.5", + pos="e,2828.7,195.15 2441.8,252.33 2467.8,250.54 2494.3,248.71 2519.4,247 2579.2,242.93 2733.6,253.23 2788.4,229 2801.4,223.25 2813.1,\ +212.75 2822.1,202.85", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3172.4,178", + pos="2953.4,178", width=1.0652]; "molecular activity to chemical entity association" -> "object closure" [color=blue, label="object closure", - lp="3214.4,221.5", - pos="e,3170.3,196.32 2656.1,252.05 2683.2,250.24 2711.1,248.48 2737.4,247 2760.4,245.7 3133.6,242.35 3152.4,229 3160,223.64 3164.7,214.92 \ -3167.6,206.26", + lp="2988.4,221.5", + pos="e,2948,196.03 2438.4,252.05 2465.5,250.25 2493.2,248.49 2519.4,247 2564.3,244.44 2884.8,252 2923.4,229 2932.4,223.62 2939.1,214.36 \ +2943.8,205.27", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3305.4,178", + pos="3086.4,178", width=2.1304]; "molecular activity to chemical entity association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3372.9,221.5", - pos="e,3297.7,196.16 2654.4,251.94 2682.1,250.12 2710.6,248.38 2737.4,247 2766.9,245.48 3242.3,242.73 3268.4,229 3278.5,223.67 3286.6,\ -214.17 3292.6,204.87", + lp="3148.9,221.5", + pos="e,3076.5,196.23 2436.8,251.93 2464.3,250.11 2492.7,248.39 2519.4,247 2577.5,243.99 2989.8,253.86 3042.4,229 3053.7,223.65 3063.3,\ +213.88 3070.7,204.38", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3497.4,178", + pos="3279.4,178", width=2.1304]; "molecular activity to chemical entity association" -> "object category closure" [color=blue, label="object category closure", - lp="3563.9,221.5", - pos="e,3491.1,196.15 2653.1,251.82 2681.2,249.99 2710.1,248.28 2737.4,247 2777.8,245.1 3429.1,248.58 3464.4,229 3473.9,223.71 3481.2,\ -214.34 3486.5,205.14", + lp="3341.9,221.5", + pos="e,3271.1,196.22 2435.1,251.83 2463.2,249.99 2492.1,248.29 2519.4,247 2559.4,245.11 3204.6,247.03 3240.4,229 3250.8,223.75 3259.3,\ +214.26 3265.7,204.95", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3687.4,178", + pos="3469.4,178", width=1.0652]; "molecular activity to chemical entity association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3736.4,221.5", - pos="e,3680.3,195.72 2652.1,251.77 2680.5,249.92 2709.8,248.23 2737.4,247 2788.1,244.74 3606.4,252.6 3651.4,229 3661.6,223.65 3669.6,\ -213.97 3675.4,204.53", + lp="3515.4,221.5", + pos="e,3461.1,195.76 2434.1,251.77 2462.5,249.92 2491.8,248.23 2519.4,247 2569.9,244.75 3384,251.35 3429.4,229 3440.2,223.66 3449.1,213.83 \ +3455.7,204.3", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3846.4,178", + pos="3628.4,178", width=1.0652]; "molecular activity to chemical entity association" -> "object namespace" [color=blue, label="object namespace", - lp="3890.4,221.5", - pos="e,3838.7,195.75 2651.8,251.72 2680.3,249.88 2709.7,248.19 2737.4,247 2767.1,245.72 3781.9,242.45 3808.4,229 3818.9,223.7 3827.2,\ -214.02 3833.4,204.58", + lp="3669.4,221.5", + pos="e,3619.8,195.79 2433.8,251.72 2462.3,249.88 2491.7,248.19 2519.4,247 2549,245.72 3560.7,241.92 3587.4,229 3598.4,223.69 3607.4,213.87 \ +3614.2,204.33", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3997.4,178", + pos="3779.4,178", width=1.0652]; "molecular activity to chemical entity association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4050.4,221.5", - pos="e,3989.4,195.77 2651.5,251.7 2680.1,249.85 2709.6,248.17 2737.4,247 2771.3,245.58 3928,244.11 3958.4,229 3969.1,223.67 3977.8,213.85 \ -3984.2,204.31", + lp="3831.4,221.5", + pos="e,3770.5,195.81 2433.5,251.7 2462.1,249.85 2491.6,248.17 2519.4,247 2553.2,245.58 3706.8,243.52 3737.4,229 3748.5,223.71 3757.8,\ +213.9 3764.7,204.35", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4168.4,178", + pos="3950.4,178", width=1.0652]; "molecular activity to chemical entity association" -> "object label closure" [color=blue, label="object label closure", - lp="4215.9,221.5", - pos="e,4160.1,195.79 2651.1,251.68 2679.8,249.82 2709.5,248.15 2737.4,247 2776,245.41 4093.7,245.96 4128.4,229 4139.3,223.69 4148.1,213.88 \ -4154.7,204.34", + lp="3998.9,221.5", + pos="e,3941.8,195.8 2433.1,251.68 2461.8,249.82 2491.5,248.15 2519.4,247 2558,245.41 3874.6,245.74 3909.4,229 3920.4,223.71 3929.4,213.89 \ +3936.2,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4330.4,178", + pos="4112.4,178", width=2.347]; "molecular activity to chemical entity association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4378.9,221.5", - pos="e,4321.5,196.3 2650.8,251.67 2679.6,249.81 2709.4,248.13 2737.4,247 2780.5,245.26 4250.5,247.67 4289.4,229 4300.2,223.79 4309.2,\ -214.18 4315.9,204.76", + lp="4160.9,221.5", + pos="e,4103.8,196.29 2432.8,251.67 2461.6,249.81 2491.4,248.13 2519.4,247 2562.5,245.26 4033.6,247.91 4072.4,229 4083.1,223.78 4091.9,\ +214.16 4098.4,204.75", style=solid]; type [height=0.5, - pos="4464.4,178", + pos="4246.4,178", width=0.86659]; "molecular activity to chemical entity association" -> type [color=blue, label=type, - lp="4478.4,221.5", - pos="e,4465.2,196.18 2650.5,251.66 2679.4,249.8 2709.3,248.12 2737.4,247 2761.2,246.05 4433.8,243.85 4452.4,229 4459.2,223.54 4462.6,\ -214.92 4464.1,206.37", + lp="4260.4,221.5", + pos="e,4247.2,196.18 2432.5,251.66 2461.4,249.8 2491.3,248.12 2519.4,247 2543.2,246.05 4215.8,243.85 4234.4,229 4241.2,223.54 4244.6,\ +214.92 4246.1,206.37", style=solid]; category [height=0.5, - pos="4565.4,178", + pos="4347.4,178", width=1.4263]; "molecular activity to chemical entity association" -> category [color=blue, label=category, - lp="4558.9,221.5", - pos="e,4549.8,195.25 2650.5,251.66 2679.4,249.79 2709.3,248.12 2737.4,247 2786.3,245.06 4452,244.65 4498.4,229 4514.6,223.53 4530.1,212.5 \ -4542.1,202.2", + lp="4340.9,221.5", + pos="e,4331.8,195.25 2432.5,251.66 2461.4,249.79 2491.3,248.12 2519.4,247 2568.3,245.06 4234,244.65 4280.4,229 4296.6,223.53 4312.1,212.5 \ +4324.1,202.2", style=solid]; subject [height=0.5, - pos="4679.4,178", + pos="4461.4,178", width=1.2277]; "molecular activity to chemical entity association" -> subject [color=blue, label=subject, - lp="4655.4,221.5", - pos="e,4660.1,194.33 2650.5,251.64 2679.4,249.78 2709.3,248.11 2737.4,247 2840.5,242.93 4495,256.59 4594.4,229 4615.1,223.24 4636,211.08 \ -4651.9,200.2", + lp="4437.4,221.5", + pos="e,4442.1,194.33 2432.5,251.64 2461.4,249.78 2491.3,248.11 2519.4,247 2622.5,242.93 4277,256.59 4376.4,229 4397.1,223.24 4418,211.08 \ +4433.9,200.2", style=solid]; object [height=0.5, - pos="4722.4,91", + pos="4504.4,91", width=1.0832]; "molecular activity to chemical entity association" -> object [color=blue, label=object, - lp="4766.4,178", - pos="e,4735.8,108.09 2650.5,251.63 2679.4,249.77 2709.3,248.1 2737.4,247 2791.5,244.88 4633.9,245.54 4685.4,229 4709.7,221.2 4718,217.1 \ -4732.4,196 4746.3,175.59 4742.5,166.51 4745.4,142 4746.2,135.38 4747.3,133.39 4745.4,127 4744.4,123.55 4742.9,120.13 4741.1,116.85", + lp="4548.4,178", + pos="e,4517.8,108.09 2432.5,251.63 2461.4,249.77 2491.3,248.1 2519.4,247 2573.5,244.88 4415.9,245.54 4467.4,229 4491.7,221.2 4500,217.1 \ +4514.4,196 4528.3,175.59 4524.5,166.51 4527.4,142 4528.2,135.38 4529.3,133.39 4527.4,127 4526.4,123.55 4524.9,120.13 4523.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2784.4,265", + pos="2566.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2915.4,265", + pos="2697.4,265", width=2.0762]; subject -> object [label=relation, - lp="4717.4,134.5", - pos="e,4704.5,107.23 4680.5,159.55 4681.7,149.57 4684.2,137.07 4689.4,127 4691.6,122.68 4694.5,118.52 4697.7,114.66"]; + lp="4499.4,134.5", + pos="e,4486.5,107.23 4462.5,159.55 4463.7,149.57 4466.2,137.07 4471.4,127 4473.6,122.68 4476.5,118.52 4479.7,114.66"]; relation [height=0.5, - pos="4667.4,18", + pos="4449.4,18", width=1.2999]; - subject -> relation [pos="e,4668.7,36.188 4678.1,159.79 4676,132.48 4672,78.994 4669.5,46.38", + subject -> relation [pos="e,4450.7,36.188 4460.1,159.79 4458,132.48 4454,78.994 4451.5,46.38", style=dotted]; "molecular activity to chemical entity association_subject" [color=blue, height=0.5, label="molecular activity", - pos="3102.4,265", + pos="2884.4,265", width=2.6178]; - object -> relation [pos="e,4680.2,35.54 4709.9,73.889 4703,64.939 4694.2,53.617 4686.4,43.584", + object -> relation [pos="e,4462.2,35.54 4491.9,73.889 4485,64.939 4476.2,53.617 4468.4,43.584", style=dotted]; "molecular activity to chemical entity association_object" [color=blue, height=0.5, label="chemical entity", - pos="3296.4,265", + pos="3078.4,265", width=2.2748]; } diff --git a/graphviz/molecular_activity_to_chemical_entity_association.svg b/graphviz/molecular_activity_to_chemical_entity_association.svg index 36e1ee2bcb..95d98e586c 100644 --- a/graphviz/molecular_activity_to_chemical_entity_association.svg +++ b/graphviz/molecular_activity_to_chemical_entity_association.svg @@ -4,16 +4,16 @@ - + %3 - + molecular activity to chemical entity association - -molecular activity to chemical entity association + +molecular activity to chemical entity association @@ -24,9 +24,9 @@ molecular activity to chemical entity association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ molecular activity to chemical entity association->id - - -id + + +id @@ -50,9 +50,9 @@ molecular activity to chemical entity association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ molecular activity to chemical entity association->name - - -name + + +name @@ -76,9 +76,9 @@ molecular activity to chemical entity association->description - - -description + + +description @@ -89,9 +89,9 @@ molecular activity to chemical entity association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ molecular activity to chemical entity association->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ molecular activity to chemical entity association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ molecular activity to chemical entity association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ molecular activity to chemical entity association->publications - - -publications + + +publications @@ -154,344 +154,344 @@ molecular activity to chemical entity association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string molecular activity to chemical entity association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string molecular activity to chemical entity association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string molecular activity to chemical entity association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type molecular activity to chemical entity association->timepoint - - -timepoint + + +timepoint original subject - -string + +string molecular activity to chemical entity association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie molecular activity to chemical entity association->original predicate - - -original predicate + + +original predicate original object - -string + +string molecular activity to chemical entity association->original object - - -original object + + +original object subject category - -ontology class + +ontology class molecular activity to chemical entity association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class molecular activity to chemical entity association->object category - - -object category + + +object category subject closure - -string + +string molecular activity to chemical entity association->subject closure - - -subject closure + + +subject closure object closure - -string + +string molecular activity to chemical entity association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class molecular activity to chemical entity association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class molecular activity to chemical entity association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string molecular activity to chemical entity association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string molecular activity to chemical entity association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string molecular activity to chemical entity association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string molecular activity to chemical entity association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source molecular activity to chemical entity association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type molecular activity to chemical entity association->type - - -type + + +type category - -category + +category molecular activity to chemical entity association->category - - -category + + +category subject - -subject + +subject molecular activity to chemical entity association->subject - - -subject + + +subject object - -object + +object molecular activity to chemical entity association->object - - -object + + +object association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + molecular activity to chemical entity association_subject - -molecular activity + +molecular activity object->relation - - + + molecular activity to chemical entity association_object - -chemical entity + +chemical entity diff --git a/graphviz/molecular_activity_to_molecular_activity_association.gv b/graphviz/molecular_activity_to_molecular_activity_association.gv index 69f54a6cde..7b9b9d412b 100644 --- a/graphviz/molecular_activity_to_molecular_activity_association.gv +++ b/graphviz/molecular_activity_to_molecular_activity_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4788.4,283"]; + graph [bb="0,0,4570.4,283"]; node [label="\N"]; "molecular activity to molecular activity association" [height=0.5, label="molecular activity to molecular activity association", - pos="2492.4,265", + pos="2274.4,265", width=6.8605]; association [height=0.5, pos="62.394,178", width=1.7332]; "molecular activity to molecular activity association" -> association [label=is_a, - lp="281.39,221.5", - pos="e,103.12,191.79 2246.6,263.23 1708.5,261.1 458.93,253.55 267.39,229 213.85,222.14 154.03,206.61 112.9,194.67"]; + lp="280.39,221.5", + pos="e,102.91,191.77 2028.8,262.79 1531.2,259.88 436.47,251.04 266.39,229 213.11,222.09 153.58,206.57 112.65,194.64"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "molecular activity to molecular activity association" -> id [color=blue, label=id, - lp="398.39,221.5", - pos="e,210.38,190 2247.8,262.46 1733.2,258.85 571.19,248.64 391.39,229 318.35,221.02 300.2,215.65 229.39,196 226.29,195.14 223.09,194.17 \ -219.89,193.16", + lp="396.39,221.5", + pos="e,210.38,189.98 2030.9,261.99 1558,257.72 547.93,246.67 389.39,229 317.23,220.96 299.34,215.5 229.39,196 226.29,195.13 223.09,194.17 \ +219.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "molecular activity to molecular activity association" -> iri [color=blue, label=iri, - lp="515.39,221.5", - pos="e,315.29,190.23 2248.3,262.05 1755.9,257.77 675.86,246.51 507.39,229 429.97,220.95 410.81,215.26 335.39,196 332.02,195.14 328.54,\ -194.18 325.05,193.17", + lp="509.39,221.5", + pos="e,315.3,190.2 2027.3,264.51 1611.5,264.45 789.3,260.21 501.39,229 426.61,220.89 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ +325.06,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "molecular activity to molecular activity association" -> name [color=blue, label=name, - lp="627.39,221.5", - pos="e,440.01,191.15 2247.9,262.36 1774.6,258.77 765.56,248.88 607.39,229 552.58,222.11 491.21,206.11 449.83,194.05", + lp="617.39,221.5", + pos="e,439.19,191.41 2030.8,261.98 1599.7,257.95 735.1,247.67 597.39,229 545.74,222 488.1,206.31 448.78,194.36", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "molecular activity to molecular activity association" -> description [color=blue, label=description, - lp="755.89,221.5", - pos="e,588.8,193.65 2247,262.92 1794.7,260.38 862.19,252.36 715.39,229 675.03,222.58 630.79,208.66 598.44,197.14", + lp="739.89,221.5", + pos="e,586.19,194.12 2029.3,262.63 1619.2,259.73 826.25,251.3 699.39,229 663.52,222.69 624.55,209.24 595.6,197.88", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "molecular activity to molecular activity association" -> "has attribute" [color=blue, label="has attribute", - lp="913.39,221.5", - pos="e,729.98,191.75 2247.8,262.3 1827.1,258.84 998.67,249.5 866.39,229 822.26,222.16 773.51,207 739.58,195.15", + lp="887.39,221.5", + pos="e,726.83,192.67 2030.4,262.15 1651.7,258.67 953.69,249.53 840.39,229 804.17,222.43 764.8,208.24 736.39,196.65", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "molecular activity to molecular activity association" -> predicate [color=blue, label=predicate, - lp="1074.4,221.5", - pos="e,887.81,193.09 2245.4,264.77 1893.5,264.71 1265.5,260.02 1040.4,229 991.17,222.22 936.47,207.65 897.4,195.99", + lp="1031.4,221.5", + pos="e,880.43,194.06 2033.1,261.13 1691.2,256.5 1096.1,246.1 997.39,229 960.25,222.56 919.77,209.02 889.78,197.66", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "molecular activity to molecular activity association" -> negated [color=blue, label=negated, - lp="1220.4,221.5", - pos="e,1022.3,190.23 2246.8,262.98 1927.7,260.69 1388.4,253.24 1191.4,229 1135.6,222.13 1072.9,205.38 1032,193.16", + lp="1151.4,221.5", + pos="e,1015.6,192.51 2033.9,260.84 1722.4,256.1 1208.9,245.87 1122.4,229 1088.3,222.36 1051.5,208.2 1024.9,196.64", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "molecular activity to molecular activity association" -> qualifiers [color=blue, label=qualifiers, - lp="1356.9,221.5", - pos="e,1171.6,193.02 2246.6,263.01 1957.4,260.73 1495,253.26 1323.4,229 1274.6,222.11 1220.5,207.65 1181.6,196.05", + lp="1254.9,221.5", + pos="e,1151.6,195.39 2031.3,261.76 1744.6,258.19 1297.2,249.42 1221.4,229 1199.7,223.15 1177.4,211.43 1160.1,200.81", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "molecular activity to molecular activity association" -> publications [color=blue, label=publications, - lp="1499.4,221.5", - pos="e,1321.9,192.66 2247.2,262.84 1989.6,260.34 1601.9,252.63 1455.4,229 1412.5,222.09 1365.3,207.61 1331.5,196.01", + lp="1346.4,221.5", + pos="e,1286.4,196.26 2030.6,262.08 1752.2,258.86 1331.2,250.46 1302.4,229 1295.1,223.57 1290.9,214.84 1288.5,206.19", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,261 +110,262 @@ digraph { width=2.0943]; "molecular activity to molecular activity association" -> "has evidence" [color=blue, label="has evidence", - lp="1652.9,221.5", - pos="e,1479.4,193.55 2250.3,261.34 2031.3,257.67 1725.5,249.05 1606.4,229 1566,222.2 1521.6,208.38 1489.1,196.99", + lp="1444.9,221.5", + pos="e,1413.8,194.93 2029.8,262.46 1778.3,259.64 1420.2,251.65 1398.4,229 1390,220.25 1395.9,210.18 1405.7,201.37", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1643.4,178", - width=3.015]; + label=string, + pos="1573.4,178", + width=1.0652]; "molecular activity to molecular activity association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1802.9,221.5", - pos="e,1667.9,195.78 2245.5,264.07 2063,261.95 1830.7,254.09 1738.4,229 1716.6,223.09 1694.2,211.61 1676.7,201.13", + lp="1562.9,221.5", + pos="e,1543.3,189.28 2033.1,261.09 1812.2,257.2 1516.9,248.39 1498.4,229 1493.8,224.18 1494.8,219.62 1498.4,214 1502.8,207.12 1518,199.47 \ +1533.6,193.08", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1878.4,178", - width=3.015]; + label=string, + pos="1668.4,178", + width=1.0652]; "molecular activity to molecular activity association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1972.4,221.5", - pos="e,1872.6,196 2263.2,258.23 2094.1,252.82 1891,243.37 1877.4,229 1871.6,222.9 1870.4,214.27 1871,205.9", + lp="1729.4,221.5", + pos="e,1648.1,193.48 2042.6,258.73 1865.3,253.53 1648.7,244.13 1634.4,229 1626.3,220.46 1631.8,209.82 1640.6,200.55", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2113.4,178", - width=3.015]; + label=string, + pos="1810.4,178", + width=1.0652]; "molecular activity to molecular activity association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2180.9,221.5", - pos="e,2087.6,195.53 2265.2,257.9 2174.7,253.08 2088.6,244.44 2074.4,229 2066.7,220.62 2071.6,210.86 2080.1,202.2", + lp="1949.9,221.5", + pos="e,1816.9,195.93 2066.6,255.23 1966.4,249.54 1863.5,240.92 1843.4,229 1834,223.44 1826.8,214.03 1821.5,204.86", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2295.4,178", + pos="2037.4,178", width=1.5346]; "molecular activity to molecular activity association" -> timepoint [color=blue, label=timepoint, - lp="2332.4,221.5", - pos="e,2291.1,196.26 2348.1,250.32 2324.8,245.29 2305.6,238.4 2297.4,229 2292,222.83 2290.3,214.43 2290.3,206.27", + lp="2112.4,221.5", + pos="e,2046.6,196.08 2152.1,249.31 2120.3,243.94 2091.1,237.14 2077.4,229 2067.4,223.06 2058.9,213.63 2052.3,204.55", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2407.4,178", + pos="2149.4,178", width=1.0652]; "molecular activity to molecular activity association" -> "original subject" [color=blue, label="original subject", - lp="2430.4,221.5", - pos="e,2387.4,193.75 2397.2,248.35 2388.3,243.45 2380.5,237.13 2374.4,229 2367.7,220.01 2372.5,209.73 2380.3,200.83", + lp="2214.4,221.5", + pos="e,2148.2,196.23 2184.4,248.16 2174.6,243.34 2165.6,237.09 2158.4,229 2152.9,222.8 2150.2,214.39 2149,206.23", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2521.4,178", + pos="2274.4,178", width=1.5887]; "molecular activity to molecular activity association" -> "original predicate" [color=blue, label="original predicate", - lp="2556.9,221.5", - pos="e,2504.6,195.4 2490.1,246.84 2489.4,236.95 2489.6,224.45 2493.4,214 2494.7,210.42 2496.5,206.94 2498.6,203.64", + lp="2337.9,221.5", + pos="e,2274.4,196.18 2274.4,246.8 2274.4,235.16 2274.4,219.55 2274.4,206.24", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2635.4,178", + pos="2403.4,178", width=1.0652]; "molecular activity to molecular activity association" -> "original object" [color=blue, label="original object", - lp="2681.9,221.5", - pos="e,2634.3,196.46 2591,248.4 2601.8,243.53 2612,237.21 2620.4,229 2626.5,223.04 2630.2,214.69 2632.3,206.52", + lp="2459.9,221.5", + pos="e,2407.8,195.99 2362,248.17 2380.6,243.02 2396.4,236.63 2402.4,229 2407.4,222.62 2408.9,214.26 2408.7,206.21", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2768.4,178", + pos="2536.4,178", width=2.1304]; "molecular activity to molecular activity association" -> "subject category" [color=blue, label="subject category", - lp="2811.9,221.5", - pos="e,2762.2,196.16 2654.2,251.34 2690.2,246.16 2722.2,238.96 2737.4,229 2746.2,223.28 2752.9,214.13 2757.8,205.22", + lp="2586.9,221.5", + pos="e,2533.7,196.01 2441.2,251.7 2473.8,246.56 2502.1,239.29 2515.4,229 2522.8,223.28 2527.6,214.49 2530.7,205.86", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2939.4,178", + pos="2707.4,178", width=2.1304]; "molecular activity to molecular activity association" -> "object category" [color=blue, label="object category", - lp="2956.9,221.5", - pos="e,2923.4,195.77 2669,252.4 2759.8,245.62 2855.5,236.87 2875.4,229 2890.3,223.11 2904.5,212.62 2915.8,202.76", + lp="2728.9,221.5", + pos="e,2693.3,196.01 2451.6,252.45 2539.7,245.8 2631.4,237.18 2650.4,229 2663.9,223.19 2676.4,212.95 2686.3,203.24", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3072.4,178", + pos="2840.4,178", width=1.0652]; "molecular activity to molecular activity association" -> "subject closure" [color=blue, label="subject closure", - lp="3093.9,221.5", - pos="e,3059.6,195.16 2667.9,252.32 2820.1,242.19 3016.1,229.11 3016.4,229 3030.2,223.21 3042.9,212.56 3052.7,202.58", + lp="2864.9,221.5", + pos="e,2828.3,195.63 2449.4,252.26 2598,242.26 2787.4,229.44 2788.4,229 2801.2,223.32 2812.8,213.03 2821.7,203.26", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3172.4,178", + pos="2953.4,178", width=1.0652]; "molecular activity to molecular activity association" -> "object closure" [color=blue, label="object closure", - lp="3214.4,221.5", - pos="e,3170.3,196.32 2664.5,252.06 2692.5,250.26 2721.3,248.5 2748.4,247 2770.8,245.76 3134.1,242.01 3152.4,229 3160,223.63 3164.7,214.92 \ -3167.6,206.26", + lp="2988.4,221.5", + pos="e,2948,196.02 2446.5,252.08 2474.5,250.28 2503.3,248.52 2530.4,247 2574,244.55 2885.9,251.4 2923.4,229 2932.4,223.61 2939.1,214.36 \ +2943.8,205.27", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3305.4,178", + pos="3086.4,178", width=2.1304]; "molecular activity to molecular activity association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3372.9,221.5", - pos="e,3297.7,196.16 2662.8,251.93 2691.3,250.12 2720.7,248.4 2748.4,247 2777.3,245.54 3242.8,242.45 3268.4,229 3278.5,223.67 3286.6,\ -214.17 3292.6,204.87", + lp="3148.9,221.5", + pos="e,3076.5,196.23 2444.8,251.94 2473.3,250.13 2502.7,248.41 2530.4,247 2587.2,244.11 2990.9,253.36 3042.4,229 3053.7,223.64 3063.3,\ +213.87 3070.7,204.38", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3497.4,178", + pos="3279.4,178", width=2.1304]; "molecular activity to molecular activity association" -> "object category closure" [color=blue, label="object category closure", - lp="3563.9,221.5", - pos="e,3491.1,196.15 2661,251.81 2690.2,249.99 2720.1,248.29 2748.4,247 2788.1,245.18 3429.6,248.3 3464.4,229 3473.9,223.7 3481.2,214.34 \ -3486.5,205.14", + lp="3341.9,221.5", + pos="e,3271.1,196.22 2443,251.82 2472.2,249.99 2502.1,248.3 2530.4,247 2569.8,245.19 3205.2,246.76 3240.4,229 3250.8,223.74 3259.3,214.26 \ +3265.7,204.95", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3687.4,178", + pos="3469.4,178", width=1.0652]; "molecular activity to molecular activity association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3736.4,221.5", - pos="e,3680.3,195.72 2660,251.75 2689.4,249.92 2719.8,248.23 2748.4,247 2798.5,244.84 3607,252.32 3651.4,229 3661.6,223.65 3669.6,213.96 \ -3675.4,204.53", + lp="3515.4,221.5", + pos="e,3461.1,195.76 2442,251.75 2471.4,249.92 2501.8,248.23 2530.4,247 2580.3,244.84 3384.6,251.09 3429.4,229 3440.2,223.66 3449.1,213.83 \ +3455.7,204.3", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3846.4,178", + pos="3628.4,178", width=1.0652]; "molecular activity to molecular activity association" -> "object namespace" [color=blue, label="object namespace", - lp="3890.4,221.5", - pos="e,3838.7,195.75 2659.3,251.72 2689,249.88 2719.6,248.2 2748.4,247 2777.8,245.77 3782.1,242.31 3808.4,229 3818.9,223.7 3827.2,214.02 \ -3833.4,204.58", + lp="3669.4,221.5", + pos="e,3619.8,195.79 2441.3,251.72 2471,249.88 2501.6,248.2 2530.4,247 2589.1,244.55 3534.5,254.57 3587.4,229 3598.4,223.69 3607.4,213.87 \ +3614.2,204.33", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3997.4,178", + pos="3779.4,178", width=1.0652]; "molecular activity to molecular activity association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4050.4,221.5", - pos="e,3989.4,195.77 2659,251.69 2688.7,249.85 2719.5,248.17 2748.4,247 2782,245.64 3928.3,243.97 3958.4,229 3969.1,223.67 3977.8,213.85 \ -3984.2,204.31", + lp="3831.4,221.5", + pos="e,3770.5,195.81 2441,251.69 2470.7,249.85 2501.5,248.18 2530.4,247 2563.9,245.64 3707.1,243.39 3737.4,229 3748.5,223.71 3757.8,213.9 \ +3764.7,204.35", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4168.4,178", + pos="3950.4,178", width=1.0652]; "molecular activity to molecular activity association" -> "object label closure" [color=blue, label="object label closure", - lp="4215.9,221.5", - pos="e,4160.1,195.79 2658.6,251.67 2688.5,249.82 2719.4,248.15 2748.4,247 2786.7,245.48 4094,245.83 4128.4,229 4139.3,223.69 4148.1,213.88 \ -4154.7,204.34", + lp="3998.9,221.5", + pos="e,3941.8,195.8 2440.6,251.67 2470.5,249.82 2501.4,248.15 2530.4,247 2568.7,245.48 3874.9,245.61 3909.4,229 3920.4,223.71 3929.4,\ +213.89 3936.2,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4330.4,178", + pos="4112.4,178", width=2.347]; "molecular activity to molecular activity association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4378.9,221.5", - pos="e,4321.5,196.3 2658.3,251.66 2688.2,249.81 2719.2,248.14 2748.4,247 2791.2,245.33 4250.8,247.54 4289.4,229 4300.2,223.79 4309.2,\ -214.18 4315.9,204.76", + lp="4160.9,221.5", + pos="e,4103.8,196.29 2440.3,251.66 2470.2,249.81 2501.2,248.14 2530.4,247 2573.2,245.33 4033.9,247.78 4072.4,229 4083.1,223.78 4091.9,\ +214.16 4098.4,204.75", style=solid]; type [height=0.5, - pos="4464.4,178", + pos="4246.4,178", width=0.86659]; "molecular activity to molecular activity association" -> type [color=blue, label=type, - lp="4478.4,221.5", - pos="e,4465.2,196.18 2658.3,251.63 2688.2,249.78 2719.2,248.12 2748.4,247 2772,246.09 4433.9,243.75 4452.4,229 4459.2,223.54 4462.6,214.92 \ -4464.1,206.37", + lp="4260.4,221.5", + pos="e,4247.2,196.18 2440.3,251.63 2470.2,249.78 2501.2,248.12 2530.4,247 2554,246.09 4215.9,243.75 4234.4,229 4241.2,223.54 4244.6,214.92 \ +4246.1,206.37", style=solid]; category [height=0.5, - pos="4565.4,178", + pos="4347.4,178", width=1.4263]; "molecular activity to molecular activity association" -> category [color=blue, label=category, - lp="4558.9,221.5", - pos="e,4549.8,195.25 2658.3,251.62 2688.2,249.78 2719.2,248.12 2748.4,247 2797,245.14 4452.3,244.55 4498.4,229 4514.6,223.53 4530.1,212.5 \ -4542.1,202.2", + lp="4340.9,221.5", + pos="e,4331.8,195.25 2440.3,251.62 2470.2,249.78 2501.2,248.12 2530.4,247 2579,245.14 4234.3,244.55 4280.4,229 4296.6,223.53 4312.1,212.5 \ +4324.1,202.2", style=solid]; subject [height=0.5, - pos="4679.4,178", + pos="4461.4,178", width=1.2277]; "molecular activity to molecular activity association" -> subject [color=blue, label=subject, - lp="4655.4,221.5", - pos="e,4660.1,194.33 2657.9,251.63 2688,249.78 2719.1,248.11 2748.4,247 2850.9,243.1 4495.6,256.43 4594.4,229 4615.1,223.24 4636,211.08 \ -4651.9,200.2", + lp="4437.4,221.5", + pos="e,4442.1,194.33 2439.9,251.63 2470,249.78 2501.1,248.11 2530.4,247 2632.9,243.1 4277.6,256.43 4376.4,229 4397.1,223.24 4418,211.08 \ +4433.9,200.2", style=solid]; object [height=0.5, - pos="4722.4,91", + pos="4504.4,91", width=1.0832]; "molecular activity to molecular activity association" -> object [color=blue, label=object, - lp="4766.4,178", - pos="e,4735.8,108.09 2657.9,251.62 2688,249.77 2719.1,248.11 2748.4,247 2802.2,244.97 4634.2,245.45 4685.4,229 4709.7,221.2 4718,217.1 \ -4732.4,196 4746.3,175.59 4742.5,166.51 4745.4,142 4746.2,135.38 4747.3,133.39 4745.4,127 4744.4,123.55 4742.9,120.13 4741.1,116.85", + lp="4548.4,178", + pos="e,4517.8,108.09 2439.9,251.62 2470,249.77 2501.1,248.11 2530.4,247 2584.2,244.97 4416.2,245.45 4467.4,229 4491.7,221.2 4500,217.1 \ +4514.4,196 4528.3,175.59 4524.5,166.51 4527.4,142 4528.2,135.38 4529.3,133.39 4527.4,127 4526.4,123.55 4524.9,120.13 4523.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2795.4,265", + pos="2577.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2926.4,265", + pos="2708.4,265", width=2.0762]; subject -> object [label=relation, - lp="4717.4,134.5", - pos="e,4704.5,107.23 4680.5,159.55 4681.7,149.57 4684.2,137.07 4689.4,127 4691.6,122.68 4694.5,118.52 4697.7,114.66"]; + lp="4499.4,134.5", + pos="e,4486.5,107.23 4462.5,159.55 4463.7,149.57 4466.2,137.07 4471.4,127 4473.6,122.68 4476.5,118.52 4479.7,114.66"]; relation [height=0.5, - pos="4667.4,18", + pos="4449.4,18", width=1.2999]; - subject -> relation [pos="e,4668.7,36.188 4678.1,159.79 4676,132.48 4672,78.994 4669.5,46.38", + subject -> relation [pos="e,4450.7,36.188 4460.1,159.79 4458,132.48 4454,78.994 4451.5,46.38", style=dotted]; "molecular activity to molecular activity association_subject" [color=blue, height=0.5, label="molecular activity", - pos="3113.4,265", + pos="2895.4,265", width=2.6178]; - object -> relation [pos="e,4680.2,35.54 4709.9,73.889 4703,64.939 4694.2,53.617 4686.4,43.584", + object -> relation [pos="e,4462.2,35.54 4491.9,73.889 4485,64.939 4476.2,53.617 4468.4,43.584", style=dotted]; "molecular activity to molecular activity association_object" [color=blue, height=0.5, label="molecular activity", - pos="3319.4,265", + pos="3101.4,265", width=2.6178]; } diff --git a/graphviz/molecular_activity_to_molecular_activity_association.svg b/graphviz/molecular_activity_to_molecular_activity_association.svg index 1949412c8e..49a63d1bf6 100644 --- a/graphviz/molecular_activity_to_molecular_activity_association.svg +++ b/graphviz/molecular_activity_to_molecular_activity_association.svg @@ -4,16 +4,16 @@ - + %3 - + molecular activity to molecular activity association - -molecular activity to molecular activity association + +molecular activity to molecular activity association @@ -24,9 +24,9 @@ molecular activity to molecular activity association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ molecular activity to molecular activity association->id - - -id + + +id @@ -50,9 +50,9 @@ molecular activity to molecular activity association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ molecular activity to molecular activity association->name - - -name + + +name @@ -76,9 +76,9 @@ molecular activity to molecular activity association->description - - -description + + +description @@ -89,9 +89,9 @@ molecular activity to molecular activity association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ molecular activity to molecular activity association->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ molecular activity to molecular activity association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ molecular activity to molecular activity association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ molecular activity to molecular activity association->publications - - -publications + + +publications @@ -154,344 +154,344 @@ molecular activity to molecular activity association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string molecular activity to molecular activity association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string molecular activity to molecular activity association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string molecular activity to molecular activity association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type molecular activity to molecular activity association->timepoint - - -timepoint + + +timepoint original subject - -string + +string molecular activity to molecular activity association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie molecular activity to molecular activity association->original predicate - - -original predicate + + +original predicate original object - -string + +string molecular activity to molecular activity association->original object - - -original object + + +original object subject category - -ontology class + +ontology class molecular activity to molecular activity association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class molecular activity to molecular activity association->object category - - -object category + + +object category subject closure - -string + +string molecular activity to molecular activity association->subject closure - - -subject closure + + +subject closure object closure - -string + +string molecular activity to molecular activity association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class molecular activity to molecular activity association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class molecular activity to molecular activity association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string molecular activity to molecular activity association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string molecular activity to molecular activity association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string molecular activity to molecular activity association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string molecular activity to molecular activity association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source molecular activity to molecular activity association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type molecular activity to molecular activity association->type - - -type + + +type category - -category + +category molecular activity to molecular activity association->category - - -category + + +category subject - -subject + +subject molecular activity to molecular activity association->subject - - -subject + + +subject object - -object + +object molecular activity to molecular activity association->object - - -object + + +object association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + molecular activity to molecular activity association_subject - -molecular activity + +molecular activity object->relation - - + + molecular activity to molecular activity association_object - -molecular activity + +molecular activity diff --git a/graphviz/molecular_activity_to_pathway_association.gv b/graphviz/molecular_activity_to_pathway_association.gv index f4e2df3211..9ee195f6ce 100644 --- a/graphviz/molecular_activity_to_pathway_association.gv +++ b/graphviz/molecular_activity_to_pathway_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4748,283"]; + graph [bb="0,0,4563,283"]; node [label="\N"]; "molecular activity to pathway association" [height=0.5, label="molecular activity to pathway association", - pos="2468.4,265", + pos="2283.4,265", width=5.6509]; association [height=0.5, pos="62.394,178", width=1.7332]; "molecular activity to pathway association" -> association [label=is_a, lp="280.39,221.5", - pos="e,102.91,191.79 2265.6,263.37 1758.2,261.43 460.92,254.06 266.39,229 213.1,222.13 153.57,206.61 112.64,194.66"]; + pos="e,102.91,191.77 2080.7,263.05 1604.8,260.44 442.44,251.81 266.39,229 213.11,222.1 153.58,206.57 112.65,194.64"]; id [color=blue, height=0.5, label=string, @@ -18,8 +18,8 @@ digraph { width=1.0652]; "molecular activity to pathway association" -> id [color=blue, label=id, - lp="396.39,221.5", - pos="e,210.38,189.98 2266.3,262.74 1780.2,259.41 572.1,249.2 389.39,229 317.23,221.02 299.34,215.5 229.39,196 226.29,195.13 223.09,194.17 \ + lp="395.39,221.5", + pos="e,210.38,189.98 2081.7,262.4 1627.9,258.49 552.77,247.41 388.39,229 316.67,220.97 298.9,215.43 229.39,196 226.29,195.13 223.09,194.17 \ 219.89,193.15", style=solid]; iri [color=blue, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "molecular activity to pathway association" -> iri [color=blue, label=iri, - lp="509.39,221.5", - pos="e,315.3,190.2 2266.9,262.45 1800.5,258.58 673.05,247.44 501.39,229 426.6,220.97 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ -325.06,193.15", + lp="501.39,221.5", + pos="e,315.32,190.15 2079.8,264.79 1677.7,265.56 794.91,263.13 493.39,229 422.11,220.93 404.75,214.31 335.39,196 332.02,195.11 328.55,\ +194.13 325.07,193.11", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "molecular activity to pathway association" -> name [color=blue, label=name, - lp="616.39,221.5", - pos="e,439.35,191.54 2266.2,262.87 1816,259.96 757.96,250.87 596.39,229 545.26,222.08 488.24,206.51 449.14,194.57", + lp="604.39,221.5", + pos="e,437.98,191.87 2081.6,262.63 1663.3,259.38 728.7,249.87 584.39,229 537.02,222.15 484.46,206.96 447.86,195.11", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "molecular activity to pathway association" -> description [color=blue, label=description, - lp="736.89,221.5", - pos="e,585.45,194.14 2265.6,263.55 1833,262.07 847.02,255.77 696.39,229 661.33,222.77 623.33,209.4 595.03,198.06", + lp="717.89,221.5", + pos="e,581.77,194.62 2080.2,263.6 1678.8,262.21 811.12,256.08 677.39,229 647.36,222.92 615.28,210.09 591.01,198.95", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "molecular activity to pathway association" -> "has attribute" [color=blue, label="has attribute", - lp="882.39,221.5", - pos="e,725.98,192.82 2265.8,263.32 1859.5,261.42 972.23,254.38 835.39,229 800.43,222.52 762.57,208.39 735.2,196.8", + lp="852.39,221.5", + pos="e,721.33,194.01 2080.1,263.74 1703.8,262.6 925.99,256.84 805.39,229 778.89,222.88 751.04,209.98 730.13,198.82", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "molecular activity to pathway association" -> negated [color=blue, label=negated, - lp="1038.4,221.5", - pos="e,847.59,190.46 2264.9,264.29 1922.7,263.9 1245.8,259.17 1009.4,229 956.09,222.2 896.47,205.66 857.14,193.46", + lp="990.39,221.5", + pos="e,843.03,191.96 2082.8,261.99 1740.1,258.06 1068.4,248.04 961.39,229 923.37,222.23 881.85,207.52 852.5,195.8", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "molecular activity to pathway association" -> qualifiers [color=blue, label=qualifiers, - lp="1178.9,221.5", - pos="e,996.68,193.07 2264.9,264.32 1949,263.84 1355.1,258.82 1145.4,229 1097.6,222.2 1044.5,207.74 1006.5,196.11", + lp="1101.9,221.5", + pos="e,982.4,194.93 2082,262.41 1762.1,259.24 1164.1,250.52 1068.4,229 1041.6,222.97 1013.3,210.59 991.57,199.66", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "molecular activity to pathway association" -> publications [color=blue, label=publications, - lp="1326.4,221.5", - pos="e,1148.1,192.71 2265,264.24 1977.1,263.51 1465.4,257.97 1282.4,229 1239.3,222.18 1191.8,207.69 1157.8,196.06", + lp="1202.4,221.5", + pos="e,1121.9,195.78 2083.2,261.73 1771.1,257.62 1199.7,247.62 1158.4,229 1146.3,223.57 1135.9,213.45 1128,203.73", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,275 +100,275 @@ digraph { width=2.0943]; "molecular activity to pathway association" -> "has evidence" [color=blue, label="has evidence", - lp="1480.9,221.5", - pos="e,1305.9,193.61 2265.8,263.31 2011.2,261.36 1588.7,254.27 1434.4,229 1393.5,222.3 1348.6,208.48 1315.7,197.06", + lp="1300.9,221.5", + pos="e,1255.9,195.88 2080.1,264.24 1788.4,263.57 1282.6,258.17 1254.4,229 1248.2,222.63 1248.8,213.73 1251.7,205.2", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1469.4,178", - width=3.015]; + label=string, + pos="1399.4,178", + width=1.0652]; "molecular activity to pathway association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1635.9,221.5", - pos="e,1495.5,195.59 2271,260.63 2027.3,255.79 1637.1,245.59 1571.4,229 1547.9,223.07 1523.5,211.31 1504.4,200.68", + lp="1419.9,221.5", + pos="e,1375.2,192.24 2080.7,263.4 1815.2,261.6 1380.2,254.72 1355.4,229 1345.9,219.09 1354.7,207.6 1366.9,198.13", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1704.4,178", - width=3.015]; + label=string, + pos="1494.4,178", + width=1.0652]; "molecular activity to pathway association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1807.4,221.5", - pos="e,1702.1,196.41 2270.1,260.97 2053.1,256.74 1733,247.41 1712.4,229 1706.1,223.34 1703.4,214.82 1702.5,206.41", + lp="1589.4,221.5", + pos="e,1489,196.04 2082.9,261.93 1855.9,258.58 1514.5,250.05 1494.4,229 1488.6,222.94 1487.2,214.32 1487.7,205.94", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1939.4,178", - width=3.015]; + label=string, + pos="1669.4,178", + width=1.0652]; "molecular activity to pathway association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2015.9,221.5", - pos="e,1918.7,195.97 2279.4,258.27 2122.2,252.55 1922.2,242.65 1909.4,229 1902.4,221.54 1905.6,212.18 1912,203.58", + lp="1809.9,221.5", + pos="e,1676.1,196.02 2085.9,260.62 1931,256.56 1736.4,247.76 1703.4,229 1693.8,223.55 1686.4,214.16 1680.9,204.98", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2121.4,178", + pos="1895.4,178", width=1.5346]; "molecular activity to pathway association" -> timepoint [color=blue, label=timepoint, - lp="2171.4,221.5", - pos="e,2121.9,196.47 2302.4,254.58 2226.4,248.79 2150,240.31 2136.4,229 2129.6,223.41 2125.9,214.91 2123.8,206.49", + lp="1972.4,221.5", + pos="e,1904.8,195.92 2097.7,257.61 2031.4,252.73 1966,244.14 1937.4,229 1926.7,223.32 1917.5,213.63 1910.6,204.28", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2233.4,178", + pos="2007.4,178", width=1.0652]; "molecular activity to pathway association" -> "original subject" [color=blue, label="original subject", - lp="2270.4,221.5", - pos="e,2219.6,194.92 2290.5,256.25 2255.7,250.98 2226.2,242.51 2214.4,229 2208.1,221.83 2209.9,212.39 2214.3,203.65", + lp="2076.4,221.5", + pos="e,2007.3,196.33 2109.5,255.6 2070,250.43 2035.3,242.16 2020.4,229 2013.9,223.25 2010.5,214.72 2008.7,206.31", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2347.4,178", + pos="2133.4,178", width=1.5887]; "molecular activity to pathway association" -> "original predicate" [color=blue, label="original predicate", - lp="2397.9,221.5", - pos="e,2336.3,195.76 2377.3,248.84 2357.5,243.66 2340.6,237.09 2334.4,229 2329.1,222.16 2329.6,213.39 2332.4,205.11", + lp="2207.9,221.5", + pos="e,2132.9,196.42 2192.6,248.81 2171,243.52 2152.1,236.9 2144.4,229 2138.6,222.99 2135.5,214.63 2134,206.47", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2461.4,178", + pos="2267.4,178", width=1.0652]; "molecular activity to pathway association" -> "original object" [color=blue, label="original object", - lp="2516.9,221.5", - pos="e,2462.8,196.18 2467,246.8 2466,235.16 2464.7,219.55 2463.6,206.24", + lp="2327.9,221.5", + pos="e,2270.6,196.18 2280.2,246.8 2278,235.16 2275,219.55 2272.5,206.24", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2594.4,178", + pos="2400.4,178", width=2.1304]; "molecular activity to pathway association" -> "subject category" [color=blue, label="subject category", - lp="2642.9,221.5", - pos="e,2590.6,196.4 2541.5,248.12 2552.7,243.33 2563.5,237.1 2572.4,229 2579.1,222.84 2583.9,214.24 2587.3,205.9", + lp="2452.9,221.5", + pos="e,2398.4,196.3 2354.8,248.12 2365.4,243.33 2375.4,237.1 2383.4,229 2389.5,222.8 2393.5,214.29 2396,206.04", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2765.4,178", + pos="2571.4,178", width=2.1304]; "molecular activity to pathway association" -> "object category" [color=blue, label="object category", - lp="2785.9,221.5", - pos="e,2750.6,195.73 2625.6,253.54 2653.3,248.18 2681.3,240.35 2706.4,229 2720,222.83 2733,212.54 2743.3,202.9", + lp="2593.9,221.5", + pos="e,2557.8,195.72 2439.8,253.49 2466.2,248.1 2492.7,240.28 2516.4,229 2529.3,222.88 2541.3,212.74 2550.8,203.17", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="2898.4,178", + pos="2704.4,178", width=1.0652]; "molecular activity to pathway association" -> "subject closure" [color=blue, label="subject closure", - lp="2921.9,221.5", - pos="e,2886,195.51 2609.3,251.97 2714.1,242.87 2839.8,231.51 2845.4,229 2858.3,223.16 2870.1,212.86 2879.2,203.11", + lp="2728.9,221.5", + pos="e,2692.6,195.5 2429.4,252.45 2528.3,244.25 2642.9,233.87 2653.4,229 2665.9,223.2 2677.1,213.04 2685.8,203.39", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="2998.4,178", + pos="2812.4,178", width=1.0652]; "molecular activity to pathway association" -> "object closure" [color=blue, label="object closure", - lp="3042.4,221.5", - pos="e,2996.9,196.21 2611.6,252.19 2634.9,250.37 2658.8,248.58 2681.4,247 2714.6,244.68 2953.8,248.95 2980.4,229 2987.7,223.52 2992.1,\ -214.77 2994.7,206.12", + lp="2851.4,221.5", + pos="e,2808.5,196.37 2426.9,252.2 2450.1,250.39 2473.9,248.59 2496.4,247 2528.7,244.71 2760.4,246.87 2787.4,229 2795.6,223.57 2801.2,\ +214.61 2805,205.75", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3131.4,178", + pos="2945.4,178", width=2.1304]; "molecular activity to pathway association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3200.9,221.5", - pos="e,3124.4,196.1 2609.6,252.01 2633.5,250.18 2658.2,248.43 2681.4,247 2727.5,244.16 3055.9,251.2 3096.4,229 3106.1,223.65 3113.8,214.28 \ -3119.4,205.08", + lp="3010.9,221.5", + pos="e,2936.7,196.15 2424.6,252.02 2448.5,250.19 2473.2,248.44 2496.4,247 2541.8,244.19 2864.8,249.6 2905.4,229 2916,223.6 2924.8,213.96 \ +2931.3,204.57", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3323.4,178", + pos="3138.4,178", width=2.1304]; "molecular activity to pathway association" -> "object category closure" [color=blue, label="object category closure", - lp="3390.9,221.5", - pos="e,3317.7,196.1 2607.8,251.86 2632.3,250.02 2657.6,248.3 2681.4,247 2715.3,245.15 3263,245.95 3292.4,229 3301.6,223.7 3308.4,214.47 \ -3313.3,205.37", + lp="3202.9,221.5", + pos="e,3131.1,196.17 2422.8,251.87 2447.3,250.02 2472.6,248.3 2496.4,247 2530,245.16 3072.6,244.8 3102.4,229 3112.4,223.68 3120.3,214.18 \ +3126.1,204.88", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3513.4,178", + pos="3328.4,178", width=1.0652]; "molecular activity to pathway association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3563.4,221.5", - pos="e,3506.4,196.18 2607,251.79 2631.7,249.93 2657.3,248.23 2681.4,247 2725.6,244.74 3439.3,249.9 3478.4,229 3488.2,223.75 3495.9,214.4 \ -3501.5,205.19", + lp="3375.4,221.5", + pos="e,3320.7,195.73 2422,251.79 2446.7,249.94 2472.3,248.23 2496.4,247 2540.5,244.74 3251.1,249.05 3290.4,229 3300.8,223.67 3309.2,213.98 \ +3315.4,204.55", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3672.4,178", + pos="3487.4,178", width=1.0652]; "molecular activity to pathway association" -> "object namespace" [color=blue, label="object namespace", - lp="3716.4,221.5", - pos="e,3665,195.73 2606.4,251.76 2631.3,249.89 2657.1,248.2 2681.4,247 2734.3,244.39 3588.3,253.3 3635.4,229 3645.7,223.67 3653.9,213.99 \ -3659.9,204.55", + lp="3529.4,221.5", + pos="e,3479.1,195.77 2421.4,251.76 2446.3,249.89 2472.1,248.2 2496.4,247 2549.2,244.4 3400,252.34 3447.4,229 3458.2,223.66 3467.1,213.84 \ +3473.7,204.31", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3823.4,178", + pos="3638.4,178", width=1.0652]; "molecular activity to pathway association" -> "subject label closure" [color=blue, label="subject label closure", - lp="3876.4,221.5", - pos="e,3815.4,195.77 2606.1,251.73 2631.1,249.86 2657,248.17 2681.4,247 2712,245.53 3757,242.67 3784.4,229 3795.1,223.66 3803.8,213.84 \ -3810.2,204.3", + lp="3689.4,221.5", + pos="e,3629.8,195.79 2421.1,251.73 2446.1,249.86 2472,248.17 2496.4,247 2526.9,245.53 3569.9,242.31 3597.4,229 3608.4,223.69 3617.4,213.87 \ +3624.2,204.33", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="3994.4,178", + pos="3809.4,178", width=1.0652]; "molecular activity to pathway association" -> "object label closure" [color=blue, label="object label closure", - lp="4041.9,221.5", - pos="e,3986.1,195.79 2605.8,251.7 2630.9,249.83 2656.9,248.15 2681.4,247 2716.7,245.34 3922.6,244.54 3954.4,229 3965.3,223.69 3974.1,\ -213.87 3980.7,204.33", + lp="3856.9,221.5", + pos="e,3800.5,195.81 2420.8,251.7 2445.9,249.83 2471.9,248.15 2496.4,247 2531.7,245.34 3735.5,244.14 3767.4,229 3778.5,223.72 3787.8,\ +213.9 3794.7,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4147.4,178", + pos="3962.4,178", width=2.347]; "molecular activity to pathway association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4200.9,221.5", - pos="e,4141.4,196.18 2605.5,251.69 2630.7,249.82 2656.8,248.13 2681.4,247 2721.2,245.16 4080.6,248.34 4115.4,229 4124.9,223.75 4131.9,\ -214.39 4137,205.18", + lp="4015.9,221.5", + pos="e,3956.4,196.18 2420.5,251.69 2445.7,249.82 2471.8,248.13 2496.4,247 2536.2,245.16 3895.6,248.34 3930.4,229 3939.9,223.75 3946.9,\ +214.39 3952,205.18", style=solid]; type [height=0.5, - pos="4281.4,178", + pos="4096.4,178", width=0.86659]; "molecular activity to pathway association" -> type [color=blue, label=type, - lp="4299.4,221.5", - pos="e,4284.1,195.98 2605.5,251.67 2630.7,249.79 2656.8,248.12 2681.4,247 2703.5,245.99 4257.8,243.61 4274.4,229 4280.9,223.32 4283.4,\ -214.65 4284.1,206.12", + lp="4114.4,221.5", + pos="e,4099.1,195.98 2420.5,251.67 2445.7,249.79 2471.8,248.12 2496.4,247 2518.5,245.99 4072.8,243.61 4089.4,229 4095.9,223.32 4098.4,\ +214.65 4099.1,206.12", style=solid]; category [height=0.5, - pos="4382.4,178", + pos="4197.4,178", width=1.4263]; "molecular activity to pathway association" -> category [color=blue, label=category, - lp="4377.9,221.5", - pos="e,4367.7,195.48 2605.5,251.66 2630.7,249.79 2656.8,248.11 2681.4,247 2726.9,244.94 4276.5,244.21 4319.4,229 4334.6,223.59 4349,212.83 \ -4360.1,202.68", + lp="4192.9,221.5", + pos="e,4182.7,195.48 2420.5,251.66 2445.7,249.79 2471.8,248.11 2496.4,247 2541.9,244.94 4091.5,244.21 4134.4,229 4149.6,223.59 4164,212.83 \ +4175.1,202.68", style=solid]; subject [height=0.5, - pos="4496.4,178", + pos="4311.4,178", width=1.2277]; "molecular activity to pathway association" -> subject [color=blue, label=subject, - lp="4473.4,221.5", - pos="e,4477.7,194.32 2605.2,251.67 2630.5,249.79 2656.8,248.11 2681.4,247 2777.5,242.67 4320.8,255.25 4413.4,229 4433.6,223.28 4453.7,\ -211.29 4469.2,200.49", + lp="4288.4,221.5", + pos="e,4292.7,194.32 2420.2,251.67 2445.5,249.79 2471.8,248.11 2496.4,247 2592.5,242.67 4135.8,255.25 4228.4,229 4248.6,223.28 4268.7,\ +211.29 4284.2,200.49", style=solid]; object [height=0.5, - pos="4539.4,91", + pos="4354.4,91", width=1.0832]; "molecular activity to pathway association" -> object [color=blue, label=object, - lp="4583.4,178", - pos="e,4552.8,108.09 2605.2,251.66 2630.5,249.78 2656.7,248.1 2681.4,247 2732,244.74 4455.3,244.73 4503.4,229 4527.3,221.18 4535.3,216.87 \ -4549.4,196 4563.2,175.52 4559.5,166.51 4562.4,142 4563.2,135.38 4564.3,133.39 4562.4,127 4561.4,123.55 4559.9,120.13 4558.1,116.85", + lp="4398.4,178", + pos="e,4367.8,108.09 2420.2,251.66 2445.5,249.78 2471.7,248.1 2496.4,247 2547,244.74 4270.3,244.73 4318.4,229 4342.3,221.18 4350.3,216.87 \ +4364.4,196 4378.2,175.52 4374.5,166.51 4377.4,142 4378.2,135.38 4379.3,133.39 4377.4,127 4376.4,123.55 4374.9,120.13 4373.1,116.85", style=solid]; predicate [height=0.5, - pos="4693.4,178", + pos="4508.4,178", width=1.5165]; "molecular activity to pathway association" -> predicate [color=blue, label=predicate, - lp="4666.4,221.5", - pos="e,4669.6,194.35 2605.2,251.65 2630.5,249.77 2656.7,248.1 2681.4,247 2787.3,242.28 4487.1,253.25 4590.4,229 4615.3,223.15 4641.2,\ -210.56 4660.8,199.47", + lp="4480.4,221.5", + pos="e,4484.6,194.35 2420.2,251.65 2445.5,249.77 2471.7,248.1 2496.4,247 2602.3,242.28 4302.1,253.25 4405.4,229 4430.3,223.15 4456.2,\ +210.56 4475.8,199.47", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2728.4,265", + pos="2543.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2859.4,265", + pos="2674.4,265", width=2.0762]; subject -> object [label=relation, - lp="4534.4,134.5", - pos="e,4521.5,107.23 4497.5,159.55 4498.7,149.57 4501.2,137.07 4506.4,127 4508.6,122.68 4511.5,118.52 4514.7,114.66"]; + lp="4349.4,134.5", + pos="e,4336.5,107.23 4312.5,159.55 4313.7,149.57 4316.2,137.07 4321.4,127 4323.6,122.68 4326.5,118.52 4329.7,114.66"]; relation [height=0.5, - pos="4484.4,18", + pos="4299.4,18", width=1.2999]; - subject -> relation [pos="e,4485.7,36.188 4495.1,159.79 4493,132.48 4489,78.994 4486.5,46.38", + subject -> relation [pos="e,4300.7,36.188 4310.1,159.79 4308,132.48 4304,78.994 4301.5,46.38", style=dotted]; "molecular activity to pathway association_subject" [color=blue, height=0.5, label="molecular activity", - pos="3046.4,265", + pos="2861.4,265", width=2.6178]; - object -> relation [pos="e,4497.2,35.54 4526.9,73.889 4520,64.939 4511.2,53.617 4503.4,43.584", + object -> relation [pos="e,4312.2,35.54 4341.9,73.889 4335,64.939 4326.2,53.617 4318.4,43.584", style=dotted]; "molecular activity to pathway association_object" [color=blue, height=0.5, label=pathway, - pos="3208.4,265", + pos="3023.4,265", width=1.3902]; "molecular activity to pathway association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3354.4,265", + pos="3169.4,265", width=2.1665]; } diff --git a/graphviz/molecular_activity_to_pathway_association.svg b/graphviz/molecular_activity_to_pathway_association.svg index b426010864..179daa95e2 100644 --- a/graphviz/molecular_activity_to_pathway_association.svg +++ b/graphviz/molecular_activity_to_pathway_association.svg @@ -4,16 +4,16 @@ - + %3 - + molecular activity to pathway association - -molecular activity to pathway association + +molecular activity to pathway association @@ -24,8 +24,8 @@ molecular activity to pathway association->association - - + + is_a @@ -37,9 +37,9 @@ molecular activity to pathway association->id - - -id + + +id @@ -50,9 +50,9 @@ molecular activity to pathway association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ molecular activity to pathway association->name - - -name + + +name @@ -76,9 +76,9 @@ molecular activity to pathway association->description - - -description + + +description @@ -89,9 +89,9 @@ molecular activity to pathway association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ molecular activity to pathway association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ molecular activity to pathway association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ molecular activity to pathway association->publications - - -publications + + +publications @@ -141,363 +141,363 @@ molecular activity to pathway association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string molecular activity to pathway association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string molecular activity to pathway association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string molecular activity to pathway association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type molecular activity to pathway association->timepoint - - -timepoint + + +timepoint original subject - -string + +string molecular activity to pathway association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie molecular activity to pathway association->original predicate - - -original predicate + + +original predicate original object - -string + +string molecular activity to pathway association->original object - - -original object + + +original object subject category - -ontology class + +ontology class molecular activity to pathway association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class molecular activity to pathway association->object category - - -object category + + +object category subject closure - -string + +string molecular activity to pathway association->subject closure - - -subject closure + + +subject closure object closure - -string + +string molecular activity to pathway association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class molecular activity to pathway association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class molecular activity to pathway association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string molecular activity to pathway association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string molecular activity to pathway association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string molecular activity to pathway association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string molecular activity to pathway association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source molecular activity to pathway association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type molecular activity to pathway association->type - - -type + + +type category - -category + +category molecular activity to pathway association->category - - -category + + +category subject - -subject + +subject molecular activity to pathway association->subject - - -subject + + +subject object - -object + +object molecular activity to pathway association->object - - -object + + +object predicate - -predicate + +predicate molecular activity to pathway association->predicate - - -predicate + + +predicate association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + molecular activity to pathway association_subject - -molecular activity + +molecular activity object->relation - - + + molecular activity to pathway association_object - -pathway + +pathway molecular activity to pathway association_predicate - -predicate type + +predicate type diff --git a/graphviz/named_thing_associated_with_likelihood_of_named_thing_association.gv b/graphviz/named_thing_associated_with_likelihood_of_named_thing_association.gv index 9a67d67f2e..946c19aabc 100644 --- a/graphviz/named_thing_associated_with_likelihood_of_named_thing_association.gv +++ b/graphviz/named_thing_associated_with_likelihood_of_named_thing_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,5810.7,283"]; + graph [bb="0,0,5592.7,283"]; node [label="\N"]; "named thing associated with likelihood of named thing association" [height=0.5, label="named thing associated with likelihood of named thing association", - pos="2706.4,265", + pos="2488.4,265", width=8.8825]; association [height=0.5, pos="62.394,178", width=1.7332]; "named thing associated with likelihood of named thing association" -> association [label=is_a, lp="279.39,221.5", - pos="e,102.71,191.81 2387.7,263.46 1773.9,261.84 469.9,255.3 265.39,229 212.35,222.18 153.11,206.64 112.39,194.69"]; + pos="e,102.71,191.79 2170.5,262.97 1600.9,260.52 448.6,252.69 265.39,229 212.35,222.14 153.12,206.61 112.39,194.67"]; id [color=blue, height=0.5, label=string, @@ -19,7 +19,7 @@ digraph { "named thing associated with likelihood of named thing association" -> id [color=blue, label=id, lp="394.39,221.5", - pos="e,210.38,189.97 2389.3,262.58 1800.5,259.44 580.49,250.42 387.39,229 316.09,221.09 298.47,215.35 229.39,196 226.29,195.13 223.09,\ + pos="e,210.38,189.97 2172.8,262.04 1629.6,258.17 559.29,248.21 387.39,229 316.1,221.03 298.47,215.35 229.39,196 226.29,195.13 223.09,\ 194.16 219.89,193.14", style=solid]; iri [color=blue, @@ -30,7 +30,7 @@ digraph { "named thing associated with likelihood of named thing association" -> iri [color=blue, label=iri, lp="490.39,221.5", - pos="e,315.53,190.04 2389.2,262.61 1819.8,259.58 666.01,250.82 482.39,229 427.19,222.44 365.34,205.43 325.24,193.07", + pos="e,315.53,190.02 2172.9,262.02 1649.9,258.21 644.89,248.45 482.39,229 427.19,222.39 365.34,205.39 325.24,193.05", style=solid]; name [color=blue, height=0.5, @@ -40,7 +40,7 @@ digraph { "named thing associated with likelihood of named thing association" -> name [color=blue, label=name, lp="586.39,221.5", - pos="e,435.51,192.39 2387.2,263.66 1834.4,262.35 740.71,256.29 566.39,229 524.32,222.41 478.05,207.7 445.24,195.93", + pos="e,435.51,192.37 2170.5,263 1665.2,260.68 719.72,253.15 566.39,229 524.33,222.37 478.05,207.67 445.24,195.91", style=solid]; description [color=blue, height=0.5, @@ -50,7 +50,7 @@ digraph { "named thing associated with likelihood of named thing association" -> description [color=blue, label=description, lp="689.89,221.5", - pos="e,575.53,195.27 2390,262.36 1833.9,258.94 732.04,249.61 649.39,229 626.41,223.27 602.69,211.35 584.34,200.59", + pos="e,575.54,195.25 2173.9,261.68 1667.8,257.43 721.73,247.12 649.39,229 626.41,223.24 602.69,211.33 584.35,200.57", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,7 +60,7 @@ digraph { "named thing associated with likelihood of named thing association" -> "has attribute" [color=blue, label="has attribute", lp="808.39,221.5", - pos="e,711.72,195.45 2387.7,263.47 1855.5,261.85 836.5,255.3 761.39,229 745.67,223.49 730.74,212.58 719.17,202.35", + pos="e,711.73,195.43 2170.9,262.68 1690.2,259.95 826.47,251.87 761.39,229 745.68,223.48 730.75,212.56 719.17,202.33", style=solid]; subject [color=blue, height=0.5, @@ -70,7 +70,7 @@ digraph { "named thing associated with likelihood of named thing association" -> subject [color=blue, label=subject, lp="902.39,221.5", - pos="e,844.99,196.26 2386.4,264.9 1879.6,265.33 942.71,261.66 876.39,229 865.7,223.74 856.95,214.11 850.39,204.71", + pos="e,845,196.25 2169,263.97 1715.5,262.93 933.18,257.05 876.39,229 865.71,223.72 856.96,214.1 850.4,204.69", style=solid]; object [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { "named thing associated with likelihood of named thing association" -> object [color=blue, label=object, lp="973.39,178", - pos="e,931.68,109.09 2392,261.63 2012.4,257.93 1396.4,249.01 1167.4,229 1070.6,220.55 1020.4,264.31 951.39,196 931.43,176.25 929.3,142.79 \ -930.79,119.17", + pos="e,931.78,108.99 2174.1,261.63 1837,258.07 1324.1,249.42 1129.4,229 1049.4,220.6 1007.7,253.5 951.39,196 931.75,175.93 929.55,142.54 \ +930.94,119.02", style=solid]; negated [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.2999]; "named thing associated with likelihood of named thing association" -> negated [color=blue, label=negated, - lp="1276.4,221.5", - pos="e,1085.6,190.46 2387,264 2025.5,262.65 1459.4,256.06 1247.4,229 1194.1,222.2 1134.5,205.66 1095.1,193.46", + lp="1215.4,221.5", + pos="e,1079.6,192.54 2176.7,260.96 1822.3,256.65 1280.6,247.2 1186.4,229 1152.3,222.41 1115.4,208.25 1088.9,196.67", style=solid]; qualifiers [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=2.1304]; "named thing associated with likelihood of named thing association" -> qualifiers [color=blue, label=qualifiers, - lp="1416.9,221.5", - pos="e,1234.7,193.07 2387,263.96 2058.6,262.4 1569.6,255.47 1383.4,229 1335.6,222.2 1282.5,207.74 1244.5,196.11", + lp="1318.9,221.5", + pos="e,1215.6,195.42 2172,262.31 1844.3,259.36 1368.7,251.26 1285.4,229 1263.7,223.2 1241.4,211.48 1224.1,200.85", style=solid]; publications [color=blue, height=0.5, @@ -110,8 +110,8 @@ digraph { width=1.7332]; "named thing associated with likelihood of named thing association" -> publications [color=blue, label=publications, - lp="1564.4,221.5", - pos="e,1386.1,192.71 2387.3,263.72 2093.9,261.79 1680.9,254.4 1520.4,229 1477.3,222.18 1429.8,207.69 1395.8,196.06", + lp="1410.4,221.5", + pos="e,1350.4,196.28 2170.6,262.9 1850.3,260.45 1398.5,252.78 1366.4,229 1359.1,223.59 1354.9,214.87 1352.5,206.21", style=solid]; "has evidence" [color=blue, height=0.5, @@ -120,257 +120,258 @@ digraph { width=2.0943]; "named thing associated with likelihood of named thing association" -> "has evidence" [color=blue, label="has evidence", - lp="1718.9,221.5", - pos="e,1543.9,193.61 2390.4,262.18 2138,259.06 1805.4,250.8 1672.4,229 1631.5,222.3 1586.6,208.48 1553.7,197.06", + lp="1508.9,221.5", + pos="e,1477.8,194.95 2169.4,263.71 1877.4,261.82 1487,254.49 1462.4,229 1454,220.27 1459.9,210.2 1469.7,201.4", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1707.4,178", - width=3.015]; + label=string, + pos="1637.4,178", + width=1.0652]; "named thing associated with likelihood of named thing association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1873.9,221.5", - pos="e,1733.5,195.59 2408,258.48 2169.8,253.04 1866.6,243.44 1809.4,229 1785.9,223.07 1761.5,211.31 1742.4,200.68", + lp="1626.9,221.5", + pos="e,1607.3,189.28 2171.9,262.35 1912.2,259.38 1583.8,251.23 1562.4,229 1557.8,224.2 1558.8,219.62 1562.4,214 1566.8,207.12 1582,199.47 \ +1597.6,193.08", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1942.4,178", - width=3.015]; + label=string, + pos="1732.4,178", + width=1.0652]; "named thing associated with likelihood of named thing association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2045.4,221.5", - pos="e,1940.1,196.41 2406.4,258.75 2203,253.78 1968,244.69 1950.4,229 1944.1,223.34 1941.4,214.82 1940.5,206.41", + lp="1793.4,221.5", + pos="e,1712,193.51 2180.5,260.09 1966.1,255.8 1715.6,246.96 1698.4,229 1690.3,220.5 1695.8,209.86 1704.5,200.59", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2177.4,178", - width=3.015]; + label=string, + pos="1874.4,178", + width=1.0652]; "named thing associated with likelihood of named thing association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2253.9,221.5", - pos="e,2156.7,195.97 2438.5,255.16 2300.3,249.24 2158.1,240.44 2147.4,229 2140.4,221.54 2143.6,212.18 2150,203.58", + lp="2013.9,221.5", + pos="e,1880.8,196.01 2195.4,257.79 2064.6,252.91 1933.8,244.26 1907.4,229 1897.9,223.54 1890.7,214.14 1885.4,204.96", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2359.4,178", + pos="2101.4,178", width=1.5346]; "named thing associated with likelihood of named thing association" -> timepoint [color=blue, label=timepoint, - lp="2409.4,221.5", - pos="e,2359.9,196.47 2500.1,251.23 2439.2,245.68 2385.6,238.29 2374.4,229 2367.6,223.41 2363.9,214.91 2361.8,206.49", + lp="2176.4,221.5", + pos="e,2110.2,195.91 2248,253.09 2202.2,247.89 2162.1,240.25 2141.4,229 2131,223.36 2122.4,213.81 2115.8,204.56", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2471.4,178", + pos="2213.4,178", width=1.0652]; "named thing associated with likelihood of named thing association" -> "original subject" [color=blue, label="original subject", - lp="2508.4,221.5", - pos="e,2457.6,194.92 2501.4,251.17 2478.9,245.97 2460.9,238.82 2452.4,229 2446.1,221.83 2447.9,212.39 2452.3,203.65", + lp="2279.4,221.5", + pos="e,2212.1,196.24 2281.2,251.23 2255.2,246.07 2234,238.91 2223.4,229 2217.2,223.22 2214.3,214.78 2213,206.47", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2585.4,178", + pos="2338.4,178", width=1.5887]; "named thing associated with likelihood of named thing association" -> "original predicate" [color=blue, label="original predicate", - lp="2635.9,221.5", - pos="e,2574.3,195.76 2611.1,247.72 2593.2,242.73 2578.2,236.52 2572.4,229 2567.1,222.16 2567.6,213.39 2570.4,205.11", + lp="2409.9,221.5", + pos="e,2336.7,196.34 2389.4,247.81 2369.9,242.77 2353.3,236.52 2346.4,229 2340.8,222.91 2338.2,214.52 2337.2,206.36", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2699.4,178", + pos="2467.4,178", width=1.0652]; "named thing associated with likelihood of named thing association" -> "original object" [color=blue, label="original object", - lp="2754.9,221.5", - pos="e,2700.8,196.18 2705,246.8 2704,235.16 2702.7,219.55 2701.6,206.24", + lp="2530.9,221.5", + pos="e,2471.6,196.18 2484.1,246.8 2481.3,235.16 2477.4,219.55 2474.1,206.24", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2832.4,178", + pos="2600.4,178", width=2.1304]; "named thing associated with likelihood of named thing association" -> "subject category" [color=blue, label="subject category", - lp="2880.9,221.5", - pos="e,2828.6,196.4 2781.1,247.43 2791.8,242.73 2802,236.71 2810.4,229 2817.1,222.84 2821.9,214.24 2825.3,205.9", + lp="2654.9,221.5", + pos="e,2599.5,196.22 2560.8,247.33 2570.3,242.65 2579.2,236.66 2586.4,229 2592.2,222.79 2595.6,214.38 2597.6,206.22", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3003.4,178", + pos="2771.4,178", width=2.1304]; "named thing associated with likelihood of named thing association" -> "object category" [color=blue, label="object category", - lp="3023.9,221.5", - pos="e,2988.6,195.73 2880.9,249.86 2902.8,244.76 2924.5,237.99 2944.4,229 2958,222.83 2971,212.54 2981.3,202.9", + lp="2795.9,221.5", + pos="e,2758,196.2 2632.8,248.94 2669,243.62 2702.1,236.94 2718.4,229 2730.7,223.02 2742,213.21 2751,203.86", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3136.4,178", + pos="2904.4,178", width=1.0652]; "named thing associated with likelihood of named thing association" -> "subject closure" [color=blue, label="subject closure", - lp="3159.9,221.5", - pos="e,3124,195.51 2952.2,253.41 3007.8,248.23 3057.9,240.5 3083.4,229 3096.3,223.16 3108.1,212.86 3117.2,203.11", + lp="2930.9,221.5", + pos="e,2893.2,195.49 2731.8,253.33 2784.4,248.14 2831.4,240.44 2855.4,229 2867.6,223.19 2878.4,213.03 2886.7,203.37", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3236.4,178", + pos="3017.4,178", width=1.0652]; "named thing associated with likelihood of named thing association" -> "object closure" [color=blue, label="object closure", - lp="3280.4,221.5", - pos="e,3234.9,196.19 2923.8,251.78 3060.4,243.67 3212.2,233.69 3218.4,229 3225.7,223.49 3230,214.74 3232.6,206.09", + lp="3053.4,221.5", + pos="e,3012.6,195.9 2720.7,252.62 2845.9,245.66 2977.3,236.66 2989.4,229 2998,223.52 3004.2,214.38 3008.6,205.4", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3369.4,178", + pos="3150.4,178", width=2.1304]; "named thing associated with likelihood of named thing association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3437.9,221.5", - pos="e,3362.3,196.05 2929.8,252.11 3109.3,242.46 3332.1,230.27 3334.4,229 3344.1,223.59 3351.8,214.21 3357.4,205.02", + lp="3213.9,221.5", + pos="e,3140.8,196.12 2714.4,252.23 2889.4,242.96 3102.9,231.24 3107.4,229 3118.4,223.57 3127.7,213.92 3134.9,204.54", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3561.4,178", + pos="3343.4,178", width=2.1304]; "named thing associated with likelihood of named thing association" -> "object category closure" [color=blue, label="object category closure", - lp="3628.9,221.5", - pos="e,3555.4,196.09 2928.9,252.04 2964.5,250.26 3001,248.52 3035.4,247 3062.8,245.79 3505.5,242.62 3529.4,229 3538.8,223.63 3545.9,214.26 \ -3550.9,205.06", + lp="3405.9,221.5", + pos="e,3335.4,196.16 2710.9,252.06 2746.5,250.27 2783,248.52 2817.4,247 2871.6,244.6 3257.2,254 3305.4,229 3315.7,223.67 3323.9,214.17 \ +3330.1,204.87", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3751.4,178", + pos="3533.4,178", width=1.0652]; "named thing associated with likelihood of named thing association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3801.4,221.5", - pos="e,3744.4,196.17 2925.8,251.89 2962.4,250.09 3000,248.38 3035.4,247 3073.2,245.52 3683.1,246.92 3716.4,229 3726.2,223.73 3733.8,214.37 \ -3739.5,205.17", + lp="3579.4,221.5", + pos="e,3525.1,195.73 2707.8,251.9 2744.4,250.1 2782,248.39 2817.4,247 2854.9,245.53 3459.8,245.72 3493.4,229 3504.2,223.62 3513.1,213.79 \ +3519.7,204.26", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3910.4,178", + pos="3692.4,178", width=1.0652]; "named thing associated with likelihood of named thing association" -> "object namespace" [color=blue, label="object namespace", - lp="3954.4,221.5", - pos="e,3903,195.72 2924.5,251.81 2961.5,250 2999.5,248.31 3035.4,247 3081.9,245.3 3832,250.4 3873.4,229 3883.7,223.66 3891.9,213.97 3897.9,\ -204.54", + lp="3733.4,221.5", + pos="e,3683.8,195.77 2706.5,251.81 2743.5,250 2781.5,248.31 2817.4,247 2863.7,245.3 3609.7,249.27 3651.4,229 3662.4,223.66 3671.4,213.84 \ +3678.2,204.3", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4061.4,178", + pos="3843.4,178", width=1.0652]; "named thing associated with likelihood of named thing association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4114.4,221.5", - pos="e,4053.4,195.76 2923.6,251.75 2960.9,249.94 2999.2,248.26 3035.4,247 3090.2,245.08 3973.3,253.51 4022.4,229 4033.1,223.65 4041.7,\ -213.83 4048.2,204.29", + lp="3894.4,221.5", + pos="e,3834.5,195.79 2705.6,251.75 2742.9,249.94 2781.2,248.26 2817.4,247 2872,245.09 3752,252.55 3801.4,229 3812.5,223.69 3821.8,213.87 \ +3828.7,204.34", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4232.4,178", + pos="4014.4,178", width=1.0652]; "named thing associated with likelihood of named thing association" -> "object label closure" [color=blue, label="object label closure", - lp="4279.9,221.5", - pos="e,4224.1,195.78 2922.7,251.71 2960.3,249.89 2999,248.22 3035.4,247 3067.5,245.92 4163.5,243.15 4192.4,229 4203.2,223.68 4212.1,213.86 \ -4218.7,204.32", + lp="4061.9,221.5", + pos="e,4005.5,195.8 2704.7,251.71 2742.3,249.89 2781,248.23 2817.4,247 2849.5,245.92 3943.4,242.78 3972.4,229 3983.5,223.71 3992.8,213.89 \ +3999.7,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4376.4,178", + pos="4158.4,178", width=2.347]; "named thing associated with likelihood of named thing association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4435.9,221.5", - pos="e,4373.4,196 2921.8,251.69 2959.7,249.87 2998.7,248.2 3035.4,247 3072,245.81 4322.7,248.96 4353.4,229 4361.5,223.7 4366.8,214.72 \ -4370.3,205.82", + lp="4217.9,221.5", + pos="e,4155.4,196 2703.8,251.69 2741.7,249.87 2780.7,248.2 2817.4,247 2854,245.81 4104.7,248.96 4135.4,229 4143.5,223.7 4148.8,214.72 \ +4152.3,205.82", style=solid]; type [height=0.5, - pos="4510.4,178", + pos="4292.4,178", width=0.86659]; "named thing associated with likelihood of named thing association" -> type [color=blue, label=type, - lp="4532.4,221.5", - pos="e,4515.5,196.18 2921.4,251.67 2959.3,249.84 2998.5,248.18 3035.4,247 3055.9,246.35 4494.9,243.42 4509.4,229 4515.4,223.09 4517,214.51 \ -4516.6,206.12", + lp="4314.4,221.5", + pos="e,4297.5,196.18 2703.4,251.67 2741.3,249.84 2780.5,248.18 2817.4,247 2837.9,246.35 4276.9,243.42 4291.4,229 4297.4,223.09 4299,214.51 \ +4298.6,206.12", style=solid]; category [height=0.5, - pos="4611.4,178", + pos="4393.4,178", width=1.4263]; "named thing associated with likelihood of named thing association" -> category [color=blue, label=category, - lp="4609.9,221.5", - pos="e,4597.8,195.45 2921.4,251.66 2959.3,249.83 2998.5,248.17 3035.4,247 3077.5,245.66 4512.9,243.74 4552.4,229 4567,223.56 4580.4,212.8 \ -4590.8,202.65", + lp="4391.9,221.5", + pos="e,4379.8,195.45 2703.4,251.66 2741.3,249.83 2780.5,248.17 2817.4,247 2859.5,245.66 4294.9,243.74 4334.4,229 4349,223.56 4362.4,212.8 \ +4372.8,202.65", style=solid]; predicate [height=0.5, - pos="4735.4,178", + pos="4517.4,178", width=1.5165]; "named thing associated with likelihood of named thing association" -> predicate [color=blue, label=predicate, - lp="4716.4,221.5", - pos="e,4714.2,194.81 2921.4,251.64 2959.3,249.81 2998.5,248.16 3035.4,247 3124.8,244.19 4558.9,251.92 4645.4,229 4666.8,223.32 4688.6,\ -211.41 4705.4,200.63", + lp="4498.4,221.5", + pos="e,4496.2,194.81 2703.4,251.64 2741.3,249.81 2780.5,248.16 2817.4,247 2906.8,244.19 4340.9,251.92 4427.4,229 4448.8,223.32 4470.6,\ +211.41 4487.4,200.63", style=solid]; "subject aspect qualifier" [height=0.5, - pos="4927.4,178", + pos="4709.4,178", width=3.3039]; "named thing associated with likelihood of named thing association" -> "subject aspect qualifier" [color=blue, label="subject aspect qualifier", - lp="4905.9,221.5", - pos="e,4884.7,194.84 2920.9,251.64 2959,249.81 2998.4,248.15 3035.4,247 3226.3,241.07 4565.4,256.77 4754.4,229 4795.8,222.92 4841.2,209.54 \ -4875.1,198.15", + lp="4687.9,221.5", + pos="e,4666.7,194.84 2702.9,251.64 2741,249.81 2780.4,248.15 2817.4,247 3008.3,241.07 4347.4,256.77 4536.4,229 4577.8,222.92 4623.2,209.54 \ +4657.1,198.15", style=solid]; "subject context qualifier" [height=0.5, - pos="5187.4,178", + pos="4969.4,178", width=3.4303]; "named thing associated with likelihood of named thing association" -> "subject context qualifier" [color=blue, label="subject context qualifier", - lp="5156.4,221.5", - pos="e,5139.8,194.73 2920.5,251.62 2958.7,249.78 2998.2,248.13 3035.4,247 3252.9,240.39 4777.7,257.36 4993.4,229 5040.1,222.86 5091.7,\ -209.23 5129.9,197.75", + lp="4938.4,221.5", + pos="e,4921.8,194.73 2702.5,251.62 2740.7,249.78 2780.2,248.13 2817.4,247 3034.9,240.39 4559.7,257.36 4775.4,229 4822.1,222.86 4873.7,\ +209.23 4911.9,197.75", style=solid]; "object aspect qualifier" [height=0.5, - pos="5442.4,178", + pos="5224.4,178", width=3.1594]; "named thing associated with likelihood of named thing association" -> "object aspect qualifier" [color=blue, label="object aspect qualifier", - lp="5402.9,221.5", - pos="e,5395.3,194.5 2920.5,251.59 2958.7,249.75 2998.2,248.11 3035.4,247 3158.2,243.33 5125.5,244.88 5247.4,229 5294.6,222.84 5346.9,\ -209.07 5385.4,197.53", + lp="5184.9,221.5", + pos="e,5177.3,194.5 2702.5,251.59 2740.7,249.75 2780.2,248.11 2817.4,247 2940.2,243.33 4907.5,244.88 5029.4,229 5076.6,222.84 5128.9,\ +209.07 5167.4,197.53", style=solid]; "object context qualifier" [height=0.5, - pos="5692.4,178", + pos="5474.4,178", width=3.2858]; "named thing associated with likelihood of named thing association" -> "object context qualifier" [color=blue, label="object context qualifier", - lp="5649.4,221.5", - pos="e,5643,194.38 2920,251.58 2958.4,249.74 2998.1,248.1 3035.4,247 3171.5,242.99 5351.2,245.67 5486.4,229 5536.7,222.8 5592.4,208.81 \ -5633.3,197.2", + lp="5431.4,221.5", + pos="e,5425,194.38 2702,251.58 2740.4,249.74 2780.1,248.1 2817.4,247 2953.5,242.99 5133.2,245.67 5268.4,229 5318.7,222.8 5374.4,208.81 \ +5415.3,197.2", style=solid]; subject -> object [label=relation, lp="900.39,134.5", @@ -385,36 +386,36 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="3082.4,265", + pos="2864.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3213.4,265", + pos="2995.4,265", width=2.0762]; "named thing associated with likelihood of named thing association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3384.4,265", + pos="3166.4,265", width=2.1665]; "named thing associated with likelihood of named thing association_subject aspect qualifier" [color=blue, height=0.5, label=string, - pos="3518.4,265", + pos="3300.4,265", width=1.0652]; "named thing associated with likelihood of named thing association_subject context qualifier" [color=blue, height=0.5, label="ontology class", - pos="3651.4,265", + pos="3433.4,265", width=2.1304]; "named thing associated with likelihood of named thing association_object aspect qualifier" [color=blue, height=0.5, label=string, - pos="3784.4,265", + pos="3566.4,265", width=1.0652]; "named thing associated with likelihood of named thing association_object context qualifier" [color=blue, height=0.5, label="ontology class", - pos="3917.4,265", + pos="3699.4,265", width=2.1304]; } diff --git a/graphviz/named_thing_associated_with_likelihood_of_named_thing_association.svg b/graphviz/named_thing_associated_with_likelihood_of_named_thing_association.svg index 1203f0fea3..c804afb968 100644 --- a/graphviz/named_thing_associated_with_likelihood_of_named_thing_association.svg +++ b/graphviz/named_thing_associated_with_likelihood_of_named_thing_association.svg @@ -4,16 +4,16 @@ - + %3 - + named thing associated with likelihood of named thing association - -named thing associated with likelihood of named thing association + +named thing associated with likelihood of named thing association @@ -24,8 +24,8 @@ named thing associated with likelihood of named thing association->association - - + + is_a @@ -37,7 +37,7 @@ named thing associated with likelihood of named thing association->id - + id @@ -50,8 +50,8 @@ named thing associated with likelihood of named thing association->iri - - + + iri @@ -63,8 +63,8 @@ named thing associated with likelihood of named thing association->name - - + + name @@ -76,8 +76,8 @@ named thing associated with likelihood of named thing association->description - - + + description @@ -89,8 +89,8 @@ named thing associated with likelihood of named thing association->has attribute - - + + has attribute @@ -102,8 +102,8 @@ named thing associated with likelihood of named thing association->subject - - + + subject @@ -115,8 +115,8 @@ named thing associated with likelihood of named thing association->object - - + + object @@ -128,9 +128,9 @@ named thing associated with likelihood of named thing association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ named thing associated with likelihood of named thing association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ named thing associated with likelihood of named thing association->publications - - -publications + + +publications @@ -167,334 +167,334 @@ named thing associated with likelihood of named thing association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string named thing associated with likelihood of named thing association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string named thing associated with likelihood of named thing association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string named thing associated with likelihood of named thing association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type named thing associated with likelihood of named thing association->timepoint - - -timepoint + + +timepoint original subject - -string + +string named thing associated with likelihood of named thing association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie named thing associated with likelihood of named thing association->original predicate - - -original predicate + + +original predicate original object - -string + +string named thing associated with likelihood of named thing association->original object - - -original object + + +original object subject category - -ontology class + +ontology class named thing associated with likelihood of named thing association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class named thing associated with likelihood of named thing association->object category - - -object category + + +object category subject closure - -string + +string named thing associated with likelihood of named thing association->subject closure - - -subject closure + + +subject closure object closure - -string + +string named thing associated with likelihood of named thing association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class named thing associated with likelihood of named thing association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class named thing associated with likelihood of named thing association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string named thing associated with likelihood of named thing association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string named thing associated with likelihood of named thing association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string named thing associated with likelihood of named thing association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string named thing associated with likelihood of named thing association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source named thing associated with likelihood of named thing association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type named thing associated with likelihood of named thing association->type - - -type + + +type category - -category + +category named thing associated with likelihood of named thing association->category - - -category + + +category predicate - -predicate + +predicate named thing associated with likelihood of named thing association->predicate - - -predicate + + +predicate subject aspect qualifier - -subject aspect qualifier + +subject aspect qualifier named thing associated with likelihood of named thing association->subject aspect qualifier - - -subject aspect qualifier + + +subject aspect qualifier subject context qualifier - -subject context qualifier + +subject context qualifier named thing associated with likelihood of named thing association->subject context qualifier - - -subject context qualifier + + +subject context qualifier object aspect qualifier - -object aspect qualifier + +object aspect qualifier named thing associated with likelihood of named thing association->object aspect qualifier - - -object aspect qualifier + + +object aspect qualifier object context qualifier - -object context qualifier + +object context qualifier named thing associated with likelihood of named thing association->object context qualifier - - -object context qualifier + + +object context qualifier @@ -524,44 +524,44 @@ association_type - -string + +string association_category - -category type + +category type named thing associated with likelihood of named thing association_predicate - -predicate type + +predicate type named thing associated with likelihood of named thing association_subject aspect qualifier - -string + +string named thing associated with likelihood of named thing association_subject context qualifier - -ontology class + +ontology class named thing associated with likelihood of named thing association_object aspect qualifier - -string + +string named thing associated with likelihood of named thing association_object context qualifier - -ontology class + +ontology class diff --git a/graphviz/organism_taxon_to_environment_association.gv b/graphviz/organism_taxon_to_environment_association.gv index e901318588..222f1ca27f 100644 --- a/graphviz/organism_taxon_to_environment_association.gv +++ b/graphviz/organism_taxon_to_environment_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,5125,283"]; + graph [bb="0,0,4907,283"]; node [label="\N"]; "organism taxon to environment association" [height=0.5, label="organism taxon to environment association", - pos="2770.4,265", + pos="2552.4,265", width=5.8856]; association [height=0.5, pos="62.394,178", width=1.7332]; "organism taxon to environment association" -> association [label=is_a, lp="498.39,221.5", - pos="e,106.89,190.67 2559.8,262.89 2073.6,259.99 884.19,250.82 484.39,229 327.94,220.46 287.97,221.64 133.39,196 128,195.11 122.41,194.03 \ + pos="e,106.89,190.67 2342.3,262.5 1890.9,258.93 840.8,248.74 484.39,229 327.95,220.33 287.97,221.64 133.39,196 128,195.11 122.41,194.03 \ 116.84,192.86"]; "organism taxon to entity association" [height=0.5, pos="322.39,178", width=5.0009]; "organism taxon to environment association" -> "organism taxon to entity association" [label=uses, - lp="654.89,221.5", - pos="e,399.61,194.33 2558.4,264.31 2095.5,264.36 1006.3,260.96 638.39,229 560.53,222.23 472.78,207.8 409.55,196.17"]; + lp="653.89,221.5", + pos="e,399.37,194.29 2340.8,263.85 1913.9,262.93 962.32,257.62 637.39,229 559.77,222.16 472.31,207.74 409.27,196.13"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "organism taxon to environment association" -> id [color=blue, label=id, - lp="773.39,221.5", - pos="e,587.38,189.98 2560.3,262.54 2082.1,258.91 940.62,248.32 766.39,229 694.23,221 676.34,215.5 606.39,196 603.29,195.13 600.09,194.17 \ -596.89,193.15", + lp="771.39,221.5", + pos="e,587.38,189.97 2340.4,264.8 1935,265.51 1063.5,262.86 764.39,229 693.11,220.93 675.47,215.35 606.39,196 603.29,195.13 600.09,194.16 \ +596.89,193.14", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,9 @@ digraph { width=1.2277]; "organism taxon to environment association" -> iri [color=blue, label=iri, - lp="886.39,221.5", - pos="e,692.3,190.2 2558.5,264.82 2135.1,265.68 1198.1,263.46 878.39,229 803.61,220.94 785.22,214.85 712.39,196 709.02,195.13 705.54,194.16 \ -702.06,193.15", + lp="876.39,221.5", + pos="e,692.32,190.13 2340.4,264.55 1953.5,264.73 1147,261.08 868.39,229 797.99,220.89 780.89,214.18 712.39,196 709.02,195.11 705.55,194.12 \ +702.07,193.1", style=solid]; name [color=blue, height=0.5, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "organism taxon to environment association" -> name [color=blue, label=name, - lp="993.39,221.5", - pos="e,816.35,191.53 2560.3,262.63 2119.6,259.37 1126.6,249.8 973.39,229 922.26,222.06 865.25,206.49 826.14,194.56", + lp="977.39,221.5", + pos="e,814.5,191.97 2342.8,262.32 1941,258.68 1090.5,248.74 957.39,229 911.15,222.15 859.92,207.04 824.16,195.21", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "organism taxon to environment association" -> description [color=blue, label=description, - lp="1113.9,221.5", - pos="e,962.45,194.13 2559.1,263.31 2136.5,261.4 1215.7,254.35 1073.4,229 1038.3,222.75 1000.3,209.39 972.04,198.05", + lp="1088.9,221.5", + pos="e,957.48,194.73 2341.1,263.41 1956.7,261.7 1171.1,255.03 1048.4,229 1019.9,222.95 989.57,210.27 966.56,199.2", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "organism taxon to environment association" -> "has attribute" [color=blue, label="has attribute", - lp="1259.4,221.5", - pos="e,1103,192.81 2559.8,263.04 2164.8,260.68 1341,252.92 1212.4,229 1177.4,222.5 1139.6,208.37 1112.2,196.79", + lp="1220.4,221.5", + pos="e,1096.5,194.23 2341,263.69 1982.5,262.42 1283.2,256.39 1173.4,229 1149.3,222.98 1124.3,210.48 1105.3,199.48", style=solid]; negated [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=1.2999]; "organism taxon to environment association" -> negated [color=blue, label=negated, - lp="1414.4,221.5", - pos="e,1224.4,190.44 2558.8,263.98 2228.5,263.06 1605.6,257.43 1385.4,229 1332.5,222.17 1273.3,205.69 1234.2,193.51", + lp="1352.4,221.5", + pos="e,1218.1,192.53 2343.6,261.81 2019,257.84 1420.3,248.04 1323.4,229 1289.8,222.39 1253.5,208.23 1227.3,196.66", style=solid]; qualifiers [color=blue, height=0.5, @@ -87,8 +87,8 @@ digraph { width=2.1304]; "organism taxon to environment association" -> qualifiers [color=blue, label=qualifiers, - lp="1553.9,221.5", - pos="e,1373.6,193.17 2558.6,263.96 2255.8,262.9 1714.3,256.97 1520.4,229 1473.2,222.19 1420.9,207.8 1383.3,196.2", + lp="1454.9,221.5", + pos="e,1353.8,195.41 2342,262.85 2039.2,260.37 1507.3,252.68 1421.4,229 1400.5,223.23 1379.1,211.67 1362.5,201.12", style=solid]; publications [color=blue, height=0.5, @@ -97,8 +97,8 @@ digraph { width=1.7332]; "organism taxon to environment association" -> publications [color=blue, label=publications, - lp="1700.4,221.5", - pos="e,1524.5,192.69 2558.9,263.84 2285.4,262.5 1824,256.11 1656.4,229 1614,222.15 1567.3,207.66 1533.9,196.04", + lp="1546.4,221.5", + pos="e,1488.3,196.18 2341.3,263.3 2044.2,261.4 1534.8,254.43 1502.4,229 1495.4,223.48 1491.7,214.73 1489.8,206.08", style=solid]; "has evidence" [color=blue, height=0.5, @@ -107,275 +107,276 @@ digraph { width=2.0943]; "organism taxon to environment association" -> "has evidence" [color=blue, label="has evidence", - lp="1853.9,221.5", - pos="e,1682.2,193.7 2560.1,262.76 2321.3,260.21 1946.7,252.48 1807.4,229 1767.6,222.29 1723.9,208.54 1691.8,197.15", + lp="1644.9,221.5", + pos="e,1615.2,194.71 2341.2,263.59 2068,261.99 1623.8,255.33 1598.4,229 1589.6,219.91 1596.2,209.68 1606.9,200.86", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1846.4,178", - width=3.015]; + label=string, + pos="1776.4,178", + width=1.0652]; "organism taxon to environment association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2006.9,221.5", - pos="e,1870.8,195.57 2566.6,260.01 2340.9,254.86 2000.9,244.65 1942.4,229 1920.3,223.09 1897.5,211.49 1879.7,200.95", + lp="1762.9,221.5", + pos="e,1747.6,190.14 2342.4,262.58 2096.8,259.87 1720.4,251.97 1698.4,229 1693.8,224.19 1694.8,219.6 1698.4,214 1700.9,210.08 1719.8,\ +201.57 1738.3,193.92", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2081.4,178", - width=3.015]; + label=string, + pos="1871.4,178", + width=1.0652]; "organism taxon to environment association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2176.4,221.5", - pos="e,2076,196.02 2565.3,260.39 2368.3,255.88 2098.1,246.54 2081.4,229 2075.7,222.98 2074.2,214.49 2074.7,206.2", + lp="1929.4,221.5", + pos="e,1849.9,193.09 2345.8,260.83 2140,256.62 1852,247.47 1834.4,229 1825.8,220 1832.4,208.99 1842.3,199.59", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2316.4,178", - width=3.015]; + label=string, + pos="2013.4,178", + width=1.0652]; "organism taxon to environment association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2384.9,221.5", - pos="e,2291.1,195.65 2560.9,262.19 2436.1,258.87 2298.3,250.32 2278.4,229 2270.8,220.83 2275.3,211.21 2283.5,202.59", + lp="2148.9,221.5", + pos="e,2018.5,195.92 2351.8,259.15 2220.7,254.46 2068.9,245.52 2042.4,229 2033.5,223.49 2027.1,214.21 2022.6,205.14", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2498.4,178", + pos="2239.4,178", width=1.5346]; "organism taxon to environment association" -> timepoint [color=blue, label=timepoint, - lp="2536.4,221.5", - pos="e,2494.4,195.96 2582.3,256.7 2545.5,251.41 2514.3,242.82 2501.4,229 2495.7,222.92 2493.9,214.4 2493.8,206.12", + lp="2309.4,221.5", + pos="e,2246.9,196.26 2383.9,254 2337.3,248.79 2294.1,240.9 2274.4,229 2265,223.34 2257.5,214.08 2251.9,205.06", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2610.4,178", + pos="2351.4,178", width=1.0652]; "organism taxon to environment association" -> "original subject" [color=blue, label="original subject", - lp="2634.4,221.5", - pos="e,2590.9,193.67 2632.3,251.29 2607.5,246.17 2586.8,239.02 2578.4,229 2571.2,220.34 2576,209.96 2583.8,200.9", + lp="2410.4,221.5", + pos="e,2347.5,196.32 2411.5,251.51 2385.4,246.38 2363.5,239.16 2354.4,229 2348.9,222.88 2347.1,214.5 2346.9,206.34", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2724.4,178", + pos="2477.4,178", width=1.5887]; "organism taxon to environment association" -> "original predicate" [color=blue, label="original predicate", - lp="2759.9,221.5", - pos="e,2705.7,195.47 2716.2,247.44 2708.3,242.71 2701.3,236.68 2696.4,229 2691.2,220.8 2694,211.6 2699.5,203.34", + lp="2537.9,221.5", + pos="e,2471.6,196.05 2494.5,247.47 2486.5,242.76 2479.4,236.73 2474.4,229 2470.1,222.3 2469.2,213.98 2469.9,206.06", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2838.4,178", + pos="2611.4,178", width=1.0652]; "organism taxon to environment association" -> "original object" [color=blue, label="original object", - lp="2882.9,221.5", - pos="e,2836.3,196.07 2803.6,247.16 2811,242.15 2818.1,236.08 2823.4,229 2828.4,222.25 2831.8,213.82 2834,205.82", + lp="2662.9,221.5", + pos="e,2612.8,196.39 2587.4,247.19 2594.4,242.27 2600.9,236.22 2605.4,229 2609.5,222.35 2611.5,214.25 2612.3,206.52", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2971.4,178", + pos="2744.4,178", width=2.1304]; "organism taxon to environment association" -> "subject category" [color=blue, label="subject category", - lp="3012.9,221.5", - pos="e,2964.4,195.94 2893,250.31 2909.1,245.19 2924.7,238.29 2938.4,229 2947.2,223.02 2954.3,213.82 2959.5,204.93", + lp="2790.9,221.5", + pos="e,2739.6,196.35 2656.6,249.31 2683.4,243.95 2707.7,237.15 2718.4,229 2726.1,223.15 2731.7,214.37 2735.7,205.79", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3142.4,178", + pos="2915.4,178", width=2.1304]; "organism taxon to environment association" -> "object category" [color=blue, label="object category", - lp="3157.9,221.5", - pos="e,3125.8,195.64 2931.3,253.28 2990.4,247.72 3049.5,239.79 3076.4,229 3091.7,222.87 3106.5,212.22 3118.2,202.31", + lp="2934.9,221.5", + pos="e,2900,195.89 2714.6,253.36 2771.9,247.87 2828.5,239.97 2854.4,229 2868.6,222.98 2882.1,212.57 2892.8,202.81", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3275.4,178", + pos="3048.4,178", width=1.0652]; "organism taxon to environment association" -> "subject closure" [color=blue, label="subject closure", - lp="3295.9,221.5", - pos="e,3262,195.11 2921.3,252.32 3050.7,242.28 3216.5,229.36 3217.4,229 3231.5,223.13 3244.6,212.48 3254.8,202.51", + lp="3070.9,221.5", + pos="e,3036.1,195.1 2703.4,252.33 2830.8,242.44 2992.7,229.75 2994.4,229 3007.7,223.17 3019.8,212.67 3029.2,202.79", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3375.4,178", + pos="3156.4,178", width=1.0652]; "organism taxon to environment association" -> "object closure" [color=blue, label="object closure", - lp="3416.4,221.5", - pos="e,3372.9,196.32 2918.1,252.08 2942.5,250.27 2967.7,248.5 2991.4,247 3031.7,244.45 3321.3,252.18 3354.4,229 3362.1,223.58 3367,214.74 \ -3370.1,205.98", + lp="3193.4,221.5", + pos="e,3152,195.95 2700.4,252.08 2724.8,250.27 2749.8,248.51 2773.4,247 2812.9,244.48 3095.9,250.14 3129.4,229 3138,223.59 3144,214.46 \ +3148.2,205.47", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3508.4,178", + pos="3289.4,178", width=2.1304]; "organism taxon to environment association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3574.9,221.5", - pos="e,3500.4,196.16 2916.6,251.94 2941.5,250.12 2967.2,248.39 2991.4,247 3044.6,243.96 3423.1,253.56 3470.4,229 3480.7,223.67 3488.9,\ -214.17 3495.1,204.87", + lp="3353.9,221.5", + pos="e,3280.1,196.2 2698.6,251.95 2723.5,250.13 2749.2,248.39 2773.4,247 2826,243.98 3200.1,252.16 3247.4,229 3258.3,223.66 3267.4,214.03 \ +3274.4,204.63", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3700.4,178", + pos="3482.4,178", width=2.1304]; "organism taxon to environment association" -> "object category closure" [color=blue, label="object category closure", - lp="3765.9,221.5", - pos="e,3693.7,196.15 2915.1,251.83 2940.5,249.99 2966.7,248.28 2991.4,247 3028.9,245.06 3633.5,246.99 3666.4,229 3676.1,223.71 3683.5,\ -214.35 3689,205.15", + lp="3545.9,221.5", + pos="e,3474.7,196.19 2697.1,251.83 2722.5,249.99 2748.7,248.28 2773.4,247 2810.7,245.07 3412.3,246.25 3445.4,229 3455.6,223.71 3463.6,\ +214.21 3469.6,204.91", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3890.4,178", + pos="3672.4,178", width=1.0652]; "organism taxon to environment association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3938.4,221.5", - pos="e,3883,195.72 2914.2,251.77 2939.9,249.92 2966.4,248.22 2991.4,247 3039.2,244.66 3810.8,251 3853.4,229 3863.7,223.66 3871.9,213.98 \ -3877.9,204.54", + lp="3719.4,221.5", + pos="e,3664.4,195.75 2696.2,251.77 2721.9,249.92 2748.4,248.22 2773.4,247 2821.1,244.67 3590.7,250.41 3633.4,229 3644.1,223.64 3652.7,\ +213.81 3659.1,204.28", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4049.4,178", + pos="3831.4,178", width=1.0652]; "organism taxon to environment association" -> "object namespace" [color=blue, label="object namespace", - lp="4092.4,221.5", - pos="e,4041.4,195.76 2913.9,251.72 2939.7,249.87 2966.3,248.19 2991.4,247 3048,244.33 3959.7,254.29 4010.4,229 4021.1,223.65 4029.7,213.83 \ -4036.2,204.3", + lp="3873.4,221.5", + pos="e,3823.1,195.77 2695.9,251.72 2721.7,249.87 2748.3,248.19 2773.4,247 2829.9,244.33 3740.6,253.95 3791.4,229 3802.2,223.67 3811.1,\ +213.85 3817.7,204.31", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4200.4,178", + pos="3982.4,178", width=1.0652]; "organism taxon to environment association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4252.4,221.5", - pos="e,4192.1,195.78 2913.6,251.7 2939.5,249.84 2966.2,248.16 2991.4,247 3023.8,245.5 4131.2,243.29 4160.4,229 4171.2,223.68 4180.1,213.86 \ -4186.7,204.32", + lp="4033.4,221.5", + pos="e,3973.8,195.79 2695.6,251.7 2721.5,249.84 2748.2,248.16 2773.4,247 2805.8,245.5 3912.2,243.1 3941.4,229 3952.4,223.69 3961.4,213.88 \ +3968.2,204.34", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4371.4,178", + pos="4153.4,178", width=1.0652]; "organism taxon to environment association" -> "object label closure" [color=blue, label="object label closure", - lp="4419.9,221.5", - pos="e,4362.8,195.8 2913.3,251.68 2939.2,249.82 2966.1,248.14 2991.4,247 3028.6,245.32 4296.9,245.14 4330.4,229 4341.4,223.71 4350.4,\ -213.89 4357.2,204.35", + lp="4200.9,221.5", + pos="e,4144.5,195.81 2695.3,251.68 2721.2,249.82 2748.1,248.14 2773.4,247 2810.5,245.32 4077.8,244.93 4111.4,229 4122.5,223.72 4131.8,\ +213.91 4138.7,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4524.4,178", + pos="4306.4,178", width=2.347]; "organism taxon to environment association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4577.9,221.5", - pos="e,4518.7,196.17 2913,251.67 2939,249.8 2966,248.13 2991.4,247 3033.1,245.15 4457.1,249.51 4493.4,229 4502.6,223.78 4509.5,214.56 \ -4514.4,205.45", + lp="4359.9,221.5", + pos="e,4300.4,196.18 2695,251.67 2721,249.8 2748,248.13 2773.4,247 2815.1,245.15 4237.9,249.24 4274.4,229 4283.9,223.75 4290.9,214.39 \ +4296,205.18", style=solid]; type [height=0.5, - pos="4658.4,178", + pos="4440.4,178", width=0.86659]; "organism taxon to environment association" -> type [color=blue, label=type, - lp="4676.4,221.5", - pos="e,4661.1,195.99 2913,251.65 2939,249.78 2966,248.11 2991.4,247 3014.4,245.99 4634.1,244.23 4651.4,229 4657.9,223.32 4660.4,214.65 \ -4661.1,206.12", + lp="4458.4,221.5", + pos="e,4443.1,195.99 2695,251.65 2721,249.78 2748,248.11 2773.4,247 2796.4,245.99 4416.1,244.23 4433.4,229 4439.9,223.32 4442.4,214.65 \ +4443.1,206.12", style=solid]; category [height=0.5, - pos="4759.4,178", + pos="4541.4,178", width=1.4263]; "organism taxon to environment association" -> category [color=blue, label=category, - lp="4754.9,221.5", - pos="e,4744.7,195.48 2912.7,251.66 2938.8,249.79 2965.9,248.11 2991.4,247 3038.7,244.93 4651.8,244.83 4696.4,229 4711.6,223.59 4726,212.84 \ -4737.1,202.68", + lp="4536.9,221.5", + pos="e,4526.7,195.48 2694.7,251.66 2720.8,249.79 2747.9,248.11 2773.4,247 2820.7,244.93 4433.8,244.83 4478.4,229 4493.6,223.59 4508,212.84 \ +4519.1,202.68", style=solid]; subject [height=0.5, - pos="4873.4,178", + pos="4655.4,178", width=1.2277]; "organism taxon to environment association" -> subject [color=blue, label=subject, - lp="4850.4,221.5", - pos="e,4854.7,194.32 2912.7,251.65 2938.8,249.78 2965.9,248.11 2991.4,247 3091.2,242.66 4694.2,256.25 4790.4,229 4810.6,223.29 4830.7,\ -211.3 4846.2,200.49", + lp="4632.4,221.5", + pos="e,4636.7,194.32 2694.7,251.65 2720.8,249.78 2747.9,248.11 2773.4,247 2873.2,242.66 4476.2,256.25 4572.4,229 4592.6,223.29 4612.7,\ +211.3 4628.2,200.49", style=solid]; object [height=0.5, - pos="4916.4,91", + pos="4698.4,91", width=1.0832]; "organism taxon to environment association" -> object [color=blue, label=object, - lp="4960.4,178", - pos="e,4929.8,108.09 2912.7,251.64 2938.8,249.77 2965.9,248.1 2991.4,247 3043.8,244.74 4830.5,245.3 4880.4,229 4904.3,221.18 4912.3,216.87 \ -4926.4,196 4940.2,175.52 4936.5,166.51 4939.4,142 4940.2,135.38 4941.3,133.39 4939.4,127 4938.4,123.55 4936.9,120.13 4935.1,116.85", + lp="4742.4,178", + pos="e,4711.8,108.09 2694.7,251.64 2720.8,249.77 2747.9,248.1 2773.4,247 2825.8,244.74 4612.5,245.3 4662.4,229 4686.3,221.18 4694.3,216.87 \ +4708.4,196 4722.2,175.52 4718.5,166.51 4721.4,142 4722.2,135.38 4723.3,133.39 4721.4,127 4720.4,123.55 4718.9,120.13 4717.1,116.85", style=solid]; predicate [height=0.5, - pos="5070.4,178", + pos="4852.4,178", width=1.5165]; "organism taxon to environment association" -> predicate [color=blue, label=predicate, - lp="5043.4,221.5", - pos="e,5046.6,194.36 2912.7,251.63 2938.8,249.76 2965.9,248.09 2991.4,247 3101.1,242.29 4860.5,254.08 4967.4,229 4992.3,223.16 5018.2,\ -210.56 5037.8,199.48", + lp="4825.4,221.5", + pos="e,4828.6,194.36 2694.7,251.63 2720.8,249.76 2747.9,248.09 2773.4,247 2883.1,242.29 4642.5,254.08 4749.4,229 4774.3,223.16 4800.2,\ +210.56 4819.8,199.48", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3038.4,265", + pos="2820.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3169.4,265", + pos="2951.4,265", width=2.0762]; subject -> object [label=relation, - lp="4911.4,134.5", - pos="e,4898.5,107.23 4874.5,159.55 4875.7,149.57 4878.2,137.07 4883.4,127 4885.6,122.68 4888.5,118.52 4891.7,114.66"]; + lp="4693.4,134.5", + pos="e,4680.5,107.23 4656.5,159.55 4657.7,149.57 4660.2,137.07 4665.4,127 4667.6,122.68 4670.5,118.52 4673.7,114.66"]; relation [height=0.5, - pos="4861.4,18", + pos="4643.4,18", width=1.2999]; - subject -> relation [pos="e,4862.7,36.188 4872.1,159.79 4870,132.48 4866,78.994 4863.5,46.38", + subject -> relation [pos="e,4644.7,36.188 4654.1,159.79 4652,132.48 4648,78.994 4645.5,46.38", style=dotted]; "organism taxon to environment association_subject" [color=blue, height=0.5, label="organism taxon", - pos="3345.4,265", + pos="3127.4,265", width=2.3109]; - object -> relation [pos="e,4874.2,35.54 4903.9,73.889 4897,64.939 4888.2,53.617 4880.4,43.584", + object -> relation [pos="e,4656.2,35.54 4685.9,73.889 4679,64.939 4670.2,53.617 4662.4,43.584", style=dotted]; "organism taxon to environment association_object" [color=blue, height=0.5, label="named thing", - pos="3516.4,265", + pos="3298.4,265", width=1.9318]; "organism taxon to environment association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3682.4,265", + pos="3464.4,265", width=2.1665]; } diff --git a/graphviz/organism_taxon_to_environment_association.svg b/graphviz/organism_taxon_to_environment_association.svg index 31d30146d2..c71a7a452e 100644 --- a/graphviz/organism_taxon_to_environment_association.svg +++ b/graphviz/organism_taxon_to_environment_association.svg @@ -4,16 +4,16 @@ - + %3 - + organism taxon to environment association - -organism taxon to environment association + +organism taxon to environment association @@ -24,7 +24,7 @@ organism taxon to environment association->association - + is_a @@ -37,9 +37,9 @@ organism taxon to environment association->organism taxon to entity association - - -uses + + +uses @@ -50,9 +50,9 @@ organism taxon to environment association->id - - -id + + +id @@ -63,9 +63,9 @@ organism taxon to environment association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ organism taxon to environment association->name - - -name + + +name @@ -89,9 +89,9 @@ organism taxon to environment association->description - - -description + + +description @@ -102,9 +102,9 @@ organism taxon to environment association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ organism taxon to environment association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ organism taxon to environment association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ organism taxon to environment association->publications - - -publications + + +publications @@ -154,363 +154,363 @@ organism taxon to environment association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string organism taxon to environment association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string organism taxon to environment association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string organism taxon to environment association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type organism taxon to environment association->timepoint - - -timepoint + + +timepoint original subject - -string + +string organism taxon to environment association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie organism taxon to environment association->original predicate - - -original predicate + + +original predicate original object - -string + +string organism taxon to environment association->original object - - -original object + + +original object subject category - -ontology class + +ontology class organism taxon to environment association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class organism taxon to environment association->object category - - -object category + + +object category subject closure - -string + +string organism taxon to environment association->subject closure - - -subject closure + + +subject closure object closure - -string + +string organism taxon to environment association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class organism taxon to environment association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class organism taxon to environment association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string organism taxon to environment association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string organism taxon to environment association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string organism taxon to environment association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string organism taxon to environment association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source organism taxon to environment association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type organism taxon to environment association->type - - -type + + +type category - -category + +category organism taxon to environment association->category - - -category + + +category subject - -subject + +subject organism taxon to environment association->subject - - -subject + + +subject object - -object + +object organism taxon to environment association->object - - -object + + +object predicate - -predicate + +predicate organism taxon to environment association->predicate - - -predicate + + +predicate association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + organism taxon to environment association_subject - -organism taxon + +organism taxon object->relation - - + + organism taxon to environment association_object - -named thing + +named thing organism taxon to environment association_predicate - -predicate type + +predicate type diff --git a/graphviz/organism_taxon_to_organism_taxon_association.gv b/graphviz/organism_taxon_to_organism_taxon_association.gv index a0be43289f..1a4a65f628 100644 --- a/graphviz/organism_taxon_to_organism_taxon_association.gv +++ b/graphviz/organism_taxon_to_organism_taxon_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,5165.4,283"]; + graph [bb="0,0,4947.4,283"]; node [label="\N"]; "organism taxon to organism taxon association" [height=0.5, label="organism taxon to organism taxon association", - pos="2801.4,265", + pos="2583.4,265", width=6.2467]; association [height=0.5, pos="62.394,178", width=1.7332]; "organism taxon to organism taxon association" -> association [label=is_a, - lp="499.39,221.5", - pos="e,106.89,190.67 2577.9,262.86 2079.1,259.94 887.68,250.86 485.39,229 328.5,220.47 288.41,221.69 133.39,196 128,195.11 122.41,194.03 \ + lp="498.39,221.5", + pos="e,106.89,190.67 2360.5,262.46 1897.3,258.9 843.64,248.85 484.39,229 327.95,220.35 287.97,221.64 133.39,196 128,195.11 122.41,194.03 \ 116.84,192.86"]; "organism taxon to entity association" [height=0.5, pos="322.39,178", width=5.0009]; "organism taxon to organism taxon association" -> "organism taxon to entity association" [label=uses, - lp="655.89,221.5", - pos="e,399.54,194.27 2576.2,264.36 2101.2,264.46 1009.8,261.05 639.39,229 561.15,222.23 472.96,207.76 409.5,196.11"]; + lp="654.89,221.5", + pos="e,399.62,194.29 2358.9,263.88 1920.8,263 966,257.73 638.39,229 560.53,222.17 472.79,207.74 409.55,196.13"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "organism taxon to organism taxon association" -> id [color=blue, label=id, - lp="775.39,221.5", - pos="e,587.38,190 2578.7,262.48 2088.1,258.79 944.01,248.23 768.39,229 695.35,221 677.2,215.65 606.39,196 603.29,195.14 600.09,194.17 \ -596.89,193.16", + lp="773.39,221.5", + pos="e,587.38,189.98 2358.4,264.84 1942.4,265.52 1068,262.72 766.39,229 694.24,220.93 676.34,215.5 606.39,196 603.29,195.13 600.09,194.17 \ +596.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,9 @@ digraph { width=1.2277]; "organism taxon to organism taxon association" -> iri [color=blue, label=iri, - lp="892.39,221.5", - pos="e,692.29,190.23 2576.3,264.73 2142.6,265.33 1205.8,262.52 884.39,229 806.98,220.93 787.81,215.26 712.39,196 709.02,195.14 705.54,\ -194.18 702.05,193.17", + lp="886.39,221.5", + pos="e,692.3,190.2 2358.4,264.29 1962.8,263.97 1158.2,259.44 878.39,229 803.61,220.86 785.22,214.85 712.39,196 709.02,195.13 705.54,194.16 \ +702.06,193.15", style=solid]; name [color=blue, height=0.5, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "organism taxon to organism taxon association" -> name [color=blue, label=name, - lp="1004.4,221.5", - pos="e,817.39,191.26 2578.8,262.36 2128.3,258.65 1138.3,248.4 984.39,229 929.75,222.11 868.59,206.19 827.21,194.15", + lp="994.39,221.5", + pos="e,816.19,191.4 2361.7,261.97 1952.5,257.81 1107.8,247.14 974.39,229 922.75,221.98 865.11,206.29 825.78,194.35", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "organism taxon to organism taxon association" -> description [color=blue, label=description, - lp="1132.9,221.5", - pos="e,965.8,193.64 2578,262.85 2148,260.13 1234.9,251.74 1092.4,229 1052,222.56 1007.8,208.65 975.45,197.13", + lp="1115.9,221.5", + pos="e,962.95,194.11 2360.3,262.56 1971.2,259.5 1198,250.75 1075.4,229 1039.7,222.68 1001,209.22 972.29,197.87", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "organism taxon to organism taxon association" -> "has attribute" [color=blue, label="has attribute", - lp="1290.4,221.5", - pos="e,1107,191.74 2578.9,262.24 2179.7,258.61 1371.4,248.9 1243.4,229 1199.3,222.14 1150.5,206.98 1116.6,195.14", + lp="1262.4,221.5", + pos="e,1103.7,192.78 2361.2,262.11 2002.4,258.49 1324.5,249.08 1215.4,229 1179.8,222.44 1141.1,208.32 1113.1,196.75", style=solid]; predicate [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=2.1665]; "organism taxon to organism taxon association" -> predicate [color=blue, label=predicate, - lp="1450.4,221.5", - pos="e,1264.6,193.08 2576.5,264.47 2243,264.12 1633.4,259.17 1416.4,229 1367.6,222.22 1313.5,207.75 1274.6,196.12", + lp="1406.4,221.5", + pos="e,1256.9,194.04 2363.6,261.1 2040.9,256.32 1466.8,245.63 1372.4,229 1335.9,222.57 1296.1,209.12 1266.6,197.79", style=solid]; negated [color=blue, height=0.5, @@ -87,8 +87,8 @@ digraph { width=1.2999]; "organism taxon to organism taxon association" -> negated [color=blue, label=negated, - lp="1595.4,221.5", - pos="e,1399,190.21 2578.2,262.82 2276.7,260.34 1755.4,252.67 1566.4,229 1511.1,222.07 1449.1,205.34 1408.5,193.13", + lp="1524.4,221.5", + pos="e,1392,192.62 2364.6,260.84 2071.3,256.01 1577.8,245.57 1495.4,229 1462.5,222.38 1427,208.39 1401.3,196.89", style=solid]; qualifiers [color=blue, height=0.5, @@ -97,8 +97,8 @@ digraph { width=2.1304]; "organism taxon to organism taxon association" -> qualifiers [color=blue, label=qualifiers, - lp="1730.9,221.5", - pos="e,1547.9,193 2578.2,262.8 2305.8,260.3 1861.2,252.62 1697.4,229 1649.4,222.07 1596,207.62 1557.8,196.03", + lp="1625.9,221.5", + pos="e,1526.9,195.38 2361.9,261.81 2092.3,258.27 1664.1,249.49 1592.4,229 1572,223.18 1551.4,211.62 1535.4,201.08", style=solid]; publications [color=blue, height=0.5, @@ -107,8 +107,8 @@ digraph { width=1.7332]; "organism taxon to organism taxon association" -> publications [color=blue, label=publications, - lp="1871.4,221.5", - pos="e,1698.1,192.76 2578.4,262.65 2336.6,259.99 1966.3,252.15 1827.4,229 1786.1,222.11 1740.6,207.8 1707.9,196.25", + lp="1716.4,221.5", + pos="e,1660.9,196.02 2361,262.29 2099.8,259.27 1698.3,251.05 1672.4,229 1665.8,223.37 1662.8,214.71 1661.6,206.17", style=solid]; "has evidence" [color=blue, height=0.5, @@ -117,262 +117,263 @@ digraph { width=2.0943]; "organism taxon to organism taxon association" -> "has evidence" [color=blue, label="has evidence", - lp="2022.9,221.5", - pos="e,1855.4,193.77 2581.3,261.2 2377,257.41 2088.1,248.69 1976.4,229 1938,222.24 1896.1,208.65 1865,197.35", + lp="1814.9,221.5", + pos="e,1787,194.37 2361.7,261.96 2127.4,258.69 1788.8,250.28 1768.4,229 1759.2,219.42 1766.7,209.02 1778.4,200.2", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2020.4,178", - width=3.015]; + label=string, + pos="1950.4,178", + width=1.0652]; "organism taxon to organism taxon association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2168.9,221.5", - pos="e,2041.8,195.77 2576.3,264.38 2406.8,262.48 2189.6,254.77 2104.4,229 2085.1,223.17 2065.6,212 2050.3,201.69", + lp="1932.9,221.5", + pos="e,1921.1,189.71 2365.4,260.54 2161.4,256.2 1885.6,247.03 1868.4,229 1863.8,224.17 1864.7,219.56 1868.4,214 1871.1,209.87 1891.6,\ +201.11 1911.5,193.39", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2255.4,178", - width=3.015]; + label=string, + pos="2045.4,178", + width=1.0652]; "organism taxon to organism taxon association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2336.4,221.5", - pos="e,2243.3,196.25 2595.8,257.68 2441.2,251.89 2253.8,242.21 2241.4,229 2235.4,222.6 2236,213.84 2239,205.44", + lp="2099.4,221.5", + pos="e,2022.4,192.58 2375.7,258.08 2214.9,252.45 2017.4,242.78 2004.4,229 1995.4,219.44 2003.2,208.17 2014.3,198.76", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2490.4,178", - width=3.015]; + label=string, + pos="2187.4,178", + width=1.0652]; "organism taxon to organism taxon association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2544.9,221.5", - pos="e,2456.3,195.1 2605,256.21 2526.1,251.02 2450.7,242.56 2438.4,229 2429.6,219.36 2436.6,209.3 2447.9,200.75", + lp="2316.9,221.5", + pos="e,2190.7,196.22 2398.1,254.77 2312.8,249.03 2226.6,240.52 2210.4,229 2202.6,223.46 2197.4,214.59 2193.9,205.85", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2672.4,178", + pos="2413.4,178", width=1.5346]; "organism taxon to organism taxon association" -> timepoint [color=blue, label=timepoint, - lp="2694.4,221.5", - pos="e,2661.3,195.8 2702.3,248.74 2682.5,243.65 2665.8,237.14 2659.4,229 2654.1,222.2 2654.6,213.44 2657.3,205.16", + lp="2475.4,221.5", + pos="e,2418.6,196.25 2477.9,249.05 2464.5,244.11 2451.5,237.6 2440.4,229 2432.7,223.04 2426.9,214.23 2422.7,205.66", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2784.4,178", + pos="2525.4,178", width=1.0652]; "organism taxon to organism taxon association" -> "original subject" [color=blue, label="original subject", - lp="2791.4,221.5", - pos="e,2758.3,191.31 2754.2,247.32 2746.7,242.57 2739.9,236.56 2735.4,229 2728.1,216.95 2737.5,205.59 2749.8,196.74", + lp="2573.4,221.5", + pos="e,2517.4,195.83 2536.2,247.32 2528.7,242.57 2521.9,236.56 2517.4,229 2513.2,222.01 2513.1,213.51 2514.7,205.53", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2898.4,178", + pos="2651.4,178", width=1.5887]; "organism taxon to organism taxon association" -> "original predicate" [color=blue, label="original predicate", - lp="2926.9,221.5", - pos="e,2882.4,195.75 2825.2,246.75 2832.5,241.26 2840.4,235.04 2847.4,229 2856.8,220.85 2866.7,211.38 2875.2,202.9", + lp="2701.9,221.5", + pos="e,2646.2,196.38 2610.7,246.8 2617.4,241.66 2624.2,235.62 2629.4,229 2634.8,222.12 2639.2,213.69 2642.6,205.72", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3012.4,178", + pos="2785.4,178", width=1.0652]; "organism taxon to organism taxon association" -> "original object" [color=blue, label="original object", - lp="3056.9,221.5", - pos="e,3010.6,196.32 2931.4,250.25 2959.2,245.1 2983.5,238.18 2994.4,229 3001.2,223.24 3005.4,214.7 3008.1,206.3", + lp="2831.9,221.5", + pos="e,2784.3,196.25 2709.4,250.02 2736,244.88 2759.2,238.03 2769.4,229 2776,223.17 2779.9,214.61 2782.2,206.21", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3145.4,178", + pos="2918.4,178", width=2.1304]; "organism taxon to organism taxon association" -> "subject category" [color=blue, label="subject category", - lp="3187.9,221.5", - pos="e,3138.6,196.3 2959.3,252.11 3029,245.77 3098.5,237.53 3112.4,229 3121.5,223.43 3128.6,214.32 3133.8,205.38", + lp="2961.9,221.5", + pos="e,2912.3,196.26 2739.1,252.01 2806.9,245.69 2874,237.5 2887.4,229 2896.2,223.4 2903,214.27 2907.8,205.34", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3316.4,178", + pos="3089.4,178", width=2.1304]; "organism taxon to organism taxon association" -> "object category" [color=blue, label="object category", - lp="3332.9,221.5", - pos="e,3300.2,195.85 2959.9,252.19 3088.1,242.56 3247.9,230.34 3251.4,229 3266.6,223.15 3281.2,212.53 3292.7,202.57", + lp="3106.9,221.5", + pos="e,3073.5,195.84 2743.9,252.36 2867.6,243.22 3018.7,231.62 3025.4,229 3040.3,223.2 3054.6,212.72 3065.8,202.85", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3449.4,178", + pos="3222.4,178", width=1.0652]; "organism taxon to organism taxon association" -> "subject closure" [color=blue, label="subject closure", - lp="3469.9,221.5", - pos="e,3436.3,195.25 2958.7,252.09 2984.3,250.29 3010.6,248.53 3035.4,247 3075,244.56 3355.6,243.92 3392.4,229 3406.4,223.32 3419.3,212.69 \ -3429.3,202.68", + lp="3243.9,221.5", + pos="e,3209.6,195.24 2740.7,252.12 2766.3,250.31 2792.6,248.54 2817.4,247 2856.1,244.59 3130.5,243.77 3166.4,229 3180.2,223.31 3192.9,\ +212.68 3202.7,202.67", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3549.4,178", + pos="3330.4,178", width=1.0652]; "organism taxon to organism taxon association" -> "object closure" [color=blue, label="object closure", - lp="3590.4,221.5", - pos="e,3546.9,196.37 2956.5,251.94 2982.8,250.12 3009.9,248.39 3035.4,247 3062.8,245.51 3505.8,244.58 3528.4,229 3536.2,223.63 3541.1,\ -214.8 3544.2,206.04", + lp="3366.4,221.5", + pos="e,3325.7,196.02 2738.5,251.96 2764.8,250.14 2791.9,248.4 2817.4,247 2844.3,245.52 3279.4,243.06 3302.4,229 3311.2,223.61 3317.5,\ +214.36 3321.8,205.27", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3682.4,178", + pos="3463.4,178", width=2.1304]; "organism taxon to organism taxon association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3748.9,221.5", - pos="e,3674.4,196.19 2955.5,251.86 2982.1,250.03 3009.6,248.32 3035.4,247 3069.2,245.27 3614.3,244.49 3644.4,229 3654.7,223.71 3663,214.21 \ -3669.1,204.91", + lp="3526.9,221.5", + pos="e,3453.8,196.24 2737.5,251.86 2764.1,250.04 2791.6,248.32 2817.4,247 2850.9,245.29 3390.1,243.43 3420.4,229 3431.5,223.72 3440.8,\ +214.09 3447.9,204.69", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3874.4,178", + pos="3656.4,178", width=2.1304]; "organism taxon to organism taxon association" -> "object category closure" [color=blue, label="object category closure", - lp="3939.9,221.5", - pos="e,3867.7,196.17 2954.3,251.79 2981.3,249.94 3009.2,248.25 3035.4,247 3080.1,244.88 3801.1,250.37 3840.4,229 3850.1,223.74 3857.5,\ -214.38 3863,205.17", + lp="3718.9,221.5", + pos="e,3648.4,196.22 2736.3,251.79 2763.3,249.95 2791.2,248.25 2817.4,247 2861.9,244.89 3578.7,249.23 3618.4,229 3628.7,223.74 3637,214.26 \ +3643.2,204.95", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4064.4,178", + pos="3846.4,178", width=1.0652]; "organism taxon to organism taxon association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4112.4,221.5", - pos="e,4057,195.74 2953.6,251.73 2980.8,249.89 3008.9,248.2 3035.4,247 3090.5,244.5 3978.4,254.25 4027.4,229 4037.7,223.68 4045.9,213.99 \ -4051.9,204.56", + lp="3892.4,221.5", + pos="e,3838.1,195.77 2735.6,251.74 2762.8,249.89 2790.9,248.2 2817.4,247 2872.3,244.51 3757.1,253.25 3806.4,229 3817.2,223.67 3826.1,\ +213.84 3832.7,204.31", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4223.4,178", + pos="4005.4,178", width=1.0652]; "organism taxon to organism taxon association" -> "object namespace" [color=blue, label="object namespace", - lp="4266.4,221.5", - pos="e,4215.4,195.77 2953.3,251.7 2980.6,249.85 3008.8,248.17 3035.4,247 3067.3,245.59 4155.8,243.23 4184.4,229 4195.1,223.66 4203.8,\ -213.84 4210.2,204.31", + lp="4046.4,221.5", + pos="e,3996.8,195.79 2735.3,251.7 2762.6,249.85 2790.8,248.17 2817.4,247 2849.2,245.59 3935.7,242.86 3964.4,229 3975.4,223.69 3984.4,\ +213.88 3991.2,204.34", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4374.4,178", + pos="4156.4,178", width=1.0652]; "organism taxon to organism taxon association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4426.4,221.5", - pos="e,4366.1,195.79 2953,251.68 2980.4,249.83 3008.7,248.15 3035.4,247 3071.4,245.44 4302,244.86 4334.4,229 4345.3,223.69 4354.1,213.87 \ -4360.7,204.33", + lp="4208.4,221.5", + pos="e,4147.5,195.81 2735,251.68 2762.4,249.83 2790.7,248.15 2817.4,247 2853.4,245.44 4081.8,244.45 4114.4,229 4125.5,223.72 4134.8,213.9 \ +4141.7,204.36", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4545.4,178", + pos="4327.4,178", width=1.0652]; "organism taxon to organism taxon association" -> "object label closure" [color=blue, label="object label closure", - lp="4593.9,221.5", - pos="e,4536.8,195.81 2952.7,251.67 2980.2,249.81 3008.6,248.13 3035.4,247 3076.2,245.27 4467.6,246.68 4504.4,229 4515.4,223.71 4524.4,\ -213.9 4531.2,204.36", + lp="4375.9,221.5", + pos="e,4318.8,195.81 2734.7,251.67 2762.2,249.81 2790.6,248.13 2817.4,247 2858.2,245.27 4249.6,246.68 4286.4,229 4297.4,223.71 4306.4,\ +213.9 4313.2,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4707.4,178", + pos="4489.4,178", width=2.347]; "organism taxon to organism taxon association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4755.9,221.5", - pos="e,4698.8,196.29 2952.7,251.64 2980.2,249.78 3008.6,248.12 3035.4,247 3080.7,245.11 4626.6,248.86 4667.4,229 4678.1,223.78 4686.9,\ -214.16 4693.4,204.75", + lp="4537.9,221.5", + pos="e,4480.8,196.29 2734.7,251.64 2762.2,249.78 2790.6,248.12 2817.4,247 2862.7,245.11 4408.6,248.86 4449.4,229 4460.1,223.78 4468.9,\ +214.16 4475.4,204.75", style=solid]; type [height=0.5, - pos="4841.4,178", + pos="4623.4,178", width=0.86659]; "organism taxon to organism taxon association" -> type [color=blue, label=type, - lp="4855.4,221.5", - pos="e,4842.2,196.18 2952.4,251.64 2980,249.78 3008.5,248.11 3035.4,247 3060.3,245.97 4809.9,244.53 4829.4,229 4836.2,223.54 4839.6,214.93 \ -4841.1,206.37", + lp="4637.4,221.5", + pos="e,4624.2,196.18 2734.4,251.64 2762,249.78 2790.5,248.11 2817.4,247 2842.3,245.97 4591.9,244.53 4611.4,229 4618.2,223.54 4621.6,214.93 \ +4623.1,206.37", style=solid]; category [height=0.5, - pos="4942.4,178", + pos="4724.4,178", width=1.4263]; "organism taxon to organism taxon association" -> category [color=blue, label=category, - lp="4935.9,221.5", - pos="e,4926.8,195.25 2952.4,251.63 2980,249.77 3008.5,248.11 3035.4,247 3086.5,244.9 4827,245.34 4875.4,229 4891.6,223.53 4907.1,212.51 \ -4919.1,202.2", + lp="4717.9,221.5", + pos="e,4708.8,195.25 2734.4,251.63 2762,249.77 2790.5,248.11 2817.4,247 2868.5,244.9 4609,245.34 4657.4,229 4673.6,223.53 4689.1,212.51 \ +4701.1,202.2", style=solid]; subject [height=0.5, - pos="5056.4,178", + pos="4838.4,178", width=1.2277]; "organism taxon to organism taxon association" -> subject [color=blue, label=subject, - lp="5032.4,221.5", - pos="e,5037.1,194.33 2952.4,251.62 2980,249.76 3008.5,248.1 3035.4,247 3089.1,244.8 4919.6,243.37 4971.4,229 4992.1,223.25 5013,211.09 \ -5028.9,200.2", + lp="4814.4,221.5", + pos="e,4819.1,194.33 2734.4,251.62 2762,249.76 2790.5,248.1 2817.4,247 2871.1,244.8 4701.6,243.37 4753.4,229 4774.1,223.25 4795,211.09 \ +4810.9,200.2", style=solid]; object [height=0.5, - pos="5099.4,91", + pos="4881.4,91", width=1.0832]; "organism taxon to organism taxon association" -> object [color=blue, label=object, - lp="5143.4,178", - pos="e,5112.8,108.09 2952.1,251.64 2979.8,249.77 3008.4,248.1 3035.4,247 3091.7,244.71 5008.8,246.2 5062.4,229 5086.7,221.2 5095,217.1 \ -5109.4,196 5123.3,175.59 5119.5,166.51 5122.4,142 5123.2,135.38 5124.3,133.39 5122.4,127 5121.4,123.55 5119.9,120.13 5118.1,116.85", + lp="4925.4,178", + pos="e,4894.8,108.09 2734.1,251.64 2761.8,249.77 2790.4,248.1 2817.4,247 2873.7,244.71 4790.8,246.2 4844.4,229 4868.7,221.2 4877,217.1 \ +4891.4,196 4905.3,175.59 4901.5,166.51 4904.4,142 4905.2,135.38 4906.3,133.39 4904.4,127 4903.4,123.55 4901.9,120.13 4900.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3082.4,265", + pos="2864.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3213.4,265", + pos="2995.4,265", width=2.0762]; subject -> object [label=relation, - lp="5094.4,134.5", - pos="e,5081.5,107.23 5057.5,159.55 5058.7,149.57 5061.2,137.07 5066.4,127 5068.6,122.68 5071.5,118.52 5074.7,114.66"]; + lp="4876.4,134.5", + pos="e,4863.5,107.23 4839.5,159.55 4840.7,149.57 4843.2,137.07 4848.4,127 4850.6,122.68 4853.5,118.52 4856.7,114.66"]; relation [height=0.5, - pos="5044.4,18", + pos="4826.4,18", width=1.2999]; - subject -> relation [pos="e,5045.7,36.188 5055.1,159.79 5053,132.48 5049,78.994 5046.5,46.38", + subject -> relation [pos="e,4827.7,36.188 4837.1,159.79 4835,132.48 4831,78.994 4828.5,46.38", style=dotted]; "organism taxon to organism taxon association_subject" [color=blue, height=0.5, label="organism taxon", - pos="3389.4,265", + pos="3171.4,265", width=2.3109]; - object -> relation [pos="e,5057.2,35.54 5086.9,73.889 5080,64.939 5071.2,53.617 5063.4,43.584", + object -> relation [pos="e,4839.2,35.54 4868.9,73.889 4862,64.939 4853.2,53.617 4845.4,43.584", style=dotted]; "organism taxon to organism taxon association_object" [color=blue, height=0.5, label="organism taxon", - pos="3573.4,265", + pos="3355.4,265", width=2.3109]; } diff --git a/graphviz/organism_taxon_to_organism_taxon_association.svg b/graphviz/organism_taxon_to_organism_taxon_association.svg index 6f56555ee1..2686677266 100644 --- a/graphviz/organism_taxon_to_organism_taxon_association.svg +++ b/graphviz/organism_taxon_to_organism_taxon_association.svg @@ -4,16 +4,16 @@ - + %3 - + organism taxon to organism taxon association - -organism taxon to organism taxon association + +organism taxon to organism taxon association @@ -24,9 +24,9 @@ organism taxon to organism taxon association->association - + -is_a +is_a @@ -37,9 +37,9 @@ organism taxon to organism taxon association->organism taxon to entity association - - -uses + + +uses @@ -50,9 +50,9 @@ organism taxon to organism taxon association->id - - -id + + +id @@ -63,9 +63,9 @@ organism taxon to organism taxon association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ organism taxon to organism taxon association->name - - -name + + +name @@ -89,9 +89,9 @@ organism taxon to organism taxon association->description - - -description + + +description @@ -102,9 +102,9 @@ organism taxon to organism taxon association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ organism taxon to organism taxon association->predicate - - -predicate + + +predicate @@ -128,9 +128,9 @@ organism taxon to organism taxon association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ organism taxon to organism taxon association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ organism taxon to organism taxon association->publications - - -publications + + +publications @@ -167,344 +167,344 @@ organism taxon to organism taxon association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string organism taxon to organism taxon association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string organism taxon to organism taxon association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string organism taxon to organism taxon association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type organism taxon to organism taxon association->timepoint - - -timepoint + + +timepoint original subject - -string + +string organism taxon to organism taxon association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie organism taxon to organism taxon association->original predicate - - -original predicate + + +original predicate original object - -string + +string organism taxon to organism taxon association->original object - - -original object + + +original object subject category - -ontology class + +ontology class organism taxon to organism taxon association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class organism taxon to organism taxon association->object category - - -object category + + +object category subject closure - -string + +string organism taxon to organism taxon association->subject closure - - -subject closure + + +subject closure object closure - -string + +string organism taxon to organism taxon association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class organism taxon to organism taxon association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class organism taxon to organism taxon association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string organism taxon to organism taxon association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string organism taxon to organism taxon association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string organism taxon to organism taxon association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string organism taxon to organism taxon association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source organism taxon to organism taxon association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type organism taxon to organism taxon association->type - - -type + + +type category - -category + +category organism taxon to organism taxon association->category - - -category + + +category subject - -subject + +subject organism taxon to organism taxon association->subject - - -subject + + +subject object - -object + +object organism taxon to organism taxon association->object - - -object + + +object association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + organism taxon to organism taxon association_subject - -organism taxon + +organism taxon object->relation - - + + organism taxon to organism taxon association_object - -organism taxon + +organism taxon diff --git a/graphviz/organism_taxon_to_organism_taxon_interaction.gv b/graphviz/organism_taxon_to_organism_taxon_interaction.gv index 99eca71189..b44e39e4cd 100644 --- a/graphviz/organism_taxon_to_organism_taxon_interaction.gv +++ b/graphviz/organism_taxon_to_organism_taxon_interaction.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,5414.5,283"]; + graph [bb="0,0,5229.5,283"]; node [label="\N"]; "organism taxon to organism taxon interaction" [height=0.5, label="organism taxon to organism taxon interaction", - pos="2855.9,265", + pos="2670.9,265", width=6.2106]; "organism taxon to organism taxon association" [height=0.5, pos="224.88,178", width=6.2467]; "organism taxon to organism taxon interaction" -> "organism taxon to organism taxon association" [label=is_a, lp="604.88,221.5", - pos="e,315.55,194.48 2632.6,263.97 2142,263.35 982.54,258.67 590.88,229 500.79,222.18 399.02,207.72 325.71,196.1"]; + pos="e,315.93,194.51 2447.8,263.6 1987.4,262.23 945.81,256.13 590.88,229 500.95,222.13 399.37,207.71 326.08,196.12"]; id [color=blue, height=0.5, label=string, @@ -19,8 +19,8 @@ digraph { "organism taxon to organism taxon interaction" -> id [color=blue, label=id, lp="719.88,221.5", - pos="e,534.87,189.98 2634,262.74 2124.4,259.52 899.53,249.71 712.88,229 641.15,221.04 623.39,215.43 553.88,196 550.77,195.13 547.58,194.17 \ -544.38,193.15", + pos="e,534.87,189.98 2449.2,262.37 1972.9,258.53 881.14,247.8 712.88,229 641.15,220.99 623.39,215.43 553.88,196 550.77,195.13 547.58,\ +194.17 544.38,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "organism taxon to organism taxon interaction" -> iri [color=blue, label=iri, - lp="832.88,221.5", - pos="e,639.79,190.19 2634.3,262.44 2144.8,258.66 1000.5,247.92 824.88,229 750.52,220.99 732.27,214.78 659.88,196 656.5,195.12 653.03,\ -194.16 649.54,193.14", + lp="825.88,221.5", + pos="e,639.8,190.15 2450,262.15 1993.6,257.98 975.8,246.82 817.88,229 746.6,220.95 729.24,214.31 659.88,196 656.51,195.11 653.03,194.13 \ +649.55,193.11", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "organism taxon to organism taxon interaction" -> name [color=blue, label=name, - lp="939.88,221.5", - pos="e,763.64,191.54 2633.6,262.91 2160.8,260.16 1085.4,251.51 919.88,229 869.1,222.09 812.51,206.58 773.62,194.65", + lp="928.88,221.5", + pos="e,762.47,191.87 2449.1,262.65 2009.5,259.53 1057.1,250.39 908.88,229 861.5,222.16 808.94,206.98 772.35,195.12", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "organism taxon to organism taxon interaction" -> description [color=blue, label=description, - lp="1060.4,221.5", - pos="e,909.69,194.15 2632.9,263.68 2178.4,262.44 1174.5,256.59 1019.9,229 985.04,222.78 947.3,209.42 919.2,198.07", + lp="1042.4,221.5", + pos="e,906.01,194.51 2447.6,263.73 2025.4,262.57 1139.5,256.81 1001.9,229 971.74,222.91 939.54,210.01 915.24,198.84", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "organism taxon to organism taxon interaction" -> "has attribute" [color=blue, label="has attribute", - lp="1205.9,221.5", - pos="e,1050.5,192.95 2633.1,263.45 2205.6,261.8 1299.7,255.22 1158.9,229 1124.4,222.58 1087.1,208.62 1060,197.07", + lp="1176.9,221.5", + pos="e,1045.8,194.01 2447.4,263.92 2050.9,263.05 1254.4,257.68 1129.9,229 1103.4,222.89 1075.5,210 1054.6,198.83", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "organism taxon to organism taxon interaction" -> negated [color=blue, label=negated, - lp="1360.9,221.5", - pos="e,1171.7,190.46 2632.2,264.63 2271.3,264.67 1576.2,260.46 1331.9,229 1279.3,222.23 1220.6,205.81 1181.7,193.62", + lp="1313.9,221.5", + pos="e,1167.6,192.08 2450.1,262.08 2087.8,258.38 1396,248.82 1284.9,229 1247.2,222.28 1206.1,207.64 1177,195.93", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "organism taxon to organism taxon interaction" -> qualifiers [color=blue, label=qualifiers, - lp="1499.4,221.5", - pos="e,1320.6,193.2 2632.2,264.78 2297.9,264.84 1684,260.45 1465.9,229 1419.2,222.26 1367.4,207.87 1330.2,196.25", + lp="1424.4,221.5", + pos="e,1306.4,194.94 2449.1,262.64 2109.9,259.86 1490.7,251.71 1390.9,229 1364.5,222.99 1336.7,210.62 1315.4,199.68", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "organism taxon to organism taxon interaction" -> publications [color=blue, label=publications, - lp="1644.9,221.5", - pos="e,1471.6,192.85 2632.3,264.9 2326.2,264.89 1792.7,260.16 1600.9,229 1559.5,222.28 1514,207.95 1481.3,196.35", + lp="1524.9,221.5", + pos="e,1446.1,196.26 2450.3,261.98 2118.3,258.29 1524,248.95 1480.9,229 1469.4,223.69 1459.6,213.92 1452.1,204.42", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,288 +100,288 @@ digraph { width=2.0943]; "organism taxon to organism taxon interaction" -> "has evidence" [color=blue, label="has evidence", - lp="1803.4,221.5", - pos="e,1629.9,193.63 2632.7,263.78 2361.2,262.32 1919.2,255.71 1756.9,229 1716.5,222.35 1672.1,208.52 1639.6,197.09", + lp="1623.4,221.5", + pos="e,1579.4,195.82 2447.1,264.7 2135.8,264.54 1606.6,259.72 1576.9,229 1570.6,222.5 1571.5,213.46 1574.9,204.85", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1793.9,178", - width=3.015]; + label=string, + pos="1723.9,178", + width=1.0652]; "organism taxon to organism taxon interaction" -> "knowledge source" [color=blue, label="knowledge source", - lp="1958.4,221.5", - pos="e,1819.4,195.61 2637.9,260.95 2376.2,256.52 1963.7,246.83 1893.9,229 1870.8,223.1 1846.8,211.34 1828.1,200.71", + lp="1742.4,221.5", + pos="e,1699.1,191.9 2447.7,263.88 2163,262.6 1704.2,256.28 1677.9,229 1668,218.74 1677.7,207.02 1690.7,197.5", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2028.9,178", - width=3.015]; + label=string, + pos="1818.9,178", + width=1.0652]; "organism taxon to organism taxon interaction" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2129.9,221.5", - pos="e,2025.8,196.33 2636.2,261.6 2400.5,257.99 2056.8,249.26 2034.9,229 2028.7,223.32 2026.4,214.91 2025.8,206.59", + lp="1911.9,221.5", + pos="e,1812.6,196.04 2449.3,262.45 2203.5,259.62 1838.6,251.61 1816.9,229 1811.1,222.94 1809.9,214.33 1810.8,205.95", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2263.9,178", - width=3.015]; + label=string, + pos="1993.9,178", + width=1.0652]; "organism taxon to organism taxon interaction" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2338.4,221.5", - pos="e,2242.1,195.87 2644.9,259 2469.5,253.78 2246.2,244.19 2231.9,229 2224.7,221.43 2228.2,212.05 2235,203.46", + lp="2132.4,221.5", + pos="e,2000,196.02 2450.3,261.88 2278.1,258.59 2062.3,250.22 2025.9,229 2016.6,223.61 2009.6,214.35 2004.5,205.26", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2445.9,178", + pos="2220.9,178", width=1.5346]; "organism taxon to organism taxon interaction" -> timepoint [color=blue, label=timepoint, - lp="2492.9,221.5", - pos="e,2445.3,196.43 2657.2,256.69 2565.8,251.48 2474,242.87 2457.9,229 2451.3,223.36 2448,214.85 2446.4,206.44", + lp="2294.9,221.5", + pos="e,2229.3,195.97 2452.8,260.97 2373.1,256.62 2294,247.51 2259.9,229 2249.6,223.43 2241.2,213.89 2234.8,204.63", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2557.9,178", + pos="2332.9,178", width=1.0652]; "organism taxon to organism taxon interaction" -> "original subject" [color=blue, label="original subject", - lp="2590.9,221.5", - pos="e,2542.1,194.82 2675.4,254.33 2608.1,248.85 2545.4,240.69 2534.9,229 2528.2,221.56 2530.8,211.86 2536.3,202.98", + lp="2397.9,221.5", + pos="e,2331.2,196.27 2492.4,254.08 2421.6,248.45 2354,240.25 2341.9,229 2335.7,223.25 2332.9,214.83 2331.8,206.52", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2671.9,178", + pos="2457.9,178", width=1.5887]; "organism taxon to organism taxon interaction" -> "original predicate" [color=blue, label="original predicate", - lp="2717.4,221.5", - pos="e,2658.1,195.8 2708.1,251.46 2683.1,246.35 2662.4,239.14 2653.9,229 2648,222.05 2649.3,213.06 2653.2,204.62", + lp="2528.4,221.5", + pos="e,2455.6,196.02 2524.4,251.39 2497.4,246.27 2474.7,239.08 2464.9,229 2459,222.99 2456.6,214.49 2455.8,206.2", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2785.9,178", + pos="2586.9,178", width=1.0652]; "organism taxon to organism taxon interaction" -> "original object" [color=blue, label="original object", - lp="2841.4,221.5", - pos="e,2783.3,196.07 2809.5,247.23 2801.9,242.47 2794.8,236.48 2789.9,229 2785.5,222.32 2783.7,214 2783.3,206.08", + lp="2656.4,221.5", + pos="e,2589.8,196.35 2628.1,247.27 2619.6,242.4 2611.3,236.35 2604.9,229 2599.3,222.53 2595.4,214.18 2592.7,206.16", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2918.9,178", + pos="2719.9,178", width=2.1304]; "organism taxon to organism taxon interaction" -> "subject category" [color=blue, label="subject category", - lp="2965.4,221.5", - pos="e,2913.5,196.22 2879.8,246.74 2885.9,241.53 2892.1,235.46 2896.9,229 2902.1,221.97 2906.4,213.49 2909.8,205.54", + lp="2777.4,221.5", + pos="e,2720,196.17 2696.3,247.12 2702.3,241.98 2708,235.86 2711.9,229 2715.7,222.15 2717.9,213.99 2719,206.26", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3089.9,178", + pos="2890.9,178", width=2.1304]; "organism taxon to organism taxon interaction" -> "object category" [color=blue, label="object category", - lp="3108.4,221.5", - pos="e,3073.8,195.91 2968.7,249.44 2989.3,244.49 3010.2,237.87 3028.9,229 3042.5,222.54 3055.7,212.41 3066.3,202.94", + lp="2917.4,221.5", + pos="e,2878.3,195.95 2787,249.55 2805.7,244.59 2824.3,237.93 2840.9,229 2852.5,222.72 2863.2,212.86 2871.7,203.55", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3222.9,178", + pos="3023.9,178", width=1.0652]; "organism taxon to organism taxon interaction" -> "subject closure" [color=blue, label="subject closure", - lp="3245.4,221.5", - pos="e,3209.8,195.42 3004.3,251.48 3077,244.6 3152.3,236.05 3167.9,229 3181.1,223.04 3193.2,212.72 3202.8,203", + lp="3051.4,221.5", + pos="e,3013.2,195.4 2820.1,251.53 2890.4,244.81 2962.1,236.4 2976.9,229 2988.6,223.13 2998.9,213.1 3006.8,203.55", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3322.9,178", + pos="3136.9,178", width=1.0652]; "organism taxon to organism taxon interaction" -> "object closure" [color=blue, label="object closure", - lp="3365.9,221.5", - pos="e,3321,196.18 3013.1,252.2 3141.6,242.48 3302.4,230.12 3303.9,229 3311.3,223.48 3315.8,214.73 3318.5,206.08", + lp="3173.9,221.5", + pos="e,3132.2,196.34 2829.1,252.25 2953.7,242.87 3106.8,230.98 3109.9,229 3118.3,223.54 3124.2,214.57 3128.4,205.72", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3455.9,178", + pos="3269.9,178", width=2.1304]; "organism taxon to organism taxon interaction" -> "subject category closure" [color=blue, label="subject category closure", - lp="3524.4,221.5", - pos="e,3448.5,196.07 3012.8,252.15 3038.3,250.35 3064.3,248.57 3088.9,247 3125.6,244.66 3387.6,246.68 3419.9,229 3429.7,223.61 3437.6,\ -214.23 3443.4,205.04", + lp="3334.4,221.5", + pos="e,3260.6,196.12 2827.8,252.17 2853.3,250.37 2879.3,248.58 2903.9,247 2939.9,244.69 3195.6,245.13 3227.9,229 3238.7,223.56 3247.9,\ +213.91 3254.8,204.53", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3647.9,178", + pos="3462.9,178", width=2.1304]; "organism taxon to organism taxon interaction" -> "object category closure" [color=blue, label="object category closure", - lp="3715.4,221.5", - pos="e,3641.8,196.1 3009.7,251.93 3036.1,250.1 3063.3,248.37 3088.9,247 3118.1,245.43 3590.4,243.5 3615.9,229 3625.3,223.64 3632.4,214.27 \ -3637.4,205.08", + lp="3526.4,221.5", + pos="e,3455.2,196.16 2825,251.92 2851.3,250.1 2878.4,248.37 2903.9,247 2932.9,245.44 3400.2,242.5 3425.9,229 3436,223.67 3444.1,214.17 \ +3450.1,204.87", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3837.9,178", + pos="3652.9,178", width=1.0652]; "organism taxon to organism taxon interaction" -> "subject namespace" [color=blue, label="subject namespace", - lp="3887.9,221.5", - pos="e,3830.9,196.17 3008.4,251.82 3035.2,249.98 3062.9,248.28 3088.9,247 3128.5,245.06 3767.9,247.77 3802.9,229 3812.7,223.74 3820.3,\ -214.38 3825.9,205.17", + lp="3699.9,221.5", + pos="e,3644.9,195.73 2823.4,251.83 2850.2,249.99 2877.9,248.28 2903.9,247 2943.3,245.06 3578.6,246.76 3613.9,229 3624.6,223.61 3633.2,\ +213.78 3639.6,204.26", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3996.9,178", + pos="3811.9,178", width=1.0652]; "organism taxon to organism taxon interaction" -> "object namespace" [color=blue, label="object namespace", - lp="4040.9,221.5", - pos="e,3989.5,195.72 3007.8,251.77 3034.8,249.92 3062.6,248.23 3088.9,247 3137.2,244.74 3916.9,251.23 3959.9,229 3970.2,223.66 3978.4,\ -213.98 3984.4,204.54", + lp="3853.9,221.5", + pos="e,3803.6,195.76 2822.8,251.77 2849.8,249.92 2877.6,248.23 2903.9,247 2952.1,244.74 3728.6,250.34 3771.9,229 3782.7,223.65 3791.6,\ +213.83 3798.2,204.3", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4147.9,178", + pos="3962.9,178", width=1.0652]; "organism taxon to organism taxon interaction" -> "subject label closure" [color=blue, label="subject label closure", - lp="4200.9,221.5", - pos="e,4139.9,195.76 3007.2,251.74 3034.3,249.89 3062.4,248.2 3088.9,247 3145.5,244.44 4058.2,254.31 4108.9,229 4119.6,223.65 4128.2,\ -213.83 4134.6,204.3", + lp="4013.9,221.5", + pos="e,3954.3,195.78 2822.2,251.74 2849.3,249.89 2877.4,248.2 2903.9,247 2960.4,244.44 3871,253.65 3921.9,229 3932.9,223.68 3941.9,213.86 \ +3948.7,204.33", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4318.9,178", + pos="4133.9,178", width=1.0652]; "organism taxon to organism taxon interaction" -> "object label closure" [color=blue, label="object label closure", - lp="4366.4,221.5", - pos="e,4310.6,195.78 3006.8,251.71 3034.1,249.85 3062.3,248.17 3088.9,247 3121.9,245.55 4249.2,243.55 4278.9,229 4289.7,223.68 4298.6,\ -213.86 4305.2,204.33", + lp="4181.4,221.5", + pos="e,4125,195.8 2821.8,251.71 2849.1,249.85 2877.3,248.17 2903.9,247 2936.9,245.55 4062.1,243.17 4091.9,229 4103,223.71 4112.3,213.89 \ +4119.2,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4462.9,178", + pos="4277.9,178", width=2.347]; "organism taxon to organism taxon interaction" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4522.4,221.5", - pos="e,4459.9,196 3006.5,251.69 3033.9,249.83 3062.2,248.15 3088.9,247 3126.4,245.38 4408.4,249.46 4439.9,229 4448,223.7 4453.3,214.72 \ -4456.8,205.82", + lp="4337.4,221.5", + pos="e,4274.9,196 2821.5,251.69 2848.9,249.83 2877.2,248.15 2903.9,247 2941.4,245.38 4223.4,249.46 4254.9,229 4263,223.7 4268.3,214.72 \ +4271.8,205.82", style=solid]; type [height=0.5, - pos="4596.9,178", + pos="4411.9,178", width=0.86659]; "organism taxon to organism taxon interaction" -> type [color=blue, label=type, - lp="4618.9,221.5", - pos="e,4602,196.18 3006.5,251.66 3033.9,249.8 3062.2,248.13 3088.9,247 3109.8,246.11 4581,243.74 4595.9,229 4601.8,223.09 4603.4,214.51 \ -4603.1,206.12", + lp="4433.9,221.5", + pos="e,4417,196.18 2821.5,251.66 2848.9,249.8 2877.2,248.13 2903.9,247 2924.8,246.11 4396,243.74 4410.9,229 4416.8,223.09 4418.4,214.51 \ +4418.1,206.12", style=solid]; category [height=0.5, - pos="4697.9,178", + pos="4512.9,178", width=1.4263]; "organism taxon to organism taxon interaction" -> category [color=blue, label=category, - lp="4696.4,221.5", - pos="e,4684.3,195.45 3006.2,251.67 3033.7,249.81 3062.1,248.13 3088.9,247 3131.9,245.18 4598.5,244.06 4638.9,229 4653.5,223.56 4666.9,\ -212.8 4677.3,202.65", + lp="4511.4,221.5", + pos="e,4499.3,195.45 2821.2,251.67 2848.7,249.81 2877.1,248.13 2903.9,247 2946.9,245.18 4413.5,244.06 4453.9,229 4468.5,223.56 4481.9,\ +212.8 4492.3,202.65", style=solid]; "associated environmental context" [height=0.5, - pos="4933.9,178", + pos="4748.9,178", width=4.6399]; "organism taxon to organism taxon interaction" -> "associated environmental context" [color=blue, label="associated environmental context", - lp="4931.4,221.5", - pos="e,4882.6,195.19 3006.2,251.66 3033.7,249.79 3062.1,248.12 3088.9,247 3271.3,239.35 4550.8,252.09 4731.9,229 4780,222.87 4833.1,209.44 \ -4872.8,198.04", + lp="4746.4,221.5", + pos="e,4697.6,195.19 2821.2,251.66 2848.7,249.79 2877.1,248.12 2903.9,247 3086.3,239.35 4365.8,252.09 4546.9,229 4595,222.87 4648.1,209.44 \ +4687.8,198.04", style=solid]; subject [height=0.5, - pos="5162.9,178", + pos="4977.9,178", width=1.2277]; "organism taxon to organism taxon interaction" -> subject [color=blue, label=subject, - lp="5124.9,221.5", - pos="e,5139.7,193.4 3005.9,251.64 3033.5,249.77 3062,248.1 3088.9,247 3198.1,242.52 4949.3,253.18 5055.9,229 5082.4,222.98 5110.2,209.77 \ -5130.8,198.44", + lp="4939.9,221.5", + pos="e,4954.7,193.4 2820.9,251.64 2848.5,249.77 2877,248.1 2903.9,247 3013.1,242.52 4764.3,253.18 4870.9,229 4897.4,222.98 4925.2,209.77 \ +4945.8,198.44", style=solid]; object [height=0.5, - pos="5205.9,91", + pos="5020.9,91", width=1.0832]; "organism taxon to organism taxon interaction" -> object [color=blue, label=object, - lp="5255.9,178", - pos="e,5219.3,108.09 3005.9,251.63 3033.5,249.76 3062,248.1 3088.9,247 3146.2,244.66 5099.3,243.33 5154.9,229 5184.7,221.31 5197.1,220.43 \ -5215.9,196 5234.9,171.26 5237.8,156.9 5228.9,127 5227.8,123.55 5226.4,120.13 5224.6,116.85", + lp="5070.9,178", + pos="e,5034.3,108.09 2820.9,251.63 2848.5,249.76 2877,248.1 2903.9,247 2961.2,244.66 4914.3,243.33 4969.9,229 4999.7,221.31 5012.1,220.43 \ +5030.9,196 5049.9,171.26 5052.8,156.9 5043.9,127 5042.8,123.55 5041.4,120.13 5039.6,116.85", style=solid]; predicate [height=0.5, - pos="5359.9,178", + pos="5174.9,178", width=1.5165]; "organism taxon to organism taxon interaction" -> predicate [color=blue, label=predicate, - lp="5332.9,221.5", - pos="e,5336.1,194.36 3005.9,251.62 3033.5,249.75 3062,248.09 3088.9,247 3209.2,242.12 5139.6,256.47 5256.9,229 5281.8,223.17 5307.7,210.57 \ -5327.2,199.48", + lp="5147.9,221.5", + pos="e,5151.1,194.36 2820.9,251.62 2848.5,249.75 2877,248.09 2903.9,247 3024.2,242.12 4954.6,256.47 5071.9,229 5096.8,223.17 5122.7,210.57 \ +5142.2,199.48", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3135.9,265", + pos="2950.9,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3266.9,265", + pos="3081.9,265", width=2.0762]; "organism taxon to organism taxon interaction_associated environmental context" [color=blue, height=0.5, label=string, - pos="3397.9,265", + pos="3212.9,265", width=1.0652]; subject -> object [label=relation, - lp="5200.9,134.5", - pos="e,5188,107.23 5164,159.55 5165.2,149.57 5167.7,137.07 5172.9,127 5175.1,122.68 5178,118.52 5181.2,114.66"]; + lp="5015.9,134.5", + pos="e,5003,107.23 4979,159.55 4980.2,149.57 4982.7,137.07 4987.9,127 4990.1,122.68 4993,118.52 4996.2,114.66"]; relation [height=0.5, - pos="5150.9,18", + pos="4965.9,18", width=1.2999]; - subject -> relation [pos="e,5152.2,36.188 5161.6,159.79 5159.5,132.48 5155.4,78.994 5153,46.38", + subject -> relation [pos="e,4967.2,36.188 4976.6,159.79 4974.5,132.48 4970.4,78.994 4968,46.38", style=dotted]; "organism taxon to organism taxon interaction_subject" [color=blue, height=0.5, label="organism taxon", - pos="3537.9,265", + pos="3352.9,265", width=2.3109]; - object -> relation [pos="e,5163.7,35.54 5193.4,73.889 5186.5,64.939 5177.7,53.617 5169.9,43.584", + object -> relation [pos="e,4978.7,35.54 5008.4,73.889 5001.5,64.939 4992.7,53.617 4984.9,43.584", style=dotted]; "organism taxon to organism taxon interaction_object" [color=blue, height=0.5, label="organism taxon", - pos="3721.9,265", + pos="3536.9,265", width=2.3109]; "organism taxon to organism taxon interaction_predicate" [color=blue, height=0.5, label="predicate type", - pos="3900.9,265", + pos="3715.9,265", width=2.1665]; } diff --git a/graphviz/organism_taxon_to_organism_taxon_interaction.svg b/graphviz/organism_taxon_to_organism_taxon_interaction.svg index 8d24f0b8d6..7579411784 100644 --- a/graphviz/organism_taxon_to_organism_taxon_interaction.svg +++ b/graphviz/organism_taxon_to_organism_taxon_interaction.svg @@ -4,16 +4,16 @@ - + %3 - + organism taxon to organism taxon interaction - -organism taxon to organism taxon interaction + +organism taxon to organism taxon interaction @@ -24,8 +24,8 @@ organism taxon to organism taxon interaction->organism taxon to organism taxon association - - + + is_a @@ -37,7 +37,7 @@ organism taxon to organism taxon interaction->id - + id @@ -50,9 +50,9 @@ organism taxon to organism taxon interaction->iri - - -iri + + +iri @@ -63,9 +63,9 @@ organism taxon to organism taxon interaction->name - - -name + + +name @@ -76,9 +76,9 @@ organism taxon to organism taxon interaction->description - - -description + + +description @@ -89,9 +89,9 @@ organism taxon to organism taxon interaction->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ organism taxon to organism taxon interaction->negated - - -negated + + +negated @@ -115,9 +115,9 @@ organism taxon to organism taxon interaction->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ organism taxon to organism taxon interaction->publications - - -publications + + +publications @@ -141,382 +141,382 @@ organism taxon to organism taxon interaction->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string organism taxon to organism taxon interaction->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string organism taxon to organism taxon interaction->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string organism taxon to organism taxon interaction->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type organism taxon to organism taxon interaction->timepoint - - -timepoint + + +timepoint original subject - -string + +string organism taxon to organism taxon interaction->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie organism taxon to organism taxon interaction->original predicate - - -original predicate + + +original predicate original object - -string + +string organism taxon to organism taxon interaction->original object - - -original object + + +original object subject category - -ontology class + +ontology class organism taxon to organism taxon interaction->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class organism taxon to organism taxon interaction->object category - - -object category + + +object category subject closure - -string + +string organism taxon to organism taxon interaction->subject closure - - -subject closure + + +subject closure object closure - -string + +string organism taxon to organism taxon interaction->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class organism taxon to organism taxon interaction->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class organism taxon to organism taxon interaction->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string organism taxon to organism taxon interaction->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string organism taxon to organism taxon interaction->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string organism taxon to organism taxon interaction->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string organism taxon to organism taxon interaction->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source organism taxon to organism taxon interaction->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type organism taxon to organism taxon interaction->type - - -type + + +type category - -category + +category organism taxon to organism taxon interaction->category - - -category + + +category associated environmental context - -associated environmental context + +associated environmental context organism taxon to organism taxon interaction->associated environmental context - - -associated environmental context + + +associated environmental context subject - -subject + +subject organism taxon to organism taxon interaction->subject - - -subject + + +subject object - -object + +object organism taxon to organism taxon interaction->object - - -object + + +object predicate - -predicate + +predicate organism taxon to organism taxon interaction->predicate - - -predicate + + +predicate association_type - -string + +string association_category - -category type + +category type organism taxon to organism taxon interaction_associated environmental context - -string + +string subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + organism taxon to organism taxon interaction_subject - -organism taxon + +organism taxon object->relation - - + + organism taxon to organism taxon interaction_object - -organism taxon + +organism taxon organism taxon to organism taxon interaction_predicate - -predicate type + +predicate type diff --git a/graphviz/organism_taxon_to_organism_taxon_specialization.gv b/graphviz/organism_taxon_to_organism_taxon_specialization.gv index d2abd3de74..344d50f822 100644 --- a/graphviz/organism_taxon_to_organism_taxon_specialization.gv +++ b/graphviz/organism_taxon_to_organism_taxon_specialization.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,5072.5,283"]; + graph [bb="0,0,4887.5,283"]; node [label="\N"]; "organism taxon to organism taxon specialization" [height=0.5, label="organism taxon to organism taxon specialization", - pos="2792.9,265", + pos="2607.9,265", width=6.5716]; "organism taxon to organism taxon association" [height=0.5, pos="224.88,178", width=6.2467]; "organism taxon to organism taxon specialization" -> "organism taxon to organism taxon association" [label=is_a, lp="604.88,221.5", - pos="e,315.93,194.53 2556.7,263.83 2069.3,262.88 966.64,257.55 590.88,229 500.95,222.17 399.37,207.75 326.08,196.15"]; + pos="e,315.93,194.49 2372.1,263.42 1916.4,261.71 930.15,255.03 590.88,229 500.95,222.1 399.37,207.69 326.08,196.11"]; id [color=blue, height=0.5, label=string, @@ -18,8 +18,8 @@ digraph { width=1.0652]; "organism taxon to organism taxon specialization" -> id [color=blue, label=id, - lp="720.88,221.5", - pos="e,534.87,189.98 2558.5,262.52 2053.3,258.97 892.66,248.77 713.88,229 641.71,221.02 623.82,215.5 553.88,196 550.77,195.13 547.57,\ + lp="719.88,221.5", + pos="e,534.87,189.98 2373.9,262.12 1903.4,257.98 873.47,246.99 712.88,229 641.16,220.97 623.39,215.43 553.88,196 550.77,195.13 547.58,\ 194.17 544.38,193.15", style=solid]; iri [color=blue, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "organism taxon to organism taxon specialization" -> iri [color=blue, label=iri, - lp="833.88,221.5", - pos="e,639.79,190.2 2558.9,262.18 2074.6,258.08 993.66,247.02 825.88,229 751.09,220.97 732.7,214.85 659.88,196 656.5,195.13 653.03,194.16 \ -649.54,193.15", + lp="825.88,221.5", + pos="e,639.8,190.15 2371.2,264.84 1955.7,265.41 1111.4,262.23 817.88,229 746.6,220.93 729.24,214.31 659.88,196 656.51,195.11 653.03,194.13 \ +649.55,193.11", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "organism taxon to organism taxon specialization" -> name [color=blue, label=name, - lp="940.88,221.5", - pos="e,763.84,191.54 2558.2,262.65 2091.6,259.53 1078.7,250.36 920.88,229 869.74,222.08 812.73,206.51 773.63,194.57", + lp="928.88,221.5", + pos="e,762.47,191.87 2373.8,262.37 1941.6,258.9 1049.6,249.35 908.88,229 861.51,222.15 808.94,206.96 772.35,195.11", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "organism taxon to organism taxon specialization" -> description [color=blue, label=description, - lp="1061.4,221.5", - pos="e,909.93,194.14 2556.8,263.43 2109.1,261.75 1167.8,255.11 1020.9,229 985.82,222.77 947.82,209.4 919.52,198.06", + lp="1042.4,221.5", + pos="e,906.26,194.62 2371.8,263.48 1957.8,261.87 1132.1,255.36 1001.9,229 971.84,222.92 939.76,210.09 915.49,198.95", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "organism taxon to organism taxon specialization" -> "has attribute" [color=blue, label="has attribute", - lp="1206.9,221.5", - pos="e,1050.5,192.82 2557.5,263.16 2138.2,261.04 1293.1,253.71 1159.9,229 1124.9,222.52 1087.1,208.39 1059.7,196.8", + lp="1176.9,221.5", + pos="e,1045.8,194.01 2371.8,263.63 1985,262.25 1247.1,256.05 1129.9,229 1103.4,222.88 1075.5,209.98 1054.6,198.82", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "organism taxon to organism taxon specialization" -> negated [color=blue, label=negated, - lp="1362.9,221.5", - pos="e,1172.1,190.46 2556.4,264.24 2205.3,263.58 1562.9,258.23 1333.9,229 1280.6,222.2 1221,205.66 1181.6,193.46", + lp="1314.9,221.5", + pos="e,1167.5,191.96 2375.5,261.62 2024.7,257.45 1389.6,247.47 1285.9,229 1247.9,222.23 1206.3,207.52 1177,195.8", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "organism taxon to organism taxon specialization" -> qualifiers [color=blue, label=qualifiers, - lp="1503.4,221.5", - pos="e,1321.2,193.07 2556.3,264.25 2233.7,263.47 1672.5,257.81 1469.9,229 1422.1,222.2 1369,207.74 1331,196.11", + lp="1425.4,221.5", + pos="e,1306.6,194.93 2374.2,262.12 2047.7,258.76 1484.5,249.98 1391.9,229 1365.3,222.97 1337.2,210.6 1315.7,199.66", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "organism taxon to organism taxon specialization" -> publications [color=blue, label=publications, - lp="1650.9,221.5", - pos="e,1472.6,192.71 2556.5,264.14 2264,263.07 1783.1,256.9 1606.9,229 1563.8,222.18 1516.3,207.69 1482.3,196.06", + lp="1525.9,221.5", + pos="e,1446.1,195.77 2376,261.37 2058.2,257.1 1521.7,247.24 1481.9,229 1470.1,223.61 1460,213.64 1452.2,204.02", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,276 +100,275 @@ digraph { width=2.0943]; "organism taxon to organism taxon specialization" -> "has evidence" [color=blue, label="has evidence", - lp="1805.4,221.5", - pos="e,1630.4,193.61 2557.7,263.03 2300.9,260.74 1906.7,253.22 1758.9,229 1718,222.3 1673.1,208.48 1640.2,197.06", + lp="1624.4,221.5", + pos="e,1579.9,195.85 2371.3,264.16 2075.7,263.16 1605.1,257.12 1577.9,229 1571.6,222.53 1572.4,213.49 1575.6,204.88", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1793.9,178", - width=3.015]; + label=string, + pos="1723.9,178", + width=1.0652]; "organism taxon to organism taxon specialization" -> "knowledge source" [color=blue, label="knowledge source", - lp="1960.4,221.5", - pos="e,1820,195.59 2565.3,260.02 2320.9,254.96 1958.9,244.92 1895.9,229 1872.4,223.07 1847.9,211.31 1828.9,200.68", + lp="1743.4,221.5", + pos="e,1699.5,191.96 2372.4,263.17 2105.1,261.04 1702.7,253.72 1678.9,229 1669.2,218.93 1678.4,207.33 1691,197.85", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2028.9,178", - width=3.015]; + label=string, + pos="1818.9,178", + width=1.0652]; "organism taxon to organism taxon specialization" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2131.9,221.5", - pos="e,2026.6,196.41 2564.2,260.36 2348.9,255.87 2056.5,246.57 2036.9,229 2030.5,223.34 2027.9,214.82 2027,206.41", + lp="1912.9,221.5", + pos="e,1813,196.04 2375.9,261.46 2149.8,257.81 1837.1,249.13 1817.9,229 1812.1,222.93 1810.8,214.32 1811.5,205.94", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2263.9,178", - width=3.015]; + label=string, + pos="1993.9,178", + width=1.0652]; "organism taxon to organism taxon specialization" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2340.4,221.5", - pos="e,2243.1,195.97 2578.7,257.33 2426.1,251.5 2246,241.93 2233.9,229 2226.9,221.54 2230.1,212.18 2236.5,203.58", + lp="2133.4,221.5", + pos="e,2000.3,196.01 2380.6,259.95 2231.2,255.64 2057.8,246.83 2026.9,229 2017.4,223.54 2010.2,214.14 2004.9,204.96", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2445.9,178", + pos="2220.9,178", width=1.5346]; "organism taxon to organism taxon specialization" -> timepoint [color=blue, label=timepoint, - lp="2495.9,221.5", - pos="e,2446.4,196.47 2611.5,253.37 2540.8,247.64 2473.6,239.54 2460.9,229 2454.1,223.41 2450.3,214.91 2448.2,206.49", + lp="2295.9,221.5", + pos="e,2229.7,195.91 2400.1,256.31 2341.3,251.24 2286.3,242.85 2260.9,229 2250.5,223.36 2241.9,213.81 2235.3,204.56", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2557.9,178", + pos="2332.9,178", width=1.0652]; "organism taxon to organism taxon specialization" -> "original subject" [color=blue, label="original subject", - lp="2594.9,221.5", - pos="e,2544.1,194.92 2602.9,254.25 2573.4,248.91 2549.3,240.91 2538.9,229 2532.6,221.83 2534.4,212.39 2538.8,203.65", + lp="2398.9,221.5", + pos="e,2331.6,196.24 2417.8,254.24 2384.2,248.98 2355.7,241.01 2342.9,229 2336.7,223.22 2333.7,214.78 2332.5,206.47", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2671.9,178", + pos="2457.9,178", width=1.5887]; "organism taxon to organism taxon specialization" -> "original predicate" [color=blue, label="original predicate", - lp="2722.4,221.5", - pos="e,2660.8,195.76 2700,248.38 2681,243.27 2664.9,236.85 2658.9,229 2653.6,222.16 2654.1,213.39 2656.9,205.11", + lp="2529.4,221.5", + pos="e,2456.2,196.34 2511.5,248.46 2490.9,243.31 2473.1,236.85 2465.9,229 2460.3,222.91 2457.7,214.52 2456.7,206.36", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2785.9,178", + pos="2586.9,178", width=1.0652]; "organism taxon to organism taxon specialization" -> "original object" [color=blue, label="original object", - lp="2841.4,221.5", - pos="e,2787.3,196.18 2791.5,246.8 2790.5,235.16 2789.2,219.55 2788.1,206.24", + lp="2650.4,221.5", + pos="e,2591.1,196.18 2603.6,246.8 2600.8,235.16 2596.9,219.55 2593.6,206.24", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2918.9,178", + pos="2719.9,178", width=2.1304]; "organism taxon to organism taxon specialization" -> "subject category" [color=blue, label="subject category", - lp="2967.4,221.5", - pos="e,2915,196.4 2866.5,247.89 2877.6,243.13 2888.2,236.97 2896.9,229 2903.6,222.84 2908.4,214.24 2911.7,205.9", + lp="2774.4,221.5", + pos="e,2719,196.22 2679.3,247.81 2689.2,243.06 2698.5,236.93 2705.9,229 2711.7,222.79 2715.1,214.38 2717.1,206.22", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3089.9,178", + pos="2890.9,178", width=2.1304]; "organism taxon to organism taxon specialization" -> "object category" [color=blue, label="object category", - lp="3110.4,221.5", - pos="e,3075.1,195.73 2957.6,252.02 2982.8,246.73 3008,239.32 3030.9,229 3044.5,222.83 3057.5,212.54 3067.8,202.9", + lp="2915.4,221.5", + pos="e,2877.5,196.2 2743.5,250.2 2783,244.69 2820.3,237.58 2837.9,229 2850.1,223.02 2861.5,213.21 2870.5,203.86", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3222.9,178", + pos="3023.9,178", width=1.0652]; "organism taxon to organism taxon specialization" -> "subject closure" [color=blue, label="subject closure", - lp="3246.4,221.5", - pos="e,3210.4,195.51 2951.4,251.63 3049.8,243.56 3159.5,233.69 3169.9,229 3182.8,223.16 3194.6,212.86 3203.7,203.11", + lp="3050.4,221.5", + pos="e,3012.6,195.49 2781.9,252.79 2867.7,246.28 2956.7,237.68 2974.9,229 2987,223.19 2997.9,213.03 3006.2,203.37", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3322.9,178", + pos="3136.9,178", width=1.0652]; "organism taxon to organism taxon specialization" -> "object closure" [color=blue, label="object closure", - lp="3366.9,221.5", - pos="e,3321.4,196.19 2961.3,252.33 2987.3,250.54 3013.8,248.72 3038.9,247 3068.4,244.98 3281.2,246.84 3304.9,229 3312.2,223.49 3316.5,\ -214.74 3319.1,206.09", + lp="3172.9,221.5", + pos="e,3132.1,195.9 2776.2,252.35 2921.6,242.28 3108.4,229.29 3108.9,229 3117.5,223.52 3123.7,214.38 3128.1,205.4", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3455.9,178", + pos="3269.9,178", width=2.1304]; "organism taxon to organism taxon specialization" -> "subject category closure" [color=blue, label="subject category closure", - lp="3525.4,221.5", - pos="e,3448.8,196.09 2957.9,252.09 2985,250.29 3012.7,248.52 3038.9,247 3081.3,244.54 3383.7,249.5 3420.9,229 3430.6,223.63 3438.3,214.25 \ -3443.9,205.06", + lp="3333.4,221.5", + pos="e,3260.3,196.16 2773.3,252.1 2800.2,250.3 2827.8,248.53 2853.9,247 2895.3,244.57 3189.6,247.21 3226.9,229 3237.9,223.61 3247.2,213.97 \ +3254.4,204.58", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3647.9,178", + pos="3462.9,178", width=2.1304]; "organism taxon to organism taxon specialization" -> "object category closure" [color=blue, label="object category closure", - lp="3715.4,221.5", - pos="e,3642.2,196.09 2955.3,251.9 2983.1,250.08 3011.8,248.36 3038.9,247 3071,245.39 3589.1,245.06 3616.9,229 3626.1,223.69 3632.9,214.46 \ -3637.8,205.36", + lp="3525.4,221.5", + pos="e,3454.9,196.18 2770.6,251.89 2798.4,250.07 2826.9,248.35 2853.9,247 2885.6,245.41 3396.7,243.55 3424.9,229 3435.2,223.7 3443.4,\ +214.2 3449.6,204.9", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3837.9,178", + pos="3652.9,178", width=1.0652]; "organism taxon to organism taxon specialization" -> "subject namespace" [color=blue, label="subject namespace", - lp="3887.9,221.5", - pos="e,3830.9,196.18 2954.3,251.8 2982.5,249.96 3011.5,248.27 3038.9,247 3081.3,245.04 3765.5,249.05 3802.9,229 3812.7,223.75 3820.3,\ -214.39 3826,205.18", + lp="3698.9,221.5", + pos="e,3644.6,195.75 2769.3,251.8 2797.5,249.97 2826.5,248.27 2853.9,247 2896,245.05 3575.1,247.72 3612.9,229 3623.7,223.64 3632.6,213.81 \ +3639.1,204.28", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3996.9,178", + pos="3811.9,178", width=1.0652]; "organism taxon to organism taxon specialization" -> "object namespace" [color=blue, label="object namespace", - lp="4040.9,221.5", - pos="e,3989.5,195.73 2953.3,251.77 2981.8,249.92 3011.2,248.23 3038.9,247 3090,244.74 3914.4,252.48 3959.9,229 3970.2,223.67 3978.4,213.98 \ -3984.4,204.55", + lp="3852.9,221.5", + pos="e,3803.3,195.77 2768.6,251.75 2797,249.91 2826.3,248.22 2853.9,247 2904.8,244.74 3725,251.25 3770.9,229 3781.9,223.67 3790.9,213.85 \ +3797.7,204.32", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4147.9,178", + pos="3962.9,178", width=1.0652]; "organism taxon to organism taxon specialization" -> "subject label closure" [color=blue, label="subject label closure", - lp="4200.9,221.5", - pos="e,4139.9,195.76 2952.9,251.72 2981.5,249.88 3011.1,248.19 3038.9,247 3068.6,245.72 4082.3,242.27 4108.9,229 4119.6,223.66 4128.2,\ -213.84 4134.6,204.3", + lp="4014.9,221.5", + pos="e,3954,195.8 2767.9,251.73 2796.5,249.88 2826.1,248.19 2853.9,247 2913.1,244.46 3867.4,254.49 3920.9,229 3932,223.7 3941.3,213.88 \ +3948.2,204.34", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4318.9,178", + pos="4133.9,178", width=1.0652]; "organism taxon to organism taxon specialization" -> "object label closure" [color=blue, label="object label closure", - lp="4366.4,221.5", - pos="e,4310.6,195.79 2952.6,251.69 2981.3,249.84 3011,248.17 3038.9,247 3073.3,245.56 4247.9,244.15 4278.9,229 4289.7,223.69 4298.6,213.87 \ -4305.2,204.33", + lp="4182.4,221.5", + pos="e,4125.3,195.8 2767.6,251.69 2796.3,249.84 2826,248.17 2853.9,247 2888.3,245.56 4061.9,243.95 4092.9,229 4103.9,223.7 4112.9,213.88 \ +4119.7,204.34", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4471.9,178", + pos="4286.9,178", width=2.347]; "organism taxon to organism taxon specialization" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4525.4,221.5", - pos="e,4465.9,196.18 2952.3,251.67 2981.1,249.82 3010.9,248.15 3038.9,247 3077.8,245.41 4405.9,247.9 4439.9,229 4449.3,223.74 4456.4,\ -214.39 4461.5,205.18", + lp="4340.4,221.5", + pos="e,4281.2,196.16 2767.3,251.67 2796.1,249.82 2825.9,248.15 2853.9,247 2892.8,245.41 4222,248.16 4255.9,229 4265.1,223.78 4272,214.56 \ +4276.8,205.45", style=solid]; type [height=0.5, - pos="4605.9,178", + pos="4420.9,178", width=0.86659]; "organism taxon to organism taxon specialization" -> type [color=blue, label=type, - lp="4623.9,221.5", - pos="e,4608.6,195.98 2951.9,251.67 2980.8,249.81 3010.8,248.13 3038.9,247 3060.5,246.13 4582.6,243.31 4598.9,229 4605.3,223.32 4607.9,\ -214.65 4608.5,206.11", + lp="4438.9,221.5", + pos="e,4423.6,195.98 2766.9,251.67 2795.8,249.81 2825.8,248.13 2853.9,247 2875.5,246.13 4397.6,243.31 4413.9,229 4420.3,223.32 4422.9,\ +214.65 4423.5,206.11", style=solid]; category [height=0.5, - pos="4706.9,178", + pos="4521.9,178", width=1.4263]; "organism taxon to organism taxon specialization" -> category [color=blue, label=category, - lp="4702.4,221.5", - pos="e,4692.1,195.48 2951.9,251.66 2980.8,249.8 3010.8,248.13 3038.9,247 3083.4,245.21 4601.9,243.91 4643.9,229 4659.1,223.59 4673.5,\ -212.83 4684.6,202.68", + lp="4517.4,221.5", + pos="e,4507.1,195.48 2766.9,251.66 2795.8,249.8 2825.8,248.13 2853.9,247 2898.4,245.21 4416.9,243.91 4458.9,229 4474.1,223.59 4488.5,\ +212.83 4499.6,202.68", style=solid]; subject [height=0.5, - pos="4820.9,178", + pos="4635.9,178", width=1.2277]; "organism taxon to organism taxon specialization" -> subject [color=blue, label=subject, - lp="4797.9,221.5", - pos="e,4802.1,194.32 2951.9,251.64 2980.8,249.79 3010.8,248.12 3038.9,247 3133.2,243.24 4647.1,254.76 4737.9,229 4758,223.28 4778.2,211.29 \ -4793.6,200.49", + lp="4612.9,221.5", + pos="e,4617.1,194.32 2766.9,251.64 2795.8,249.79 2825.8,248.12 2853.9,247 2948.2,243.24 4462.1,254.76 4552.9,229 4573,223.28 4593.2,211.29 \ +4608.6,200.49", style=solid]; object [height=0.5, - pos="4863.9,91", + pos="4678.9,91", width=1.0832]; "organism taxon to organism taxon specialization" -> object [color=blue, label=object, - lp="4907.9,178", - pos="e,4877.3,108.09 2951.9,251.63 2980.8,249.77 3010.8,248.11 3038.9,247 3088.5,245.04 4780.6,244.45 4827.9,229 4851.8,221.18 4859.8,\ -216.87 4873.9,196 4887.7,175.52 4884,166.51 4886.9,142 4887.7,135.38 4888.8,133.39 4886.9,127 4885.8,123.55 4884.4,120.13 4882.6,\ + lp="4722.9,178", + pos="e,4692.3,108.09 2766.9,251.63 2795.8,249.77 2825.8,248.11 2853.9,247 2903.5,245.04 4595.6,244.45 4642.9,229 4666.8,221.18 4674.8,\ +216.87 4688.9,196 4702.7,175.52 4699,166.51 4701.9,142 4702.7,135.38 4703.8,133.39 4701.9,127 4700.8,123.55 4699.4,120.13 4697.6,\ 116.85", style=solid]; predicate [height=0.5, - pos="5017.9,178", + pos="4832.9,178", width=1.5165]; "organism taxon to organism taxon specialization" -> predicate [color=blue, label=predicate, - lp="4990.9,221.5", - pos="e,4994.1,194.35 2951.6,251.64 2980.6,249.78 3010.6,248.11 3038.9,247 3143,242.91 4813.4,252.84 4914.9,229 4939.8,223.15 4965.7,210.56 \ -4985.2,199.47", + lp="4805.9,221.5", + pos="e,4809.1,194.35 2766.6,251.64 2795.6,249.78 2825.6,248.11 2853.9,247 2958,242.91 4628.4,252.84 4729.9,229 4754.8,223.15 4780.7,210.56 \ +4800.2,199.47", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3085.9,265", + pos="2900.9,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3216.9,265", + pos="3031.9,265", width=2.0762]; subject -> object [label=relation, - lp="4858.9,134.5", - pos="e,4846,107.23 4822,159.55 4823.2,149.57 4825.7,137.07 4830.9,127 4833.1,122.68 4836,118.52 4839.2,114.66"]; + lp="4673.9,134.5", + pos="e,4661,107.23 4637,159.55 4638.2,149.57 4640.7,137.07 4645.9,127 4648.1,122.68 4651,118.52 4654.2,114.66"]; relation [height=0.5, - pos="4808.9,18", + pos="4623.9,18", width=1.2999]; - subject -> relation [pos="e,4810.2,36.188 4819.6,159.79 4817.5,132.48 4813.4,78.994 4811,46.38", + subject -> relation [pos="e,4625.2,36.188 4634.6,159.79 4632.5,132.48 4628.4,78.994 4626,46.38", style=dotted]; "organism taxon to organism taxon specialization_subject" [color=blue, height=0.5, label="organism taxon", - pos="3392.9,265", + pos="3207.9,265", width=2.3109]; - object -> relation [pos="e,4821.7,35.54 4851.4,73.889 4844.5,64.939 4835.7,53.617 4827.9,43.584", + object -> relation [pos="e,4636.7,35.54 4666.4,73.889 4659.5,64.939 4650.7,53.617 4642.9,43.584", style=dotted]; "organism taxon to organism taxon specialization_object" [color=blue, height=0.5, label="organism taxon", - pos="3576.9,265", + pos="3391.9,265", width=2.3109]; "organism taxon to organism taxon specialization_predicate" [color=blue, height=0.5, label="predicate type", - pos="3755.9,265", + pos="3570.9,265", width=2.1665]; } diff --git a/graphviz/organism_taxon_to_organism_taxon_specialization.svg b/graphviz/organism_taxon_to_organism_taxon_specialization.svg index 6d1a3e2d57..18a4cafcf5 100644 --- a/graphviz/organism_taxon_to_organism_taxon_specialization.svg +++ b/graphviz/organism_taxon_to_organism_taxon_specialization.svg @@ -4,16 +4,16 @@ - + %3 - + organism taxon to organism taxon specialization - -organism taxon to organism taxon specialization + +organism taxon to organism taxon specialization @@ -24,8 +24,8 @@ organism taxon to organism taxon specialization->organism taxon to organism taxon association - - + + is_a @@ -37,9 +37,9 @@ organism taxon to organism taxon specialization->id - + -id +id @@ -50,9 +50,9 @@ organism taxon to organism taxon specialization->iri - - -iri + + +iri @@ -63,9 +63,9 @@ organism taxon to organism taxon specialization->name - - -name + + +name @@ -76,9 +76,9 @@ organism taxon to organism taxon specialization->description - - -description + + +description @@ -89,9 +89,9 @@ organism taxon to organism taxon specialization->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ organism taxon to organism taxon specialization->negated - - -negated + + +negated @@ -115,9 +115,9 @@ organism taxon to organism taxon specialization->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ organism taxon to organism taxon specialization->publications - - -publications + + +publications @@ -141,363 +141,363 @@ organism taxon to organism taxon specialization->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string organism taxon to organism taxon specialization->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string organism taxon to organism taxon specialization->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string organism taxon to organism taxon specialization->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type organism taxon to organism taxon specialization->timepoint - - -timepoint + + +timepoint original subject - -string + +string organism taxon to organism taxon specialization->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie organism taxon to organism taxon specialization->original predicate - - -original predicate + + +original predicate original object - -string + +string organism taxon to organism taxon specialization->original object - - -original object + + +original object subject category - -ontology class + +ontology class organism taxon to organism taxon specialization->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class organism taxon to organism taxon specialization->object category - - -object category + + +object category subject closure - -string + +string organism taxon to organism taxon specialization->subject closure - - -subject closure + + +subject closure object closure - -string + +string organism taxon to organism taxon specialization->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class organism taxon to organism taxon specialization->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class organism taxon to organism taxon specialization->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string organism taxon to organism taxon specialization->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string organism taxon to organism taxon specialization->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string organism taxon to organism taxon specialization->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string organism taxon to organism taxon specialization->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source organism taxon to organism taxon specialization->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type organism taxon to organism taxon specialization->type - - -type + + +type category - -category + +category organism taxon to organism taxon specialization->category - - -category + + +category subject - -subject + +subject organism taxon to organism taxon specialization->subject - - -subject + + +subject object - -object + +object organism taxon to organism taxon specialization->object - - -object + + +object predicate - -predicate + +predicate organism taxon to organism taxon specialization->predicate - - -predicate + + +predicate association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + organism taxon to organism taxon specialization_subject - -organism taxon + +organism taxon object->relation - - + + organism taxon to organism taxon specialization_object - -organism taxon + +organism taxon organism taxon to organism taxon specialization_predicate - -predicate type + +predicate type diff --git a/graphviz/organism_to_organism_association.gv b/graphviz/organism_to_organism_association.gv index eb47fd5725..2b4ff52cec 100644 --- a/graphviz/organism_to_organism_association.gv +++ b/graphviz/organism_to_organism_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4788.4,283"]; + graph [bb="0,0,4570.4,283"]; node [label="\N"]; "organism to organism association" [height=0.5, label="organism to organism association", - pos="2492.4,265", + pos="2274.4,265", width=4.6399]; association [height=0.5, pos="62.394,178", width=1.7332]; "organism to organism association" -> association [label=is_a, - lp="281.39,221.5", - pos="e,103.12,191.79 2325.6,263.53 1843.4,261.85 469.05,254.85 267.39,229 213.85,222.14 154.03,206.61 112.9,194.67"]; + lp="280.39,221.5", + pos="e,102.91,191.77 2108,263.23 1659.4,260.84 446.2,252.3 266.39,229 213.11,222.09 153.58,206.57 112.65,194.64"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "organism to organism association" -> id [color=blue, label=id, - lp="398.39,221.5", - pos="e,210.38,190 2326.4,263 1863.6,259.95 581.05,249.72 391.39,229 318.35,221.02 300.2,215.65 229.39,196 226.29,195.14 223.09,194.17 \ -219.89,193.16", + lp="396.39,221.5", + pos="e,210.38,189.98 2108.7,262.68 1680.2,259 557.28,247.71 389.39,229 317.23,220.96 299.34,215.5 229.39,196 226.29,195.13 223.09,194.17 \ +219.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "organism to organism association" -> iri [color=blue, label=iri, - lp="515.39,221.5", - pos="e,315.29,190.23 2326.4,262.71 1881.8,259.03 685.45,247.51 507.39,229 429.97,220.95 410.81,215.26 335.39,196 332.02,195.14 328.54,\ -194.18 325.05,193.17", + lp="509.39,221.5", + pos="e,315.3,190.2 2107.3,264.46 1727.7,264.91 809.2,262.37 501.39,229 426.61,220.89 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ +325.06,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "organism to organism association" -> name [color=blue, label=name, - lp="627.39,221.5", - pos="e,440.01,191.15 2326.2,262.94 1897.4,259.91 774.95,250.06 607.39,229 552.58,222.11 491.21,206.11 449.83,194.05", + lp="617.39,221.5", + pos="e,439.19,191.41 2108.4,262.68 1714.3,259.25 743.98,248.87 597.39,229 545.74,222 488.1,206.31 448.78,194.36", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "organism to organism association" -> description [color=blue, label=description, - lp="755.89,221.5", - pos="e,588.8,193.65 2326,263.34 1914.6,261.33 871.38,253.82 715.39,229 675.03,222.58 630.79,208.66 598.44,197.14", + lp="739.89,221.5", + pos="e,586.19,194.12 2108,263.15 1731.3,260.83 834.97,252.83 699.39,229 663.52,222.69 624.55,209.24 595.6,197.88", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "organism to organism association" -> "has attribute" [color=blue, label="has attribute", - lp="913.39,221.5", - pos="e,729.98,191.75 2326.5,262.91 1941.1,260.03 1007.5,250.88 866.39,229 822.26,222.16 773.51,207 739.58,195.15", + lp="887.39,221.5", + pos="e,726.83,192.67 2108.3,262.83 1757.2,259.94 962,251.04 840.39,229 804.17,222.43 764.8,208.24 736.39,196.65", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "organism to organism association" -> predicate [color=blue, label=predicate, - lp="1074.4,221.5", - pos="e,887.81,193.09 2325.2,264.7 1998,265.3 1283.8,262.54 1040.4,229 991.17,222.22 936.47,207.65 897.4,195.99", + lp="1031.4,221.5", + pos="e,880.43,194.06 2109.3,262.13 1788.7,258.1 1103.9,247.46 997.39,229 960.25,222.56 919.77,209.02 889.78,197.66", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "organism to organism association" -> negated [color=blue, label=negated, - lp="1220.4,221.5", - pos="e,1022.3,190.23 2325.7,263.48 2025.6,261.88 1405.8,255.38 1191.4,229 1135.6,222.13 1072.9,205.38 1032,193.16", + lp="1151.4,221.5", + pos="e,1015.6,192.51 2109.8,261.95 1814.4,257.82 1216.4,247.33 1122.4,229 1088.3,222.36 1051.5,208.2 1024.9,196.64", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "organism to organism association" -> qualifiers [color=blue, label=qualifiers, - lp="1356.9,221.5", - pos="e,1171.6,193.02 2325.7,263.54 2050.3,262.02 1511.7,255.62 1323.4,229 1274.6,222.11 1220.5,207.65 1181.6,196.05", + lp="1254.9,221.5", + pos="e,1151.6,195.39 2108.5,262.64 1833.4,259.76 1304.4,251.37 1221.4,229 1199.7,223.15 1177.4,211.43 1160.1,200.81", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "organism to organism association" -> publications [color=blue, label=publications, - lp="1499.4,221.5", - pos="e,1321.9,192.66 2325.9,263.48 2076.5,261.83 1617.8,255.2 1455.4,229 1412.5,222.09 1365.3,207.61 1331.5,196.01", + lp="1346.4,221.5", + pos="e,1286.4,196.26 2108.3,262.88 1839.1,260.39 1334.1,252.58 1302.4,229 1295.1,223.57 1290.9,214.84 1288.5,206.19", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,263 +110,264 @@ digraph { width=2.0943]; "organism to organism association" -> "has evidence" [color=blue, label="has evidence", - lp="1652.9,221.5", - pos="e,1479.4,193.55 2327,262.49 2109.7,259.63 1740.2,251.53 1606.4,229 1566,222.2 1521.6,208.38 1489.1,196.99", + lp="1444.9,221.5", + pos="e,1413.8,194.93 2108,263.22 1860.7,261.22 1422.5,254.13 1398.4,229 1390,220.25 1395.9,210.18 1405.7,201.37", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1643.4,178", - width=3.015]; + label=string, + pos="1573.4,178", + width=1.0652]; "organism to organism association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1802.9,221.5", - pos="e,1667.9,195.78 2325.3,264.68 2137.4,263.95 1844.9,257.94 1738.4,229 1716.6,223.09 1694.2,211.61 1676.7,201.13", + lp="1562.9,221.5", + pos="e,1543.3,189.28 2108.9,262.29 1887.2,259.16 1519.2,250.72 1498.4,229 1493.8,224.18 1494.8,219.62 1498.4,214 1502.8,207.12 1518,199.47 \ +1533.6,193.08", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1878.4,178", - width=3.015]; + label=string, + pos="1668.4,178", + width=1.0652]; "organism to organism association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1972.4,221.5", - pos="e,1872.6,196 2331,260.26 2154,255.34 1892.9,245.36 1877.4,229 1871.6,222.9 1870.4,214.27 1871,205.9", + lp="1729.4,221.5", + pos="e,1648.1,193.48 2112.2,260.63 1928,255.99 1650.7,246.18 1634.4,229 1626.3,220.46 1631.8,209.82 1640.6,200.55", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2113.4,178", - width=3.015]; + label=string, + pos="1810.4,178", + width=1.0652]; "organism to organism association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2180.9,221.5", - pos="e,2087.6,195.53 2330,260.75 2220.2,256.82 2092,248.14 2074.4,229 2066.7,220.62 2071.6,210.86 2080.1,202.2", + lp="1949.9,221.5", + pos="e,1816.9,195.93 2120.3,258.05 2006.4,252.55 1867.2,243.08 1843.4,229 1834,223.44 1826.8,214.03 1821.5,204.86", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2295.4,178", + pos="2037.4,178", width=1.5346]; "organism to organism association" -> timepoint [color=blue, label=timepoint, - lp="2332.4,221.5", - pos="e,2291.1,196.26 2364.3,253.44 2333.9,248.24 2307.4,240.51 2297.4,229 2292,222.83 2290.3,214.43 2290.3,206.27", + lp="2112.4,221.5", + pos="e,2046.6,196.08 2164.9,251.39 2128.3,245.73 2092.9,238.22 2077.4,229 2067.4,223.06 2058.9,213.63 2052.3,204.55", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2407.4,178", + pos="2149.4,178", width=1.0652]; "organism to organism association" -> "original subject" [color=blue, label="original subject", - lp="2430.4,221.5", - pos="e,2387.4,193.75 2400,249.85 2390,244.76 2381.1,237.99 2374.4,229 2367.7,220.01 2372.5,209.73 2380.3,200.83", + lp="2214.4,221.5", + pos="e,2148.2,196.23 2187.3,249.53 2176.4,244.53 2166.3,237.87 2158.4,229 2152.9,222.8 2150.2,214.39 2149,206.23", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2521.4,178", + pos="2274.4,178", width=1.5887]; "organism to organism association" -> "original predicate" [color=blue, label="original predicate", - lp="2556.9,221.5", - pos="e,2504.6,195.4 2490.1,246.84 2489.4,236.95 2489.6,224.45 2493.4,214 2494.7,210.42 2496.5,206.94 2498.6,203.64", + lp="2337.9,221.5", + pos="e,2274.4,196.18 2274.4,246.8 2274.4,235.16 2274.4,219.55 2274.4,206.24", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2635.4,178", + pos="2403.4,178", width=1.0652]; "organism to organism association" -> "original object" [color=blue, label="original object", - lp="2681.9,221.5", - pos="e,2634.3,196.46 2587.1,250.06 2599.4,244.99 2611,238.17 2620.4,229 2626.5,223.04 2630.2,214.69 2632.3,206.52", + lp="2459.9,221.5", + pos="e,2407.8,195.99 2357.7,249.34 2378.1,244.01 2396,237.22 2402.4,229 2407.4,222.62 2408.9,214.26 2408.7,206.21", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2768.4,178", + pos="2536.4,178", width=2.1304]; "organism to organism association" -> "subject category" [color=blue, label="subject category", - lp="2811.9,221.5", - pos="e,2762.2,196.16 2608,251.94 2665.8,245.1 2726,236.45 2737.4,229 2746.2,223.28 2752.9,214.13 2757.8,205.22", + lp="2586.9,221.5", + pos="e,2533.7,196.01 2391.6,252.16 2447.7,245.55 2505,237.05 2515.4,229 2522.8,223.28 2527.6,214.49 2530.7,205.86", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2939.4,178", + pos="2707.4,178", width=2.1304]; "organism to organism association" -> "object category" [color=blue, label="object category", - lp="2956.9,221.5", - pos="e,2923.5,195.8 2611.7,252.32 2630.6,250.51 2650.1,248.68 2668.4,247 2714.4,242.78 2832.4,245.91 2875.4,229 2890.3,223.14 2904.5,\ -212.65 2915.8,202.79", + lp="2728.9,221.5", + pos="e,2693.3,196.02 2393.7,252.37 2412.6,250.55 2432.1,248.71 2450.4,247 2494.8,242.85 2609.4,246.58 2650.4,229 2663.9,223.21 2676.5,\ +212.98 2686.3,203.26", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3072.4,178", + pos="2840.4,178", width=1.0652]; "organism to organism association" -> "subject closure" [color=blue, label="subject closure", - lp="3093.9,221.5", - pos="e,3059.6,195.24 2608.8,252.02 2628.7,250.19 2649.1,248.43 2668.4,247 2745.6,241.28 2944.8,258.46 3016.4,229 3030.2,223.31 3042.9,\ -212.68 3052.7,202.67", + lp="2864.9,221.5", + pos="e,2828.7,195.21 2390.8,252.04 2410.7,250.21 2431.1,248.44 2450.4,247 2487.9,244.19 2753.9,243.97 2788.4,229 2801.4,223.33 2813.2,\ +212.85 2822.1,202.94", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3172.4,178", + pos="2953.4,178", width=1.0652]; "organism to organism association" -> "object closure" [color=blue, label="object closure", - lp="3214.4,221.5", - pos="e,3170.3,196.34 2607.3,251.91 2627.7,250.05 2648.6,248.32 2668.4,247 2695.2,245.21 3130.4,244.5 3152.4,229 3160.1,223.6 3164.8,214.76 \ -3167.7,206", + lp="2988.4,221.5", + pos="e,2948,196.05 2389.3,251.92 2409.7,250.07 2430.6,248.33 2450.4,247 2502.9,243.47 2878.1,255.78 2923.4,229 2932.4,223.64 2939.1,214.4 \ +2943.8,205.3", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3305.4,178", + pos="3086.4,178", width=2.1304]; "organism to organism association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3372.9,221.5", - pos="e,3297.7,196.18 2606.9,251.83 2627.3,249.97 2648.5,248.26 2668.4,247 2701.7,244.9 3238.8,244.45 3268.4,229 3278.5,223.69 3286.6,\ -214.19 3292.6,204.89", + lp="3148.9,221.5", + pos="e,3076.5,196.25 2388.9,251.84 2409.3,249.98 2430.5,248.26 2450.4,247 2483.2,244.92 3012.6,243.01 3042.4,229 3053.7,223.67 3063.3,\ +213.9 3070.7,204.41", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3497.4,178", + pos="3279.4,178", width=2.1304]; "organism to organism association" -> "object category closure" [color=blue, label="object category closure", - lp="3563.9,221.5", - pos="e,3491.1,196.16 2606.4,251.75 2627,249.89 2648.3,248.19 2668.4,247 2712.5,244.37 3425.7,250.4 3464.4,229 3474,223.72 3481.2,214.36 \ -3486.5,205.15", + lp="3341.9,221.5", + pos="e,3271.1,196.23 2388.4,251.76 2409,249.89 2430.3,248.2 2450.4,247 2494.2,244.39 3201.2,248.71 3240.4,229 3250.8,223.76 3259.3,214.27 \ +3265.7,204.96", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3687.4,178", + pos="3469.4,178", width=1.0652]; "organism to organism association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3736.4,221.5", - pos="e,3680.3,195.72 2605.9,251.72 2626.7,249.85 2648.2,248.16 2668.4,247 2722.9,243.87 3603,254.35 3651.4,229 3661.6,223.66 3669.6,213.97 \ -3675.4,204.54", + lp="3515.4,221.5", + pos="e,3461.1,195.77 2387.9,251.73 2408.7,249.85 2430.2,248.16 2450.4,247 2504.7,243.88 3380.6,253.01 3429.4,229 3440.2,223.66 3449.1,\ +213.84 3455.7,204.31", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3846.4,178", + pos="3628.4,178", width=1.0652]; "organism to organism association" -> "object namespace" [color=blue, label="object namespace", - lp="3890.4,221.5", - pos="e,3838.7,195.76 2605.4,251.72 2626.3,249.84 2648,248.14 2668.4,247 2700,245.23 3780.1,243.3 3808.4,229 3818.9,223.7 3827.2,214.03 \ -3833.4,204.58", + lp="3669.4,221.5", + pos="e,3619.8,195.79 2387.4,251.73 2408.3,249.84 2430,248.14 2450.4,247 2481.9,245.23 3559,242.74 3587.4,229 3598.4,223.69 3607.4,213.88 \ +3614.2,204.34", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3997.4,178", + pos="3779.4,178", width=1.0652]; "organism to organism association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4050.4,221.5", - pos="e,3989.4,195.78 2605.4,251.69 2626.3,249.81 2648,248.12 2668.4,247 2704.2,245.03 3926.3,244.95 3958.4,229 3969.1,223.67 3977.8,213.85 \ -3984.2,204.32", + lp="3831.4,221.5", + pos="e,3770.5,195.81 2387.4,251.69 2408.3,249.81 2430,248.13 2450.4,247 2486.1,245.03 3705.1,244.33 3737.4,229 3748.5,223.72 3757.8,213.9 \ +3764.7,204.36", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4168.4,178", + pos="3950.4,178", width=1.0652]; "organism to organism association" -> "object label closure" [color=blue, label="object label closure", - lp="4215.9,221.5", - pos="e,4160.1,195.79 2605.4,251.67 2626.3,249.79 2648,248.11 2668.4,247 2708.9,244.8 4091.9,246.79 4128.4,229 4139.3,223.7 4148.1,213.88 \ -4154.7,204.34", + lp="3998.9,221.5", + pos="e,3941.8,195.81 2387.4,251.67 2408.3,249.79 2430,248.11 2450.4,247 2490.9,244.8 3872.9,246.56 3909.4,229 3920.4,223.71 3929.4,213.9 \ +3936.2,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4330.4,178", + pos="4112.4,178", width=2.347]; "organism to organism association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4378.9,221.5", - pos="e,4321.5,196.31 2605,251.69 2626,249.79 2647.9,248.1 2668.4,247 2713.4,244.58 4248.8,248.49 4289.4,229 4300.2,223.79 4309.2,214.18 \ -4315.9,204.77", + lp="4160.9,221.5", + pos="e,4103.8,196.29 2387,251.69 2408,249.79 2429.9,248.1 2450.4,247 2495.4,244.58 4031.9,248.74 4072.4,229 4083.1,223.78 4091.9,214.16 \ +4098.4,204.75", style=solid]; type [height=0.5, - pos="4464.4,178", + pos="4246.4,178", width=0.86659]; "organism to organism association" -> type [color=blue, label=type, - lp="4478.4,221.5", - pos="e,4465.2,196.18 2605,251.67 2626,249.78 2647.9,248.09 2668.4,247 2693.1,245.68 4433,244.44 4452.4,229 4459.2,223.54 4462.6,214.92 \ -4464.1,206.37", + lp="4260.4,221.5", + pos="e,4247.2,196.18 2387,251.67 2408,249.78 2429.9,248.09 2450.4,247 2475.1,245.68 4215,244.44 4234.4,229 4241.2,223.54 4244.6,214.92 \ +4246.1,206.37", style=solid]; category [height=0.5, - pos="4565.4,178", + pos="4347.4,178", width=1.4263]; "organism to organism association" -> category [color=blue, label=category, - lp="4558.9,221.5", - pos="e,4549.8,195.25 2605,251.67 2626,249.78 2647.9,248.09 2668.4,247 2719.2,244.3 4450.2,245.26 4498.4,229 4514.6,223.53 4530.1,212.51 \ -4542.1,202.2", + lp="4340.9,221.5", + pos="e,4331.8,195.25 2387,251.67 2408,249.78 2429.9,248.09 2450.4,247 2501.2,244.3 4232.2,245.26 4280.4,229 4296.6,223.53 4312.1,212.51 \ +4324.1,202.2", style=solid]; subject [height=0.5, - pos="4679.4,178", + pos="4461.4,178", width=1.2277]; "organism to organism association" -> subject [color=blue, label=subject, - lp="4655.4,221.5", - pos="e,4660.1,194.33 2605,251.66 2626,249.77 2647.9,248.09 2668.4,247 2775.2,241.35 4491.3,257.6 4594.4,229 4615.1,223.25 4636,211.09 \ -4651.9,200.2", + lp="4437.4,221.5", + pos="e,4442.1,194.33 2387,251.66 2408,249.77 2429.9,248.09 2450.4,247 2557.2,241.35 4273.3,257.6 4376.4,229 4397.1,223.25 4418,211.09 \ +4433.9,200.2", style=solid]; object [height=0.5, - pos="4722.4,91", + pos="4504.4,91", width=1.0832]; "organism to organism association" -> object [color=blue, label=object, - lp="4766.4,178", - pos="e,4735.8,108.09 2605,251.65 2626,249.76 2647.9,248.08 2668.4,247 2724.3,244.05 4632,246.12 4685.4,229 4709.7,221.2 4718,217.1 4732.4,\ -196 4746.3,175.59 4742.5,166.51 4745.4,142 4746.2,135.38 4747.3,133.39 4745.4,127 4744.4,123.55 4742.9,120.13 4741.1,116.85", + lp="4548.4,178", + pos="e,4517.8,108.09 2387,251.65 2408,249.76 2429.9,248.08 2450.4,247 2506.3,244.05 4414,246.12 4467.4,229 4491.7,221.2 4500,217.1 4514.4,\ +196 4528.3,175.59 4524.5,166.51 4527.4,142 4528.2,135.38 4529.3,133.39 4527.4,127 4526.4,123.55 4524.9,120.13 4523.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2715.4,265", + pos="2497.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2846.4,265", + pos="2628.4,265", width=2.0762]; subject -> object [label=relation, - lp="4717.4,134.5", - pos="e,4704.5,107.23 4680.5,159.55 4681.7,149.57 4684.2,137.07 4689.4,127 4691.6,122.68 4694.5,118.52 4697.7,114.66"]; + lp="4499.4,134.5", + pos="e,4486.5,107.23 4462.5,159.55 4463.7,149.57 4466.2,137.07 4471.4,127 4473.6,122.68 4476.5,118.52 4479.7,114.66"]; relation [height=0.5, - pos="4667.4,18", + pos="4449.4,18", width=1.2999]; - subject -> relation [pos="e,4668.7,36.188 4678.1,159.79 4676,132.48 4672,78.994 4669.5,46.38", + subject -> relation [pos="e,4450.7,36.188 4460.1,159.79 4458,132.48 4454,78.994 4451.5,46.38", style=dotted]; "organism to organism association_subject" [color=blue, height=0.5, label="individual organism", - pos="3041.4,265", + pos="2823.4,265", width=2.8525]; - object -> relation [pos="e,4680.2,35.54 4709.9,73.889 4703,64.939 4694.2,53.617 4686.4,43.584", + object -> relation [pos="e,4462.2,35.54 4491.9,73.889 4485,64.939 4476.2,53.617 4468.4,43.584", style=dotted]; "organism to organism association_object" [color=blue, height=0.5, label="individual organism", - pos="3264.4,265", + pos="3046.4,265", width=2.8525]; } diff --git a/graphviz/organism_to_organism_association.svg b/graphviz/organism_to_organism_association.svg index 5e3520b9bf..7ab8d76911 100644 --- a/graphviz/organism_to_organism_association.svg +++ b/graphviz/organism_to_organism_association.svg @@ -4,16 +4,16 @@ - + %3 - + organism to organism association - -organism to organism association + +organism to organism association @@ -24,9 +24,9 @@ organism to organism association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ organism to organism association->id - - -id + + +id @@ -50,9 +50,9 @@ organism to organism association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ organism to organism association->name - - -name + + +name @@ -76,9 +76,9 @@ organism to organism association->description - - -description + + +description @@ -89,9 +89,9 @@ organism to organism association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ organism to organism association->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ organism to organism association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ organism to organism association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ organism to organism association->publications - - -publications + + +publications @@ -154,344 +154,344 @@ organism to organism association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string organism to organism association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string organism to organism association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string organism to organism association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type organism to organism association->timepoint - - -timepoint + + +timepoint original subject - -string + +string organism to organism association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie organism to organism association->original predicate - - -original predicate + + +original predicate original object - -string + +string organism to organism association->original object - - -original object + + +original object subject category - -ontology class + +ontology class organism to organism association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class organism to organism association->object category - - -object category + + +object category subject closure - -string + +string organism to organism association->subject closure - - -subject closure + + +subject closure object closure - -string + +string organism to organism association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class organism to organism association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class organism to organism association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string organism to organism association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string organism to organism association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string organism to organism association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string organism to organism association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source organism to organism association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type organism to organism association->type - - -type + + +type category - -category + +category organism to organism association->category - - -category + + +category subject - -subject + +subject organism to organism association->subject - - -subject + + +subject object - -object + +object organism to organism association->object - - -object + + +object association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + organism to organism association_subject - -individual organism + +individual organism object->relation - - + + organism to organism association_object - -individual organism + +individual organism diff --git a/graphviz/organismal_entity_as_a_model_of_disease_association.gv b/graphviz/organismal_entity_as_a_model_of_disease_association.gv index 335ce5f944..02fdef42a1 100644 --- a/graphviz/organismal_entity_as_a_model_of_disease_association.gv +++ b/graphviz/organismal_entity_as_a_model_of_disease_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,5972.4,283"]; + graph [bb="0,0,5707.4,283"]; node [label="\N"]; "organismal entity as a model of disease association" [height=0.5, label="organismal entity as a model of disease association", - pos="3219.4,265", + pos="2954.4,265", width=6.9147]; association [height=0.5, pos="62.394,178", width=1.7332]; "organismal entity as a model of disease association" -> association [label=is_a, lp="626.39,221.5", - pos="e,107.11,190.75 2972.8,262.44 2414.4,258.62 1066.8,247.72 612.39,229 399.62,220.23 344.94,227.91 134.39,196 128.7,195.14 122.79,\ -194.05 116.92,192.86"]; + pos="e,107.11,190.75 2705.1,264.69 2277,264.88 1374.4,260.98 612.39,229 399.63,220.07 344.94,227.91 134.39,196 128.7,195.14 122.79,194.05 \ +116.92,192.86"]; "model to disease association mixin" [height=0.5, pos="315.39,178", width=4.7843]; "organismal entity as a model of disease association" -> "model to disease association mixin" [label=uses, lp="843.89,221.5", - pos="e,423.07,192.13 2971.9,262.98 2447.4,260.38 1238.4,252.04 827.39,229 691.91,221.41 536.89,205.21 433.25,193.3"]; + pos="e,423.07,192.07 2707.7,262.45 2228.1,259.02 1186.1,249.43 827.39,229 691.91,221.28 536.89,205.11 433.25,193.24"]; "entity to disease association mixin" [height=0.5, pos="676.39,178", width=4.7482]; "organismal entity as a model of disease association" -> "entity to disease association mixin" [label=uses, lp="998.89,221.5", - pos="e,750.52,194.23 2970.4,264.7 2470.7,265.34 1361.4,262.75 982.39,229 906.84,222.27 821.76,207.8 760.52,196.15"]; + pos="e,750.84,194.25 2705.4,264.06 2252.3,263.42 1309.3,258.45 982.39,229 906.98,222.21 822.05,207.78 760.83,196.16"]; id [color=blue, height=0.5, label=string, @@ -32,7 +32,7 @@ digraph { "organismal entity as a model of disease association" -> id [color=blue, label=id, lp="1116.4,221.5", - pos="e,932.38,189.97 2972.8,262.53 2455.5,259.08 1289.8,249.15 1109.4,229 1038.1,221.04 1020.5,215.35 951.39,196 948.29,195.13 945.09,\ + pos="e,932.38,189.97 2708.9,261.9 2243.1,257.54 1263.7,246.43 1109.4,229 1038.1,220.95 1020.5,215.35 951.39,196 948.29,195.13 945.09,\ 194.16 941.89,193.14", style=solid]; iri [color=blue, @@ -43,7 +43,7 @@ digraph { "organismal entity as a model of disease association" -> iri [color=blue, label=iri, lp="1213.4,221.5", - pos="e,1037.7,190.02 2972.7,262.5 2473.4,259.07 1376.1,249.31 1205.4,229 1149.9,222.4 1087.8,205.4 1047.5,193.05", + pos="e,1037.7,189.99 2709.1,261.8 2262.8,257.41 1350.2,246.42 1205.4,229 1149.9,222.33 1087.8,205.35 1047.5,193.02", style=solid]; name [color=blue, height=0.5, @@ -53,7 +53,7 @@ digraph { "organismal entity as a model of disease association" -> name [color=blue, label=name, lp="1309.4,221.5", - pos="e,1157.7,192.37 2971.3,263.29 2487.5,261.36 1450.9,254.29 1289.4,229 1247.1,222.37 1200.5,207.67 1167.5,195.91", + pos="e,1157.7,192.34 2707.8,262.51 2278.2,259.35 1425.2,250.47 1289.4,229 1247.1,222.31 1200.5,207.61 1167.5,195.87", style=solid]; description [color=blue, height=0.5, @@ -63,7 +63,7 @@ digraph { "organismal entity as a model of disease association" -> description [color=blue, label=description, lp="1412.9,221.5", - pos="e,1297.8,195.26 2973.3,262.24 2488.2,258.36 1448.6,247.91 1372.4,229 1349.1,223.22 1325,211.22 1306.5,200.42", + pos="e,1297.8,195.23 2705.3,264.53 2292.1,264.51 1497.7,260.31 1372.4,229 1349.1,223.18 1325,211.18 1306.5,200.4", style=solid]; "has attribute" [color=blue, height=0.5, @@ -73,7 +73,7 @@ digraph { "organismal entity as a model of disease association" -> "has attribute" [color=blue, label="has attribute", lp="1532.4,221.5", - pos="e,1434,195.2 2971.7,262.99 2509.1,260.54 1554.3,252.64 1485.4,229 1469.2,223.45 1453.7,212.42 1441.7,202.13", + pos="e,1434,195.17 2708.5,262.03 2305.2,258.24 1542,248.53 1485.4,229 1469.2,223.42 1453.8,212.39 1441.8,202.1", style=solid]; predicate [color=blue, height=0.5, @@ -83,18 +83,18 @@ digraph { "organismal entity as a model of disease association" -> predicate [color=blue, label=predicate, lp="1632.4,221.5", - pos="e,1572.4,196.14 2970.3,264.74 2530.5,265.19 1657,261.9 1598.4,229 1589,223.7 1581.9,214.34 1576.8,205.14", + pos="e,1572.4,196.13 2706.1,263.57 2327.8,262.07 1645.6,255.66 1598.4,229 1589,223.68 1581.9,214.32 1576.8,205.12", style=solid]; object [color=blue, height=0.5, label="named thing", - pos="5358.4,91", + pos="5093.4,91", width=1.9318]; "organismal entity as a model of disease association" -> object [color=blue, label=object, lp="1711.4,178", - pos="e,5288.9,91.949 2976.2,261.08 2655.5,256.61 2108.5,246.68 1908.4,229 1806.7,220.02 1617.9,232.83 1689.4,160 1754.5,93.7 4748.8,91.768 \ -5278.7,91.946", + pos="e,5023.6,92.052 2710.1,261.47 2434.6,257.7 2003.9,248.8 1842.4,229 1768.4,219.93 1637.2,213.27 1689.4,160 1749.5,98.687 4505.8,92.655 \ +5013.5,92.064", style=solid]; negated [color=blue, height=0.5, @@ -103,8 +103,8 @@ digraph { width=1.2999]; "organismal entity as a model of disease association" -> negated [color=blue, label=negated, - lp="2019.4,221.5", - pos="e,1824.1,190.32 2972.4,262.62 2669.4,259.94 2173.4,252.06 1990.4,229 1935.6,222.1 1874.3,205.5 1833.9,193.31", + lp="1912.4,221.5", + pos="e,1811,194.18 2709.1,261.83 2417.6,258.33 1960.7,249.62 1883.4,229 1860.7,222.95 1837.4,210.62 1819.7,199.71", style=solid]; qualifiers [color=blue, height=0.5, @@ -113,8 +113,8 @@ digraph { width=2.1304]; "organismal entity as a model of disease association" -> qualifiers [color=blue, label=qualifiers, - lp="2153.9,221.5", - pos="e,1972.8,193.12 2972.6,262.6 2700,259.9 2278.5,252.03 2120.4,229 2073,222.1 2020.4,207.72 1982.6,196.15", + lp="1992.9,221.5", + pos="e,1935.4,196.04 2710.5,261.3 2426.3,257.28 1991.1,248.04 1959.4,229 1950.5,223.64 1944,214.39 1939.5,205.3", style=solid]; publications [color=blue, height=0.5, @@ -123,8 +123,8 @@ digraph { width=1.7332]; "organismal entity as a model of disease association" -> publications [color=blue, label=publications, - lp="2293.4,221.5", - pos="e,2122.8,192.88 2972.8,262.47 2732,259.64 2383.1,251.64 2249.4,229 2208.9,222.14 2164.4,207.9 2132.3,196.37", + lp="2078.4,221.5", + pos="e,2055.5,193.49 2706.8,262.97 2442.3,260.61 2057.5,253.05 2034.4,229 2024.5,218.74 2033.6,207.83 2046.8,198.82", style=solid]; "has evidence" [color=blue, height=0.5, @@ -133,281 +133,284 @@ digraph { width=2.0943]; "organismal entity as a model of disease association" -> "has evidence" [color=blue, label="has evidence", - lp="2442.9,221.5", - pos="e,2279.5,193.89 2976.7,260.98 2774.8,257.12 2503.6,248.42 2396.4,229 2359.3,222.28 2318.8,208.76 2288.8,197.47", + lp="2175.9,221.5", + pos="e,2186.4,189.91 2709.4,261.77 2473.5,258.38 2149.5,249.93 2129.4,229 2124.8,224.19 2125.4,219.36 2129.4,214 2135.7,205.45 2155.3,\ +198.12 2176.6,192.41", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2445.4,178", - width=3.015]; + label=string, + pos="2375.4,178", + width=1.0652]; "organismal entity as a model of disease association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2586.9,221.5", - pos="e,2464.8,195.77 2988.1,258.34 2802.5,252.81 2566.1,243.14 2522.4,229 2504.6,223.23 2486.9,212.21 2472.9,201.98", + lp="2306.9,221.5", + pos="e,2346.4,189.96 2715.1,260.02 2514.8,255.47 2258.9,246.31 2242.4,229 2197.3,181.64 2186.1,235.8 2327.4,196 2330.5,195.13 2333.7,\ +194.15 2336.9,193.13", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2680.4,178", - width=3.015]; + label=string, + pos="2470.4,178", + width=1.0652]; "organismal entity as a model of disease association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2754.4,221.5", - pos="e,2664.7,195.98 2996.1,257.01 2845.3,251.16 2671.3,241.71 2659.4,229 2653,222.18 2654.7,213.11 2659.2,204.57", + lp="2473.4,221.5", + pos="e,2440.9,189.76 2728.8,257.36 2572.7,251.63 2390.8,242.18 2378.4,229 2373.8,224.15 2374.6,219.49 2378.4,214 2379.2,212.77 2406.6,\ +202.43 2431.3,193.3", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2915.4,178", - width=3.015]; + label=string, + pos="2565.4,178", + width=1.0652]; "organismal entity as a model of disease association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2963.9,221.5", - pos="e,2877,194.99 3010.1,255.25 2936.5,249.99 2869,241.75 2857.4,229 2848.2,218.83 2855.8,208.72 2868.3,200.28", + lp="2688.9,221.5", + pos="e,2566.6,196.08 2753.5,254.36 2673.6,248.8 2597,240.56 2582.4,229 2575.3,223.36 2571.1,214.59 2568.7,205.95", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="3097.4,178", + pos="2785.4,178", width=1.5346]; "organismal entity as a model of disease association" -> timepoint [color=blue, label=timepoint, - lp="3112.4,221.5", - pos="e,3082.8,195.52 3119.2,248.45 3099.9,243.41 3083.7,236.99 3077.4,229 3071.7,221.76 3073.4,212.7 3077.5,204.28", + lp="2846.4,221.5", + pos="e,2790.3,196.24 2847.3,248.66 2834.4,243.77 2822,237.37 2811.4,229 2803.8,223.03 2798.2,214.22 2794.2,205.65", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="3209.4,178", + pos="2897.4,178", width=1.0652]; "organismal entity as a model of disease association" -> "original subject" [color=blue, label="original subject", - lp="3209.4,221.5", - pos="e,3180.7,190.29 3172.2,247.32 3164.7,242.57 3157.9,236.56 3153.4,229 3145.4,215.65 3157,203.87 3171.8,195.09", + lp="2944.4,221.5", + pos="e,2888.9,195.81 2907.2,247.32 2899.7,242.57 2892.9,236.56 2888.4,229 2884.2,221.99 2884.2,213.49 2885.9,205.5", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3323.4,178", + pos="3022.4,178", width=1.5887]; "organismal entity as a model of disease association" -> "original predicate" [color=blue, label="original predicate", - lp="3346.9,221.5", - pos="e,3305.1,195.28 3242.5,246.83 3249.9,241.23 3258.1,234.94 3265.4,229 3276.1,220.35 3287.6,210.53 3297.5,201.9", + lp="3072.9,221.5", + pos="e,3017.2,196.38 2981.7,246.8 2988.4,241.66 2995.2,235.62 3000.4,229 3005.8,222.12 3010.2,213.69 3013.6,205.72", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3437.4,178", + pos="3151.4,178", width=1.0652]; "organismal entity as a model of disease association" -> "original object" [color=blue, label="original object", - lp="3478.9,221.5", - pos="e,3433.9,195.93 3350.5,249.67 3378.5,244.53 3403.1,237.76 3414.4,229 3422,223.14 3427.1,214.2 3430.6,205.49", + lp="3200.9,221.5", + pos="e,3152.1,196.11 3085.8,249.71 3110.3,244.66 3131.2,237.92 3140.4,229 3146.5,223.08 3149.6,214.61 3151,206.32", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3570.4,178", + pos="3284.4,178", width=2.1304]; "organismal entity as a model of disease association" -> "subject category" [color=blue, label="subject category", - lp="3610.9,221.5", - pos="e,3562.6,196.33 3420.9,254.39 3469.5,249.21 3513.4,241.25 3534.4,229 3544,223.42 3551.7,214.17 3557.5,205.14", + lp="3329.9,221.5", + pos="e,3279.3,196.22 3156,254.39 3199.6,249.19 3238.1,241.22 3256.4,229 3264.8,223.41 3270.9,214.41 3275.3,205.57", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3741.4,178", + pos="3455.4,178", width=2.1304]; "organismal entity as a model of disease association" -> "object category" [color=blue, label="object category", - lp="3756.9,221.5", - pos="e,3724.8,195.61 3390.7,251.92 3516.8,242.85 3667.5,231.57 3674.4,229 3690.1,223.12 3705.2,212.38 3717.1,202.36", + lp="3473.9,221.5", + pos="e,3439.8,196.08 3131.1,252.3 3247.6,244.21 3380.8,234.01 3393.4,229 3407.9,223.23 3421.6,212.86 3432.5,203.05", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3874.4,178", + pos="3588.4,178", width=1.0652]; "organismal entity as a model of disease association" -> "subject closure" [color=blue, label="subject closure", - lp="3892.9,221.5", - pos="e,3858.6,194.67 3394.2,252.18 3422.1,250.38 3450.5,248.6 3477.4,247 3552.7,242.52 3746.4,257.14 3816.4,229 3824.3,225.84 3838.7,\ -213.42 3851.2,201.75", + lp="3610.9,221.5", + pos="e,3575.9,195.21 3129.9,252.2 3157.5,250.41 3185.7,248.63 3212.4,247 3283.7,242.65 3467.5,256.62 3533.4,229 3547.1,223.28 3559.5,\ +212.64 3569.1,202.64", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3970.4,178", + pos="3701.4,178", width=1.0652]; "organismal entity as a model of disease association" -> "object closure" [color=blue, label="object closure", - lp="4011.4,221.5", - pos="e,3967.9,196.36 3391.8,251.98 3420.4,250.17 3449.7,248.44 3477.4,247 3503.6,245.64 3927.8,243.94 3949.4,229 3957.2,223.63 3962.1,\ -214.79 3965.2,206.03", + lp="3735.4,221.5", + pos="e,3695.3,196.08 3126.8,252.01 3155.4,250.2 3184.7,248.46 3212.4,247 3263.1,244.33 3625.3,254.27 3669.4,229 3678.8,223.62 3685.9,\ +214.24 3690.9,205.05", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="4103.4,178", + pos="3834.4,178", width=2.1304]; "organismal entity as a model of disease association" -> "subject category closure" [color=blue, label="subject category closure", - lp="4169.9,221.5", - pos="e,4095.4,196.19 3390.4,251.88 3419.4,250.07 3449.3,248.36 3477.4,247 3510,245.43 4036.3,243.97 4065.4,229 4075.7,223.7 4084,214.21 \ -4090.1,204.91", + lp="3896.9,221.5", + pos="e,3824.2,196.25 3125.4,251.9 3154.4,250.08 3184.3,248.37 3212.4,247 3244.4,245.45 3760.3,242.5 3789.4,229 3800.9,223.68 3810.7,213.91 \ +3818.2,204.41", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="4292.4,178", + pos="4027.4,178", width=2.1304]; "organismal entity as a model of disease association" -> "object category closure" [color=blue, label="object category closure", - lp="4359.9,221.5", - pos="e,4286.7,196.12 3389,251.79 3418.5,249.96 3448.8,248.27 3477.4,247 3520.9,245.07 4223.6,250.62 4261.4,229 4270.6,223.73 4277.4,214.5 \ -4282.3,205.4", + lp="4089.9,221.5", + pos="e,4019.1,196.23 3124,251.79 3153.5,249.97 3183.8,248.27 3212.4,247 3255.5,245.08 3949.9,248.37 3988.4,229 3998.8,223.75 4007.3,214.27 \ +4013.7,204.96", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4482.4,178", + pos="4217.4,178", width=1.0652]; "organismal entity as a model of disease association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4532.4,221.5", - pos="e,4475.4,196.2 3388,251.74 3417.7,249.91 3448.5,248.22 3477.4,247 3531.2,244.73 4399.8,254.33 4447.4,229 4457.2,223.77 4464.9,214.42 \ -4470.5,205.21", + lp="4263.4,221.5", + pos="e,4209.1,195.77 3123,251.75 3152.7,249.91 3183.5,248.22 3212.4,247 3266,244.74 4129.3,252.68 4177.4,229 4188.2,223.66 4197.1,213.84 \ +4203.7,204.31", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4641.4,178", + pos="4376.4,178", width=1.0652]; "organismal entity as a model of disease association" -> "object namespace" [color=blue, label="object namespace", - lp="4685.4,221.5", - pos="e,4634,195.74 3387.6,251.7 3417.5,249.86 3448.4,248.19 3477.4,247 3508.7,245.72 4576.5,243.31 4604.4,229 4614.7,223.69 4622.9,214.01 \ -4628.9,204.57", + lp="4417.4,221.5", + pos="e,4367.8,195.79 3122.6,251.7 3152.5,249.86 3183.4,248.19 3212.4,247 3243.6,245.72 4307.3,242.57 4335.4,229 4346.4,223.69 4355.4,\ +213.87 4362.2,204.33", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4792.4,178", + pos="4527.4,178", width=1.0652]; "organismal entity as a model of disease association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4845.4,221.5", - pos="e,4784.4,195.78 3387.3,251.68 3417.3,249.83 3448.2,248.17 3477.4,247 3512.8,245.58 4721.7,244.78 4753.4,229 4764.1,223.67 4772.8,\ -213.85 4779.2,204.32", + lp="4579.4,221.5", + pos="e,4518.5,195.81 3122.3,251.68 3152.3,249.84 3183.2,248.17 3212.4,247 3247.7,245.59 4453.4,244.16 4485.4,229 4496.5,223.72 4505.8,\ +213.9 4512.7,204.36", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4963.4,178", + pos="4698.4,178", width=1.0652]; "organismal entity as a model of disease association" -> "object label closure" [color=blue, label="object label closure", - lp="5010.9,221.5", - pos="e,4955.1,195.79 3386.9,251.66 3417,249.81 3448.1,248.15 3477.4,247 3517.5,245.43 4887.3,246.63 4923.4,229 4934.3,223.7 4943.1,213.88 \ -4949.7,204.34", + lp="4746.9,221.5", + pos="e,4689.8,195.81 3121.9,251.66 3152,249.81 3183.1,248.15 3212.4,247 3252.5,245.43 4621.2,246.4 4657.4,229 4668.4,223.71 4677.4,213.9 \ +4684.2,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="5107.4,178", + pos="4842.4,178", width=2.347]; "organismal entity as a model of disease association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="5166.9,221.5", - pos="e,5104.4,196.01 3386.6,251.65 3416.8,249.8 3448,248.13 3477.4,247 3522,245.28 5046.9,253.29 5084.4,229 5092.5,223.71 5097.9,214.73 \ -5101.3,205.83", + lp="4902.9,221.5", + pos="e,4839.6,196.48 3121.6,251.65 3151.8,249.8 3183,248.13 3212.4,247 3234.7,246.14 4801.8,241.31 4820.4,229 4828.3,223.76 4833.4,214.95 \ +4836.7,206.18", style=solid]; type [height=0.5, - pos="5241.4,178", + pos="4976.4,178", width=0.86659]; "organismal entity as a model of disease association" -> type [color=blue, label=type, - lp="5263.4,221.5", - pos="e,5246.5,196.18 3386.6,251.62 3416.8,249.78 3448,248.12 3477.4,247 3501.9,246.07 5223,246.23 5240.4,229 5246.4,223.09 5248,214.52 \ -5247.6,206.13", + lp="4999.4,221.5", + pos="e,4981.9,196.13 3121.6,251.62 3151.8,249.78 3183,248.12 3212.4,247 3236.9,246.07 4959.2,246.41 4976.4,229 4982.3,223.04 4983.7,214.44 \ +4983.3,206.06", style=solid]; category [height=0.5, - pos="5342.4,178", + pos="5077.4,178", width=1.4263]; "organismal entity as a model of disease association" -> category [color=blue, label=category, - lp="5340.9,221.5", - pos="e,5328.8,195.46 3386.6,251.62 3416.8,249.77 3448,248.11 3477.4,247 3527.5,245.1 5236.4,246.51 5283.4,229 5298,223.57 5311.4,212.81 \ -5321.8,202.66", + lp="5075.9,221.5", + pos="e,5064.1,195.46 3121.6,251.62 3151.8,249.77 3183,248.11 3212.4,247 3262.6,245.1 4972.4,246.72 5019.4,229 5033.7,223.62 5046.8,213.01 \ +5056.9,202.95", style=solid]; subject [height=0.5, - pos="5456.4,178", + pos="5191.4,178", width=1.2277]; "organismal entity as a model of disease association" -> subject [color=blue, label=subject, - lp="5435.4,221.5", - pos="e,5438.1,194.56 3386.2,251.63 3416.5,249.77 3447.9,248.11 3477.4,247 3530.1,245.02 5325.8,243.78 5376.4,229 5395.8,223.32 5415.2,\ -211.45 5430,200.71", + lp="5170.4,221.5", + pos="e,5173.1,194.56 3121.2,251.63 3151.5,249.77 3182.9,248.11 3212.4,247 3265.1,245.02 5060.8,243.78 5111.4,229 5130.8,223.32 5150.2,\ +211.45 5165,200.71", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="5603.4,178", + pos="5338.4,178", width=2.3651]; "organismal entity as a model of disease association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="5588.4,221.5", - pos="e,5570.3,194.62 3386.2,251.62 3416.5,249.76 3447.9,248.1 3477.4,247 3587.8,242.87 5356.7,248.59 5465.4,229 5498.5,223.04 5534.1,\ -209.96 5560.8,198.68", + lp="5323.4,221.5", + pos="e,5305.3,194.62 3121.2,251.62 3151.5,249.76 3182.9,248.1 3212.4,247 3322.8,242.87 5091.7,248.59 5200.4,229 5233.5,223.04 5269.1,\ +209.96 5295.8,198.68", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="5782.4,178", + pos="5517.4,178", width=2.1123]; "organismal entity as a model of disease association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="5770.4,221.5", - pos="e,5752.8,194.86 3386.2,251.6 3416.5,249.75 3447.9,248.09 3477.4,247 3598.6,242.51 5541.5,252.93 5660.4,229 5689.4,223.17 5720.2,\ -210.48 5743.6,199.35", + lp="5505.4,221.5", + pos="e,5487.8,194.86 3121.2,251.6 3151.5,249.75 3182.9,248.09 3212.4,247 3333.6,242.51 5276.5,252.93 5395.4,229 5424.4,223.17 5455.2,\ +210.48 5478.6,199.35", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="5919.4,178", + pos="5654.4,178", width=1.011]; "organismal entity as a model of disease association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="5920.9,221.5", - pos="e,5901,193.86 3385.9,251.6 3416.3,249.74 3447.8,248.09 3477.4,247 3542.9,244.6 5772.3,246.61 5835.4,229 5856.2,223.19 5877.1,210.77 \ -5892.9,199.77", + lp="5655.9,221.5", + pos="e,5636,193.86 3120.9,251.6 3151.3,249.74 3182.8,248.09 3212.4,247 3277.9,244.6 5507.3,246.61 5570.4,229 5591.2,223.19 5612.1,210.77 \ +5627.9,199.77", style=solid]; relation [height=0.5, - pos="5407.4,18", + pos="5142.4,18", width=1.2999]; - object -> relation [pos="e,5395.9,35.705 5370,73.174 5376,64.509 5383.4,53.768 5390,44.141", + object -> relation [pos="e,5130.9,35.705 5105,73.174 5111,64.509 5118.4,53.768 5125,44.141", style=dotted]; association_type [color=blue, height=0.5, label=string, - pos="3524.4,265", + pos="3259.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3655.4,265", + pos="3390.4,265", width=2.0762]; subject -> object [label=relation, - lp="5414.4,134.5", - pos="e,5364.8,108.97 5423.9,165.59 5411.1,159.94 5397,152.13 5386.4,142 5379.4,135.31 5373.7,126.48 5369.3,118.1"]; - subject -> relation [pos="e,5418.6,35.828 5455,159.99 5452.9,139.02 5448,102.55 5437.4,73 5433.9,63.258 5428.8,53.189 5423.8,44.423", + lp="5149.4,134.5", + pos="e,5099.8,108.97 5158.9,165.59 5146.1,159.94 5132,152.13 5121.4,142 5114.4,135.31 5108.7,126.48 5104.3,118.1"]; + subject -> relation [pos="e,5153.6,35.828 5190,159.99 5187.9,139.02 5183,102.55 5172.4,73 5168.9,63.258 5163.8,53.189 5158.8,44.423", style=dotted]; "organismal entity as a model of disease association_subject" [color=blue, height=0.5, label="organismal entity", - pos="3841.4,265", + pos="3576.4,265", width=2.5817]; } diff --git a/graphviz/organismal_entity_as_a_model_of_disease_association.svg b/graphviz/organismal_entity_as_a_model_of_disease_association.svg index 3db6b721b4..981f7dcb9c 100644 --- a/graphviz/organismal_entity_as_a_model_of_disease_association.svg +++ b/graphviz/organismal_entity_as_a_model_of_disease_association.svg @@ -4,16 +4,16 @@ - + %3 - + organismal entity as a model of disease association - -organismal entity as a model of disease association + +organismal entity as a model of disease association @@ -24,7 +24,7 @@ organismal entity as a model of disease association->association - + is_a @@ -37,8 +37,8 @@ organismal entity as a model of disease association->model to disease association mixin - - + + uses @@ -50,8 +50,8 @@ organismal entity as a model of disease association->entity to disease association mixin - - + + uses @@ -63,7 +63,7 @@ organismal entity as a model of disease association->id - + id @@ -76,8 +76,8 @@ organismal entity as a model of disease association->iri - - + + iri @@ -89,8 +89,8 @@ organismal entity as a model of disease association->name - - + + name @@ -102,8 +102,8 @@ organismal entity as a model of disease association->description - - + + description @@ -115,8 +115,8 @@ organismal entity as a model of disease association->has attribute - - + + has attribute @@ -128,21 +128,21 @@ organismal entity as a model of disease association->predicate - - + + predicate object - -named thing + +named thing organismal entity as a model of disease association->object - - + + object @@ -154,9 +154,9 @@ organismal entity as a model of disease association->negated - - -negated + + +negated @@ -167,9 +167,9 @@ organismal entity as a model of disease association->qualifiers - - -qualifiers + + +qualifiers @@ -180,9 +180,9 @@ organismal entity as a model of disease association->publications - - -publications + + +publications @@ -193,364 +193,364 @@ organismal entity as a model of disease association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string organismal entity as a model of disease association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string organismal entity as a model of disease association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string organismal entity as a model of disease association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type organismal entity as a model of disease association->timepoint - - -timepoint + + +timepoint original subject - -string + +string organismal entity as a model of disease association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie organismal entity as a model of disease association->original predicate - - -original predicate + + +original predicate original object - -string + +string organismal entity as a model of disease association->original object - - -original object + + +original object subject category - -ontology class + +ontology class organismal entity as a model of disease association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class organismal entity as a model of disease association->object category - - -object category + + +object category subject closure - -string + +string organismal entity as a model of disease association->subject closure - - -subject closure + + +subject closure object closure - -string + +string organismal entity as a model of disease association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class organismal entity as a model of disease association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class organismal entity as a model of disease association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string organismal entity as a model of disease association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string organismal entity as a model of disease association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string organismal entity as a model of disease association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string organismal entity as a model of disease association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source organismal entity as a model of disease association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type organismal entity as a model of disease association->type - - -type + + +type category - -category + +category organismal entity as a model of disease association->category - - -category + + +category subject - -subject + +subject organismal entity as a model of disease association->subject - - -subject + + +subject frequency qualifier - -frequency value + +frequency value organismal entity as a model of disease association->frequency qualifier - - -frequency qualifier + + +frequency qualifier severity qualifier - -severity value + +severity value organismal entity as a model of disease association->severity qualifier - - -severity qualifier + + +severity qualifier onset qualifier - -onset + +onset organismal entity as a model of disease association->onset qualifier - - -onset qualifier + + +onset qualifier relation - -relation + +relation object->relation - - + + association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation subject->relation - - + + organismal entity as a model of disease association_subject - -organismal entity + +organismal entity diff --git a/graphviz/pairwise_gene_to_gene_interaction.gv b/graphviz/pairwise_gene_to_gene_interaction.gv index c7e85e0ee0..ae18746eee 100644 --- a/graphviz/pairwise_gene_to_gene_interaction.gv +++ b/graphviz/pairwise_gene_to_gene_interaction.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4874,283"]; + graph [bb="0,0,4689,283"]; node [label="\N"]; "pairwise gene to gene interaction" [height=0.5, label="pairwise gene to gene interaction", - pos="2594.4,265", + pos="2409.4,265", width=4.6399]; "gene to gene association" [height=0.5, pos="125.44,178", width=3.4844]; "pairwise gene to gene interaction" -> "gene to gene association" [label=is_a, lp="406.44,221.5", - pos="e,187.32,193.67 2428.2,262.98 1950,259.82 592.45,249.17 392.44,229 325.77,222.28 250.85,207.61 197.38,195.89"]; + pos="e,187.59,193.7 2243.6,262.72 1794.1,259.03 573.79,247.42 392.44,229 325.88,222.24 251.1,207.62 197.65,195.92"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "pairwise gene to gene interaction" -> id [color=blue, label=id, - lp="522.44,221.5", - pos="e,336.43,189.98 2428.1,262.98 1968.5,259.93 702.8,249.72 515.44,229 443.27,221.02 425.38,215.5 355.44,196 352.33,195.13 349.13,194.17 \ -345.93,193.15", + lp="521.44,221.5", + pos="e,336.43,189.98 2243.6,262.7 1813.4,259.09 683.31,247.92 514.44,229 442.71,220.97 424.95,215.43 355.44,196 352.33,195.13 349.13,\ +194.17 345.94,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "pairwise gene to gene interaction" -> iri [color=blue, label=iri, - lp="635.44,221.5", - pos="e,441.35,190.2 2428.4,262.75 1986.5,259.17 803.6,247.92 627.44,229 552.65,220.97 534.26,214.85 461.44,196 458.06,195.13 454.58,194.16 \ -451.1,193.15", + lp="627.44,221.5", + pos="e,441.36,190.15 2242.2,264.71 1859.8,265.68 930.41,264.2 619.44,229 548.16,220.93 530.8,214.31 461.44,196 458.07,195.11 454.59,194.13 \ +451.11,193.11", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "pairwise gene to gene interaction" -> name [color=blue, label=name, - lp="742.44,221.5", - pos="e,565.4,191.54 2428.3,263.09 2001.4,260.45 888.48,251.48 722.44,229 671.3,222.08 614.29,206.51 575.18,194.57", + lp="730.44,221.5", + pos="e,564.03,191.87 2243.5,262.9 1845.6,259.94 859.03,250.49 710.44,229 663.07,222.15 610.5,206.96 573.91,195.11", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "pairwise gene to gene interaction" -> description [color=blue, label=description, - lp="862.94,221.5", - pos="e,711.49,194.14 2427.7,263.67 2016.8,262.42 977.42,256.55 822.44,229 787.38,222.77 749.38,209.4 721.08,198.06", + lp="843.94,221.5", + pos="e,707.82,194.62 2242.6,263.71 1859.9,262.57 941.35,256.92 803.44,229 773.4,222.92 741.32,210.09 717.05,198.95", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "pairwise gene to gene interaction" -> "has attribute" [color=blue, label="has attribute", - lp="1008.4,221.5", - pos="e,852.02,192.82 2427.7,263.48 2040.5,261.83 1102.5,255.15 961.44,229 926.48,222.52 888.61,208.39 861.24,196.8", + lp="978.44,221.5", + pos="e,847.38,194.01 2242.5,263.84 1882.5,262.96 1056.1,257.77 931.44,229 904.93,222.88 877.09,209.98 856.18,198.82", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "pairwise gene to gene interaction" -> negated [color=blue, label=negated, - lp="1164.4,221.5", - pos="e,973.64,190.46 2427.5,264.31 2099.2,264.21 1380.6,260.29 1135.4,229 1082.1,222.2 1022.5,205.66 983.19,193.46", + lp="1116.4,221.5", + pos="e,969.07,191.96 2243.9,262.38 1914.3,258.76 1198.2,248.71 1087.4,229 1049.4,222.23 1007.9,207.52 978.54,195.8", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "pairwise gene to gene interaction" -> qualifiers [color=blue, label=qualifiers, - lp="1304.9,221.5", - pos="e,1122.7,193.07 2427.5,264.35 2123.2,264.2 1489.5,260.01 1271.4,229 1223.6,222.2 1170.6,207.74 1132.5,196.11", + lp="1227.9,221.5", + pos="e,1108.4,194.93 2243.6,262.75 1934.7,259.89 1293.8,251.34 1194.4,229 1167.6,222.97 1139.3,210.59 1117.6,199.66", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "pairwise gene to gene interaction" -> publications [color=blue, label=publications, - lp="1452.4,221.5", - pos="e,1274.2,192.71 2427.5,264.31 2148.6,263.95 1599.5,259.24 1408.4,229 1365.3,222.18 1317.8,207.69 1283.8,196.06", + lp="1328.4,221.5", + pos="e,1247.9,195.78 2244.3,262.18 1942.2,258.39 1327.3,248.34 1284.4,229 1272.4,223.57 1262,213.45 1254,203.73", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,276 +100,276 @@ digraph { width=2.0943]; "pairwise gene to gene interaction" -> "has evidence" [color=blue, label="has evidence", - lp="1606.9,221.5", - pos="e,1431.9,193.61 2427.9,263.56 2179.1,262.01 1722.2,255.51 1560.4,229 1519.6,222.3 1474.7,208.48 1441.7,197.06", + lp="1426.9,221.5", + pos="e,1382,195.88 2242.3,264.3 1958.5,263.99 1409.8,259.41 1380.4,229 1374.3,222.63 1374.8,213.73 1377.8,205.2", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1595.4,178", - width=3.015]; + label=string, + pos="1525.4,178", + width=1.0652]; "pairwise gene to gene interaction" -> "knowledge source" [color=blue, label="knowledge source", - lp="1761.9,221.5", - pos="e,1621.5,195.59 2430.6,261.28 2191.1,256.74 1766.2,246.38 1697.4,229 1673.9,223.07 1649.5,211.31 1630.4,200.68", + lp="1545.9,221.5", + pos="e,1501.2,192.24 2242.7,263.62 1982.7,262.2 1507.4,255.92 1481.4,229 1471.9,219.09 1480.7,207.6 1492.9,198.13", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1830.4,178", - width=3.015]; + label=string, + pos="1620.4,178", + width=1.0652]; "pairwise gene to gene interaction" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1933.4,221.5", - pos="e,1828.2,196.41 2430,261.61 2214.2,257.71 1860.1,248.4 1838.4,229 1832.1,223.34 1829.4,214.82 1828.5,206.41", + lp="1715.4,221.5", + pos="e,1615.1,196.04 2244,262.42 2018.9,259.45 1641.6,251.17 1620.4,229 1614.6,222.94 1613.2,214.32 1613.7,205.94", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2065.4,178", - width=3.015]; + label=string, + pos="1795.4,178", + width=1.0652]; "pairwise gene to gene interaction" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2141.9,221.5", - pos="e,2044.7,195.97 2435.8,259.34 2275.4,253.84 2049.1,243.55 2035.4,229 2028.4,221.54 2031.6,212.18 2038.1,203.58", + lp="1935.9,221.5", + pos="e,1802.2,196.02 2245.5,261.45 2086.8,257.8 1864.9,249.15 1829.4,229 1819.9,223.55 1812.4,214.16 1807,204.98", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2247.4,178", + pos="2021.4,178", width=1.5346]; "pairwise gene to gene interaction" -> timepoint [color=blue, label=timepoint, - lp="2297.4,221.5", - pos="e,2248,196.47 2448.9,256.08 2366.6,250.3 2277.3,241.32 2262.4,229 2255.7,223.41 2251.9,214.91 2249.8,206.49", + lp="2098.4,221.5", + pos="e,2030.9,195.92 2250.6,259.4 2175.8,254.94 2095.9,246.18 2063.4,229 2052.7,223.32 2043.6,213.63 2036.6,204.28", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2359.4,178", + pos="2133.4,178", width=1.0652]; "pairwise gene to gene interaction" -> "original subject" [color=blue, label="original subject", - lp="2396.4,221.5", - pos="e,2345.7,194.92 2436.9,258.91 2393.5,254.01 2354.4,245.06 2340.4,229 2334.2,221.83 2336,212.39 2340.4,203.65", + lp="2202.4,221.5", + pos="e,2133.3,196.33 2255.4,257.92 2208,253.03 2163.8,244.34 2146.4,229 2139.9,223.25 2136.5,214.72 2134.7,206.31", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2473.4,178", + pos="2259.4,178", width=1.5887]; "pairwise gene to gene interaction" -> "original predicate" [color=blue, label="original predicate", - lp="2523.9,221.5", - pos="e,2462.4,195.76 2506.5,249.65 2485.4,244.35 2467,237.52 2460.4,229 2455.2,222.16 2455.7,213.39 2458.4,205.11", + lp="2333.9,221.5", + pos="e,2258.9,196.42 2321.9,249.6 2299,244.19 2278.5,237.3 2270.4,229 2264.6,222.99 2261.6,214.63 2260.1,206.47", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2587.4,178", + pos="2393.4,178", width=1.0652]; "pairwise gene to gene interaction" -> "original object" [color=blue, label="original object", - lp="2642.9,221.5", - pos="e,2588.9,196.18 2593,246.8 2592.1,235.16 2590.8,219.55 2589.7,206.24", + lp="2453.9,221.5", + pos="e,2396.7,196.18 2406.2,246.8 2404,235.16 2401.1,219.55 2398.6,206.24", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2720.4,178", + pos="2526.4,178", width=2.1304]; "pairwise gene to gene interaction" -> "subject category" [color=blue, label="subject category", - lp="2768.9,221.5", - pos="e,2716.6,196.4 2666.2,248.69 2677.9,243.82 2689.2,237.42 2698.4,229 2705.2,222.84 2710,214.24 2713.3,205.9", + lp="2578.9,221.5", + pos="e,2524.4,196.3 2479.8,248.58 2490.8,243.73 2501.2,237.36 2509.4,229 2515.6,222.8 2519.5,214.29 2522,206.04", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2891.4,178", + pos="2697.4,178", width=2.1304]; "pairwise gene to gene interaction" -> "object category" [color=blue, label="object category", - lp="2911.9,221.5", - pos="e,2876.6,195.73 2714.8,252.46 2762.5,246.61 2811,238.68 2832.4,229 2846.1,222.83 2859,212.54 2869.3,202.9", + lp="2719.9,221.5", + pos="e,2683.8,195.72 2529.3,252.41 2575.4,246.61 2621.9,238.74 2642.4,229 2655.3,222.88 2667.3,212.74 2676.8,203.17", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3024.4,178", + pos="2830.4,178", width=1.0652]; "pairwise gene to gene interaction" -> "subject closure" [color=blue, label="subject closure", - lp="3047.9,221.5", - pos="e,3012,195.53 2713.7,252.37 2732.7,250.55 2752.1,248.71 2770.4,247 2815.1,242.84 2930.5,247.4 2971.4,229 2984.4,223.18 2996.1,212.88 \ -3005.3,203.13", + lp="2854.9,221.5", + pos="e,2818.6,195.51 2529.2,252.37 2548,250.56 2567.3,248.72 2585.4,247 2628.5,242.92 2740.2,247.21 2779.4,229 2791.9,223.22 2803.2,213.05 \ +2811.9,203.4", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3124.4,178", + pos="2938.4,178", width=1.0652]; "pairwise gene to gene interaction" -> "object closure" [color=blue, label="object closure", - lp="3168.4,221.5", - pos="e,3123,196.23 2710.8,252.05 2730.7,250.21 2751.2,248.45 2770.4,247 2807.7,244.2 3076.4,251.31 3106.4,229 3113.8,223.54 3118.1,214.8 \ -3120.7,206.15", + lp="2977.4,221.5", + pos="e,2934.5,196.39 2525.8,252.07 2545.7,250.23 2566.2,248.46 2585.4,247 2621.8,244.24 2882.9,249.03 2913.4,229 2921.7,223.6 2927.3,\ +214.64 2931.1,205.79", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3257.4,178", + pos="3071.4,178", width=2.1304]; "pairwise gene to gene interaction" -> "subject category closure" [color=blue, label="subject category closure", - lp="3326.9,221.5", - pos="e,3250.4,196.11 2709.9,251.91 2730,250.07 2750.8,248.34 2770.4,247 2820.6,243.58 3178.3,253.09 3222.4,229 3232.2,223.67 3239.8,214.3 \ -3245.5,205.1", + lp="3136.9,221.5", + pos="e,3062.8,196.17 2524.9,251.92 2545,250.07 2565.8,248.34 2585.4,247 2634.9,243.61 2987.2,251.38 3031.4,229 3042.1,223.62 3050.8,213.98 \ +3057.4,204.59", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3449.4,178", + pos="3264.4,178", width=2.1304]; "pairwise gene to gene interaction" -> "object category closure" [color=blue, label="object category closure", - lp="3516.9,221.5", - pos="e,3443.7,196.1 2708.4,251.84 2729,249.97 2750.4,248.25 2770.4,247 2806.4,244.77 3387.2,246.95 3418.4,229 3427.6,223.71 3434.5,214.48 \ -3439.4,205.37", + lp="3328.9,221.5", + pos="e,3257.1,196.17 2523.9,251.8 2544.4,249.94 2565.5,248.24 2585.4,247 2621.1,244.78 3196.9,245.74 3228.4,229 3238.5,223.69 3246.4,\ +214.19 3252.2,204.89", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3639.4,178", + pos="3454.4,178", width=1.0652]; "pairwise gene to gene interaction" -> "subject namespace" [color=blue, label="subject namespace", - lp="3689.4,221.5", - pos="e,3632.5,196.19 2708,251.78 2728.7,249.9 2750.2,248.19 2770.4,247 2816.7,244.27 3563.6,250.84 3604.4,229 3614.3,223.76 3621.9,214.4 \ -3627.5,205.19", + lp="3501.4,221.5", + pos="e,3446.8,195.73 2523,251.78 2543.7,249.9 2565.2,248.19 2585.4,247 2631.5,244.28 3375.3,249.97 3416.4,229 3426.9,223.67 3435.3,213.99 \ +3441.5,204.55", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3798.4,178", + pos="3613.4,178", width=1.0652]; "pairwise gene to gene interaction" -> "object namespace" [color=blue, label="object namespace", - lp="3842.4,221.5", - pos="e,3791.1,195.74 2707.9,251.72 2728.7,249.85 2750.2,248.16 2770.4,247 2825.4,243.85 3712.5,254.23 3761.4,229 3771.8,223.68 3780,213.99 \ -3786,204.56", + lp="3655.4,221.5", + pos="e,3605.1,195.77 2522.9,251.72 2543.7,249.85 2565.2,248.16 2585.4,247 2640.2,243.86 3524.2,253.23 3573.4,229 3584.3,223.67 3593.1,\ +213.84 3599.7,204.31", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3949.4,178", + pos="3764.4,178", width=1.0652]; "pairwise gene to gene interaction" -> "subject label closure" [color=blue, label="subject label closure", - lp="4002.4,221.5", - pos="e,3941.5,195.77 2707.5,251.72 2728.4,249.84 2750.1,248.14 2770.4,247 2802.1,245.23 3882.1,243.12 3910.4,229 3921.2,223.66 3929.8,\ -213.84 3936.2,204.31", + lp="3815.4,221.5", + pos="e,3755.8,195.79 2522.5,251.73 2543.4,249.84 2565.1,248.14 2585.4,247 2617,245.23 3695,242.75 3723.4,229 3734.4,223.69 3743.5,213.88 \ +3750.3,204.34", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4120.4,178", + pos="3935.4,178", width=1.0652]; "pairwise gene to gene interaction" -> "object label closure" [color=blue, label="object label closure", - lp="4167.9,221.5", - pos="e,4112.1,195.79 2707.5,251.69 2728.4,249.81 2750.1,248.12 2770.4,247 2806.8,245 4047.7,244.99 4080.4,229 4091.3,223.69 4100.1,213.87 \ -4106.7,204.33", + lp="3982.9,221.5", + pos="e,3926.5,195.81 2522.5,251.69 2543.4,249.81 2565.1,248.12 2585.4,247 2621.7,245 3860.6,244.57 3893.4,229 3904.6,223.72 3913.8,213.9 \ +3920.8,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4273.4,178", + pos="4088.4,178", width=2.347]; "pairwise gene to gene interaction" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4326.9,221.5", - pos="e,4267.5,196.18 2707.5,251.67 2728.4,249.79 2750.1,248.11 2770.4,247 2811.2,244.78 4205.7,248.84 4241.4,229 4250.9,223.75 4258,214.39 \ -4263,205.18", + lp="4141.9,221.5", + pos="e,4082.5,196.18 2522.5,251.67 2543.4,249.79 2565.1,248.11 2585.4,247 2626.2,244.78 4020.7,248.84 4056.4,229 4065.9,223.75 4073,214.39 \ +4078,205.18", style=solid]; type [height=0.5, - pos="4407.4,178", + pos="4222.4,178", width=0.86659]; "pairwise gene to gene interaction" -> type [color=blue, label=type, - lp="4425.4,221.5", - pos="e,4410.1,195.98 2707,251.69 2728.1,249.79 2749.9,248.1 2770.4,247 2793,245.79 4383.4,243.95 4400.4,229 4406.9,223.32 4409.4,214.65 \ -4410.1,206.12", + lp="4240.4,221.5", + pos="e,4225.1,195.98 2522,251.69 2543.1,249.79 2564.9,248.1 2585.4,247 2608,245.79 4198.4,243.95 4215.4,229 4221.9,223.32 4224.4,214.65 \ +4225.1,206.12", style=solid]; category [height=0.5, - pos="4508.4,178", + pos="4323.4,178", width=1.4263]; "pairwise gene to gene interaction" -> category [color=blue, label=category, - lp="4503.9,221.5", - pos="e,4493.7,195.48 2707,251.68 2728.1,249.79 2749.9,248.1 2770.4,247 2816.9,244.51 4401.6,244.55 4445.4,229 4460.7,223.59 4475,212.84 \ -4486.2,202.68", + lp="4318.9,221.5", + pos="e,4308.7,195.48 2522,251.68 2543.1,249.79 2564.9,248.1 2585.4,247 2631.9,244.51 4216.6,244.55 4260.4,229 4275.7,223.59 4290,212.84 \ +4301.2,202.68", style=solid]; subject [height=0.5, - pos="4622.4,178", + pos="4437.4,178", width=1.2277]; "pairwise gene to gene interaction" -> subject [color=blue, label=subject, - lp="4599.4,221.5", - pos="e,4603.7,194.32 2707,251.67 2728.1,249.78 2749.9,248.09 2770.4,247 2868.6,241.77 4444.9,255.8 4539.4,229 4559.6,223.29 4579.8,211.3 \ -4595.2,200.49", + lp="4414.4,221.5", + pos="e,4418.7,194.32 2522,251.67 2543.1,249.78 2564.9,248.09 2585.4,247 2683.6,241.77 4259.9,255.8 4354.4,229 4374.6,223.29 4394.8,211.3 \ +4410.2,200.49", style=solid]; object [height=0.5, - pos="4665.4,91", + pos="4480.4,91", width=1.0832]; "pairwise gene to gene interaction" -> object [color=blue, label=object, - lp="4709.4,178", - pos="e,4678.8,108.09 2707,251.67 2728.1,249.77 2749.9,248.09 2770.4,247 2822,244.26 4580.4,245.05 4629.4,229 4653.4,221.18 4661.4,216.87 \ -4675.4,196 4689.2,175.52 4685.5,166.51 4688.4,142 4689.2,135.38 4690.3,133.39 4688.4,127 4687.4,123.55 4685.9,120.13 4684.2,116.85", + lp="4524.4,178", + pos="e,4493.8,108.09 2522,251.67 2543.1,249.77 2564.9,248.09 2585.4,247 2637,244.26 4395.4,245.05 4444.4,229 4468.4,221.18 4476.4,216.87 \ +4490.4,196 4504.2,175.52 4500.5,166.51 4503.4,142 4504.2,135.38 4505.3,133.39 4503.4,127 4502.4,123.55 4500.9,120.13 4499.2,116.85", style=solid]; predicate [height=0.5, - pos="4819.4,178", + pos="4634.4,178", width=1.5165]; "pairwise gene to gene interaction" -> predicate [color=blue, label=predicate, - lp="4792.4,221.5", - pos="e,4795.6,194.36 2707,251.66 2728.1,249.77 2749.9,248.08 2770.4,247 2878.4,241.3 4611.2,253.71 4716.4,229 4741.3,223.16 4767.2,210.56 \ -4786.8,199.48", + lp="4607.4,221.5", + pos="e,4610.6,194.36 2522,251.66 2543.1,249.77 2564.9,248.08 2585.4,247 2693.4,241.3 4426.2,253.71 4531.4,229 4556.3,223.16 4582.2,210.56 \ +4601.8,199.48", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2817.4,265", + pos="2632.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2948.4,265", + pos="2763.4,265", width=2.0762]; subject -> object [label=relation, - lp="4660.4,134.5", - pos="e,4647.5,107.23 4623.5,159.55 4624.7,149.57 4627.2,137.07 4632.4,127 4634.7,122.68 4637.6,118.52 4640.8,114.66"]; + lp="4475.4,134.5", + pos="e,4462.5,107.23 4438.5,159.55 4439.7,149.57 4442.2,137.07 4447.4,127 4449.7,122.68 4452.6,118.52 4455.8,114.66"]; relation [height=0.5, - pos="4610.4,18", + pos="4425.4,18", width=1.2999]; - subject -> relation [pos="e,4611.7,36.188 4621.1,159.79 4619.1,132.48 4615,78.994 4612.5,46.38", + subject -> relation [pos="e,4426.7,36.188 4436.1,159.79 4434.1,132.48 4430,78.994 4427.5,46.38", style=dotted]; "gene to gene association_subject" [color=blue, height=0.5, label="gene or gene product", - pos="3151.4,265", + pos="2966.4,265", width=3.0692]; - object -> relation [pos="e,4623.3,35.54 4653,73.889 4646,64.939 4637.3,53.617 4629.5,43.584", + object -> relation [pos="e,4438.3,35.54 4468,73.889 4461,64.939 4452.3,53.617 4444.5,43.584", style=dotted]; "gene to gene association_object" [color=blue, height=0.5, label="gene or gene product", - pos="3390.4,265", + pos="3205.4,265", width=3.0692]; "pairwise gene to gene interaction_predicate" [color=blue, height=0.5, label="predicate type", - pos="3596.4,265", + pos="3411.4,265", width=2.1665]; } diff --git a/graphviz/pairwise_gene_to_gene_interaction.svg b/graphviz/pairwise_gene_to_gene_interaction.svg index 3ea0e5a47a..264d74b62a 100644 --- a/graphviz/pairwise_gene_to_gene_interaction.svg +++ b/graphviz/pairwise_gene_to_gene_interaction.svg @@ -4,16 +4,16 @@ - + %3 - + pairwise gene to gene interaction - -pairwise gene to gene interaction + +pairwise gene to gene interaction @@ -24,8 +24,8 @@ pairwise gene to gene interaction->gene to gene association - - + + is_a @@ -37,9 +37,9 @@ pairwise gene to gene interaction->id - + -id +id @@ -50,9 +50,9 @@ pairwise gene to gene interaction->iri - - -iri + + +iri @@ -63,9 +63,9 @@ pairwise gene to gene interaction->name - - -name + + +name @@ -76,9 +76,9 @@ pairwise gene to gene interaction->description - - -description + + +description @@ -89,9 +89,9 @@ pairwise gene to gene interaction->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ pairwise gene to gene interaction->negated - - -negated + + +negated @@ -115,9 +115,9 @@ pairwise gene to gene interaction->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ pairwise gene to gene interaction->publications - - -publications + + +publications @@ -141,363 +141,363 @@ pairwise gene to gene interaction->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string pairwise gene to gene interaction->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string pairwise gene to gene interaction->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string pairwise gene to gene interaction->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type pairwise gene to gene interaction->timepoint - - -timepoint + + +timepoint original subject - -string + +string pairwise gene to gene interaction->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie pairwise gene to gene interaction->original predicate - - -original predicate + + +original predicate original object - -string + +string pairwise gene to gene interaction->original object - - -original object + + +original object subject category - -ontology class + +ontology class pairwise gene to gene interaction->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class pairwise gene to gene interaction->object category - - -object category + + +object category subject closure - -string + +string pairwise gene to gene interaction->subject closure - - -subject closure + + +subject closure object closure - -string + +string pairwise gene to gene interaction->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class pairwise gene to gene interaction->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class pairwise gene to gene interaction->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string pairwise gene to gene interaction->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string pairwise gene to gene interaction->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string pairwise gene to gene interaction->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string pairwise gene to gene interaction->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source pairwise gene to gene interaction->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type pairwise gene to gene interaction->type - - -type + + +type category - -category + +category pairwise gene to gene interaction->category - - -category + + +category subject - -subject + +subject pairwise gene to gene interaction->subject - - -subject + + +subject object - -object + +object pairwise gene to gene interaction->object - - -object + + +object predicate - -predicate + +predicate pairwise gene to gene interaction->predicate - - -predicate + + +predicate association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + gene to gene association_subject - -gene or gene product + +gene or gene product object->relation - - + + gene to gene association_object - -gene or gene product + +gene or gene product pairwise gene to gene interaction_predicate - -predicate type + +predicate type diff --git a/graphviz/pairwise_molecular_interaction.gv b/graphviz/pairwise_molecular_interaction.gv index 9cec1236bf..a5a8f2f8b7 100644 --- a/graphviz/pairwise_molecular_interaction.gv +++ b/graphviz/pairwise_molecular_interaction.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,5127,283"]; + graph [bb="0,0,4955,283"]; node [label="\N"]; "pairwise molecular interaction" [height=0.5, label="pairwise molecular interaction", - pos="2800,265", + pos="2628,265", width=4.2427]; "pairwise gene to gene interaction" [height=0.5, pos="167.04,178", width=4.6399]; "pairwise molecular interaction" -> "pairwise gene to gene interaction" [label=is_a, - lp="503.04,221.5", - pos="e,243.77,193.99 2647.3,264.46 2201.9,265.35 909.98,264.7 489.04,229 408.91,222.21 318.49,207.54 253.91,195.84"]; + lp="502.04,221.5", + pos="e,243.86,194.02 2475.4,264.25 2052.9,264.49 874.34,262.09 488.04,229 408.29,222.17 318.32,207.55 253.96,195.87"]; iri [color=blue, height=0.5, label="iri type", @@ -18,9 +18,9 @@ digraph { width=1.2277]; "pairwise molecular interaction" -> iri [color=blue, label=iri, - lp="623.04,221.5", - pos="e,428.94,190.2 2647.9,263.15 2185.4,260.35 815.22,250.32 615.04,229 540.24,221.03 521.86,214.85 449.04,196 445.66,195.13 442.18,\ -194.16 438.7,193.15", + lp="616.04,221.5", + pos="e,428.96,190.15 2475.9,263.01 2037.5,259.92 791.37,249.43 608.04,229 536.31,221.01 518.83,214.38 449.04,196 445.66,195.11 442.19,\ +194.14 438.71,193.12", style=solid]; name [color=blue, height=0.5, @@ -29,8 +29,8 @@ digraph { width=1.5707]; "pairwise molecular interaction" -> name [color=blue, label=name, - lp="730.04,221.5", - pos="e,552.63,191.45 2647.8,263.5 2198.9,261.75 899.93,254.52 710.04,229 658.73,222.11 601.52,206.45 562.41,194.48", + lp="720.04,221.5", + pos="e,551.68,191.78 2475.6,263.39 2050.8,261.37 873.37,253.61 700.04,229 651.81,222.15 598.23,206.78 561.2,194.88", style=solid]; description [color=blue, height=0.5, @@ -39,8 +39,8 @@ digraph { width=2.0943]; "pairwise molecular interaction" -> description [color=blue, label=description, - lp="850.54,221.5", - pos="e,699.09,194.17 2647.3,264.07 2212.6,263.89 988.63,260.54 810.04,229 774.97,222.81 736.97,209.44 708.67,198.08", + lp="834.54,221.5", + pos="e,695.92,194.52 2475.2,264.14 2064.4,264.1 956.42,260.98 794.04,229 763.11,222.91 729.99,209.92 705.05,198.71", style=solid]; "has attribute" [color=blue, height=0.5, @@ -49,8 +49,8 @@ digraph { width=1.4443]; "pairwise molecular interaction" -> "has attribute" [color=blue, label="has attribute", - lp="996.04,221.5", - pos="e,839.62,192.85 2647.3,263.96 2234,263.46 1113.5,259.29 949.04,229 914.06,222.56 876.2,208.43 848.84,196.83", + lp="971.04,221.5", + pos="e,835.75,193.79 2475.1,264.27 2084.9,264.47 1072.8,261.79 924.04,229 896.15,222.85 866.68,209.73 844.69,198.47", style=solid]; negated [color=blue, height=0.5, @@ -59,8 +59,8 @@ digraph { width=1.2999]; "pairwise molecular interaction" -> negated [color=blue, label=negated, - lp="1151,221.5", - pos="e,961.05,190.49 2648.3,262.66 2263.7,259.01 1270.7,247.85 1122,229 1069.1,222.28 1009.9,205.79 970.8,193.57", + lp="1111,221.5", + pos="e,957.55,191.76 2476,263.05 2113.1,260.44 1216.6,251.74 1082,229 1041.9,222.22 997.91,207.26 967.08,195.46", style=solid]; qualifiers [color=blue, height=0.5, @@ -69,8 +69,8 @@ digraph { width=2.1304]; "pairwise molecular interaction" -> qualifiers [color=blue, label=qualifiers, - lp="1290.5,221.5", - pos="e,1109.9,193.12 2648.7,262.6 2286.9,258.95 1392,248.1 1257,229 1209.7,222.3 1157.2,207.82 1119.6,196.17", + lp="1226.5,221.5", + pos="e,1098.2,194.6 2475.7,263.34 2131.9,261.41 1315.8,254.2 1193,229 1163.2,222.88 1131.4,210.05 1107.3,198.92", style=solid]; publications [color=blue, height=0.5, @@ -79,8 +79,8 @@ digraph { width=1.7332]; "pairwise molecular interaction" -> publications [color=blue, label=publications, - lp="1438,221.5", - pos="e,1261.3,192.76 2648.8,262.48 2310.9,258.76 1515.1,248.07 1394,229 1351.4,222.28 1304.4,207.78 1270.9,196.12", + lp="1336,221.5", + pos="e,1240.9,195.41 2476.5,262.48 2138.3,258.77 1347.1,248.08 1292,229 1276,223.44 1260.6,212.52 1248.7,202.3", style=solid]; "has evidence" [color=blue, height=0.5, @@ -89,299 +89,299 @@ digraph { width=2.0943]; "pairwise molecular interaction" -> "has evidence" [color=blue, label="has evidence", - lp="1599.5,221.5", - pos="e,1420,193.43 2647.3,264.57 2362.3,264.82 1759.3,261.33 1553,229 1510.5,222.34 1463.7,208.27 1429.7,196.75", + lp="1439.5,221.5", + pos="e,1380.2,196.13 2475.1,264.57 2153.7,265.11 1434.3,262.53 1393,229 1386.2,223.48 1382.9,214.85 1381.3,206.3", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1583,178", - width=3.015]; + label=string, + pos="1513,178", + width=1.0652]; "pairwise molecular interaction" -> "knowledge source" [color=blue, label="knowledge source", - lp="1758.5,221.5", - pos="e,1611.2,195.4 2648.7,262.48 2367.5,259.19 1784.4,249.91 1694,229 1668.2,223.02 1641,210.9 1620,200.09", + lp="1558.5,221.5", + pos="e,1499,195.21 2475,264.85 2173.3,265.75 1527.6,263.61 1494,229 1487.3,222.1 1489.2,212.61 1493.7,203.74", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1818,178", - width=3.015]; + label=string, + pos="1608,178", + width=1.0652]; "pairwise molecular interaction" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1933,221.5", - pos="e,1820.1,196.34 2648.4,262.78 2385.7,260.08 1870.5,251.87 1838,229 1830.4,223.6 1825.6,214.77 1822.7,206.01", + lp="1737,221.5", + pos="e,1614.7,196.12 2477.1,262.21 2209.8,258.53 1677.9,248.78 1642,229 1632.4,223.67 1624.9,214.3 1619.5,205.1", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2053,178", - width=3.015]; + label=string, + pos="1817,178", + width=1.0652]; "pairwise molecular interaction" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2142.5,221.5", - pos="e,2039.4,196.19 2648.9,262.37 2432.2,259.27 2056.8,250.78 2036,229 2029.8,222.48 2030.9,213.58 2034.6,205.1", + lp="1958.5,221.5", + pos="e,1824.1,196.09 2475.3,264.3 2264.7,263.62 1905,258.13 1852,229 1842.3,223.64 1834.6,214.27 1829,205.07", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2235,178", + pos="2043,178", width=1.5346]; "pairwise molecular interaction" -> timepoint [color=blue, label=timepoint, - lp="2303,221.5", - pos="e,2241.5,195.99 2651,260.94 2505.2,256.87 2300.5,247.85 2268,229 2258.6,223.51 2251.3,214.11 2246.1,204.94", + lp="2122,221.5", + pos="e,2053,196.1 2480.7,260.24 2332.7,255.54 2121.6,245.97 2087,229 2075.8,223.48 2066.2,213.68 2058.9,204.21", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2347,178", + pos="2155,178", width=1.0652]; "pairwise molecular interaction" -> "original subject" [color=blue, label="original subject", - lp="2404,221.5", - pos="e,2342.1,196 2649.1,262.18 2525.9,259.1 2368.7,250.87 2348,229 2342.3,222.96 2340.8,214.46 2341,206.18", + lp="2227,221.5", + pos="e,2155.8,196.11 2479.3,260.8 2355.3,256.79 2195.1,247.98 2171,229 2163.9,223.39 2159.9,214.63 2157.7,205.99", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2461,178", + pos="2281,178", width=1.5887]; "pairwise molecular interaction" -> "original predicate" [color=blue, label="original predicate", - lp="2536.5,221.5", - pos="e,2460.5,196.38 2664.2,256.77 2581,251.09 2487.8,241.96 2473,229 2466.6,223.3 2463.3,214.78 2461.7,206.37", + lp="2360.5,221.5", + pos="e,2281.9,196.02 2492.7,256.63 2408.2,250.84 2312.6,241.63 2297,229 2290,223.29 2286,214.5 2283.8,205.87", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2589,178", + pos="2410,178", width=1.0652]; "pairwise molecular interaction" -> "original object" [color=blue, label="original object", - lp="2668.5,221.5", - pos="e,2594.3,195.96 2696.1,251.8 2662.5,246.24 2630.5,238.69 2617,229 2608.9,223.1 2602.8,214.04 2598.4,205.24", + lp="2494.5,221.5", + pos="e,2417,196.01 2525.3,251.68 2490.7,246.03 2457.3,238.46 2443,229 2434.2,223.1 2427.1,213.92 2421.8,205.02", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2722,178", + pos="2543,178", width=2.1304]; "pairwise molecular interaction" -> "subject category" [color=blue, label="subject category", - lp="2789.5,221.5", - pos="e,2721,196.24 2752.1,247.77 2743.7,242.93 2735.7,236.78 2730,229 2725.3,222.49 2722.9,214.23 2721.8,206.3", + lp="2617.5,221.5", + pos="e,2544.8,196.38 2582,247.75 2573.1,242.87 2564.5,236.69 2558,229 2552.6,222.56 2549.2,214.22 2546.9,206.2", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2893,178", + pos="2714,178", width=2.1304]; "pairwise molecular interaction" -> "object category" [color=blue, label="object category", - lp="2919.5,221.5", - pos="e,2879.7,196.09 2825.8,247.25 2833.6,241.78 2841.9,235.45 2849,229 2857.5,221.36 2866,212.2 2873.2,203.82", + lp="2745.5,221.5", + pos="e,2703.2,196.26 2654.7,247.26 2662.3,241.88 2670.3,235.6 2677,229 2684.5,221.69 2691.5,212.79 2697.5,204.54", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3026,178", + pos="2847,178", width=1.0652]; "pairwise molecular interaction" -> "subject closure" [color=blue, label="subject closure", - lp="3053.5,221.5", - pos="e,3014.8,195.53 2913.6,252.83 2936.2,247.62 2959.1,240.02 2979,229 2990.3,222.76 3000.5,212.86 3008.4,203.5", + lp="2877.5,221.5", + pos="e,2837.4,195.52 2742.7,253.08 2764.4,247.83 2786.2,240.15 2805,229 2815.5,222.82 2824.6,213.05 2831.6,203.78", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3132,178", + pos="2960,178", width=1.0652]; "pairwise molecular interaction" -> "object closure" [color=blue, label="object closure", - lp="3174,221.5", - pos="e,3129.7,196.09 2909.5,252.38 2998.6,242.81 3110,230.58 3112,229 3119.4,223.38 3124.1,214.61 3127,205.97", + lp="2999,221.5", + pos="e,2956.3,196.17 2736.5,252.29 2824.3,242.7 2933.9,230.49 2936,229 2943.9,223.4 2949.3,214.52 2952.9,205.79", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3265,178", + pos="3093,178", width=2.1304]; "pairwise molecular interaction" -> "subject category closure" [color=blue, label="subject category closure", - lp="3332.5,221.5", - pos="e,3257.3,196.02 2907.6,252.15 2925.8,250.31 2944.4,248.52 2962,247 3021.1,241.91 3176.1,257.44 3228,229 3238.1,223.5 3246.2,213.97 \ -3252.2,204.7", + lp="3158.5,221.5", + pos="e,3084.3,196.05 2735.6,252.16 2753.8,250.32 2772.4,248.53 2790,247 2848.4,241.94 3001.1,256.17 3053,229 3063.5,223.53 3072.1,214.01 \ +3078.7,204.73", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3458,178", + pos="3286,178", width=2.1304]; "pairwise molecular interaction" -> "object category closure" [color=blue, label="object category closure", - lp="3523.5,221.5", - pos="e,3451.3,196.1 2905.4,251.93 2924.2,250.06 2943.7,248.32 2962,247 3013.3,243.32 3379.1,253.91 3424,229 3433.7,223.66 3441.1,214.28 \ -3446.6,205.09", + lp="3350.5,221.5", + pos="e,3278.7,196.13 2733.4,251.93 2752.2,250.06 2771.7,248.32 2790,247 2841.1,243.33 3205,253.21 3250,229 3260,223.63 3267.9,214.12 \ +3273.7,204.83", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3648,178", + pos="3476,178", width=1.0652]; "pairwise molecular interaction" -> "subject namespace" [color=blue, label="subject namespace", - lp="3696,221.5", - pos="e,3640.6,195.7 2904.5,251.85 2923.6,249.96 2943.4,248.23 2962,247 2998,244.62 3579.1,245.68 3611,229 3621.3,223.63 3629.5,213.94 \ -3635.5,204.51", + lp="3523,221.5", + pos="e,3468.3,195.71 2732.5,251.85 2751.6,249.96 2771.4,248.23 2790,247 2826,244.62 3406,245.45 3438,229 3448.5,223.64 3456.8,213.95 \ +3463.1,204.52", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3807,178", + pos="3635,178", width=1.0652]; "pairwise molecular interaction" -> "object namespace" [color=blue, label="object namespace", - lp="3850,221.5", - pos="e,3799,195.74 2904.1,251.81 2923.3,249.91 2943.3,248.19 2962,247 3006.7,244.16 3728,249.1 3768,229 3778.7,223.63 3787.4,213.8 3793.8,\ -204.27", + lp="3677,221.5", + pos="e,3626.7,195.75 2732.1,251.81 2751.3,249.91 2771.3,248.19 2790,247 2834.7,244.16 3554.9,248.83 3595,229 3605.9,223.64 3614.7,213.82 \ +3621.3,204.29", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3958,178", + pos="3786,178", width=1.0652]; "pairwise molecular interaction" -> "subject label closure" [color=blue, label="subject label closure", - lp="4010,221.5", - pos="e,3949.7,195.77 2904.1,251.75 2923.3,249.86 2943.3,248.16 2962,247 3015.1,243.73 3870.4,252.46 3918,229 3928.9,223.66 3937.7,213.84 \ -3944.3,204.31", + lp="3837,221.5", + pos="e,3777.4,195.78 2732.1,251.75 2751.3,249.86 2771.3,248.16 2790,247 2843,243.73 3697.3,252.15 3745,229 3756,223.68 3765.1,213.86 \ +3771.8,204.32", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4129,178", + pos="3957,178", width=1.0652]; "pairwise molecular interaction" -> "object label closure" [color=blue, label="object label closure", - lp="4175.5,221.5", - pos="e,4120.4,195.79 2903.6,251.75 2923,249.85 2943.1,248.14 2962,247 3024.5,243.23 4031.7,256.21 4088,229 4099,223.69 4108.1,213.87 \ -4114.9,204.34", + lp="4004.5,221.5", + pos="e,3948.1,195.8 2731.6,251.75 2751,249.85 2771.1,248.14 2790,247 2852.4,243.23 3858.6,255.85 3915,229 3926.2,223.7 3935.4,213.89 \ +3942.4,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4282,178", + pos="4110,178", width=2.347]; "pairwise molecular interaction" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4334.5,221.5", - pos="e,4275.7,196.19 2903.6,251.72 2923,249.82 2943.1,248.12 2962,247 2997.7,244.88 4217.7,246.16 4249,229 4258.6,223.76 4265.9,214.4 \ -4271.1,205.19", + lp="4163.5,221.5", + pos="e,4104,196.17 2731.6,251.72 2751,249.82 2771.1,248.12 2790,247 2825.8,244.88 4046.8,246.4 4078,229 4087.5,223.74 4094.6,214.38 4099.6,\ +205.17", style=solid]; type [height=0.5, - pos="4416,178", + pos="4244,178", width=0.86659]; "pairwise molecular interaction" -> type [color=blue, label=type, - lp="4433,221.5", - pos="e,4418.4,196.02 2903.6,251.7 2923,249.8 2943.1,248.11 2962,247 2982.1,245.83 4392.8,242.13 4408,229 4414.6,223.36 4417.3,214.7 4418.1,\ -206.17", + lp="4262,221.5", + pos="e,4246.7,195.98 2731.6,251.7 2751,249.8 2771.1,248.11 2790,247 2810.1,245.82 4222,242.28 4237,229 4243.5,223.32 4246,214.65 4246.7,\ +206.11", style=solid]; category [height=0.5, - pos="4517,178", + pos="4345,178", width=1.4263]; "pairwise molecular interaction" -> category [color=blue, label=category, - lp="4512.5,221.5", - pos="e,4502,195.47 2903.6,251.69 2923,249.79 2943.1,248.1 2962,247 3044.7,242.17 4374.9,256.44 4453,229 4468.6,223.54 4483.3,212.62 4494.7,\ -202.38", + lp="4340.5,221.5", + pos="e,4330.3,195.47 2731.6,251.69 2751,249.79 2771.1,248.1 2790,247 2872.8,242.17 4203.9,256.76 4282,229 4297.3,223.58 4311.6,212.82 \ +4322.8,202.67", style=solid]; "interacting molecules category" [color=blue, height=0.5, label="ontology class", - pos="4663,178", + pos="4491,178", width=2.1304]; "pairwise molecular interaction" -> "interacting molecules category" [color=blue, label="interacting molecules category", - lp="4705,221.5", - pos="e,4635.3,194.83 2903.2,251.72 2922.7,249.81 2943,248.11 2962,247 3050,241.9 4461.9,247.43 4548,229 4575.4,223.14 4604.3,210.55 4626.3,\ + lp="4533,221.5", + pos="e,4463.3,194.83 2731.2,251.72 2750.7,249.81 2771,248.11 2790,247 2878,241.9 4289.9,247.43 4376,229 4403.4,223.14 4432.3,210.55 4454.3,\ 199.47", style=solid]; subject [height=0.5, - pos="4825,178", + pos="4653,178", width=1.2277]; "pairwise molecular interaction" -> subject [color=blue, label=subject, - lp="4852,221.5", - pos="e,4827.4,196.03 2903.2,251.7 2922.7,249.79 2943,248.09 2962,247 2987.8,245.53 4797.5,245.81 4817,229 4823.6,223.37 4826.3,214.71 \ -4827.1,206.18", + lp="4680,221.5", + pos="e,4655.4,196.03 2731.2,251.7 2750.7,249.79 2771,248.09 2790,247 2815.8,245.53 4625.5,245.81 4645,229 4651.6,223.37 4654.3,214.71 \ +4655.1,206.18", style=solid]; id [height=0.5, - pos="4914,178", + pos="4742,178", width=0.75]; "pairwise molecular interaction" -> id [color=blue, label=id, - lp="4905,221.5", - pos="e,4908.3,195.7 2903.2,251.69 2922.7,249.78 2943,248.09 2962,247 3015.3,243.96 4835.4,254.82 4882,229 4891.6,223.69 4898.8,214.14 \ -4903.9,204.8", + lp="4733,221.5", + pos="e,4736.3,195.7 2731.2,251.69 2750.7,249.78 2771,248.09 2790,247 2843.3,243.96 4663.4,254.82 4710,229 4719.6,223.69 4726.8,214.14 \ +4731.9,204.8", style=solid]; predicate [height=0.5, - pos="5014,178", + pos="4842,178", width=1.5165]; "pairwise molecular interaction" -> predicate [color=blue, label=predicate, - lp="4990,221.5", - pos="e,4991.1,194.59 2903.2,251.69 2922.7,249.78 2943,248.09 2962,247 3070.4,240.83 4810.6,254.86 4916,229 4939.6,223.21 4964,210.84 \ -4982.5,199.84", + lp="4817,221.5", + pos="e,4819.1,194.59 2731.2,251.69 2750.7,249.78 2771,248.09 2790,247 2898.4,240.83 4638.6,254.86 4744,229 4767.6,223.21 4792,210.84 \ +4810.5,199.84", style=solid]; object [height=0.5, - pos="4892,91", + pos="4720,91", width=1.0832]; "pairwise molecular interaction" -> object [color=blue, label=object, - lp="5105,178", - pos="e,4929.4,96.831 2903.2,251.68 2922.7,249.77 2943,248.08 2962,247 3019.3,243.75 4973.1,245.74 5028,229 5053.5,221.23 5065.4,219.45 \ -5078,196 5109.7,137.24 5004.4,109.66 4939.4,98.485", + lp="4933,178", + pos="e,4757.4,96.861 2731.2,251.68 2750.7,249.77 2771,248.08 2790,247 2847.3,243.75 4800.1,245.49 4855,229 4880.9,221.24 4893.1,219.72 \ +4906,196 4937.9,137.39 4832.6,109.74 4767.5,98.523", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3009,265", + pos="2837,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3140,265", + pos="2968,265", width=2.0762]; subject -> object [label=relation, - lp="4891,134.5", - pos="e,4879.4,108.05 4838,160.61 4847.9,147.95 4861.9,130.24 4873.1,115.98"]; + lp="4719,134.5", + pos="e,4707.4,108.05 4666,160.61 4675.9,147.95 4689.9,130.24 4701.1,115.98"]; relation [height=0.5, - pos="4837,18", + pos="4665,18", width=1.2999]; - subject -> relation [pos="e,4835.7,36.188 4826.3,159.79 4828.4,132.48 4832.5,78.994 4835,46.38", + subject -> relation [pos="e,4663.7,36.188 4654.3,159.79 4656.4,132.48 4660.5,78.994 4663,46.38", style=dotted]; "pairwise molecular interaction_subject" [color=blue, height=0.5, label="molecular entity", - pos="3320,265", + pos="3148,265", width=2.4192]; "pairwise molecular interaction_id" [color=blue, height=0.5, label=string, - pos="3463,265", + pos="3291,265", width=1.0652]; "pairwise molecular interaction_predicate" [color=blue, height=0.5, label="predicate type", - pos="3597,265", + pos="3425,265", width=2.1665]; - object -> relation [pos="e,4849.8,35.54 4879.6,73.889 4872.6,64.939 4863.9,53.617 4856.1,43.584", + object -> relation [pos="e,4677.8,35.54 4707.6,73.889 4700.6,64.939 4691.9,53.617 4684.1,43.584", style=dotted]; "pairwise molecular interaction_object" [color=blue, height=0.5, label="molecular entity", - pos="3780,265", + pos="3608,265", width=2.4192]; } diff --git a/graphviz/pairwise_molecular_interaction.svg b/graphviz/pairwise_molecular_interaction.svg index 325a59e207..44f2873f81 100644 --- a/graphviz/pairwise_molecular_interaction.svg +++ b/graphviz/pairwise_molecular_interaction.svg @@ -4,16 +4,16 @@ - + %3 - + pairwise molecular interaction - -pairwise molecular interaction + +pairwise molecular interaction @@ -24,9 +24,9 @@ pairwise molecular interaction->pairwise gene to gene interaction - - -is_a + + +is_a @@ -37,9 +37,9 @@ pairwise molecular interaction->iri - - -iri + + +iri @@ -50,9 +50,9 @@ pairwise molecular interaction->name - - -name + + +name @@ -63,9 +63,9 @@ pairwise molecular interaction->description - - -description + + +description @@ -76,9 +76,9 @@ pairwise molecular interaction->has attribute - - -has attribute + + +has attribute @@ -89,9 +89,9 @@ pairwise molecular interaction->negated - - -negated + + +negated @@ -102,9 +102,9 @@ pairwise molecular interaction->qualifiers - - -qualifiers + + +qualifiers @@ -115,9 +115,9 @@ pairwise molecular interaction->publications - - -publications + + +publications @@ -128,395 +128,395 @@ pairwise molecular interaction->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string pairwise molecular interaction->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string pairwise molecular interaction->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string pairwise molecular interaction->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type pairwise molecular interaction->timepoint - - -timepoint + + +timepoint original subject - -string + +string pairwise molecular interaction->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie pairwise molecular interaction->original predicate - - -original predicate + + +original predicate original object - -string + +string pairwise molecular interaction->original object - - -original object + + +original object subject category - -ontology class + +ontology class pairwise molecular interaction->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class pairwise molecular interaction->object category - - -object category + + +object category subject closure - -string + +string pairwise molecular interaction->subject closure - - -subject closure + + +subject closure object closure - -string + +string pairwise molecular interaction->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class pairwise molecular interaction->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class pairwise molecular interaction->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string pairwise molecular interaction->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string pairwise molecular interaction->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string pairwise molecular interaction->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string pairwise molecular interaction->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source pairwise molecular interaction->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type pairwise molecular interaction->type - - -type + + +type category - -category + +category pairwise molecular interaction->category - - -category + + +category interacting molecules category - -ontology class + +ontology class pairwise molecular interaction->interacting molecules category - - -interacting molecules category + + +interacting molecules category subject - -subject + +subject pairwise molecular interaction->subject - - -subject + + +subject id - -id + +id pairwise molecular interaction->id - - -id + + +id predicate - -predicate + +predicate pairwise molecular interaction->predicate - - -predicate + + +predicate object - -object + +object pairwise molecular interaction->object - - -object + + +object association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + pairwise molecular interaction_subject - -molecular entity + +molecular entity pairwise molecular interaction_id - -string + +string pairwise molecular interaction_predicate - -predicate type + +predicate type object->relation - - + + pairwise molecular interaction_object - -molecular entity + +molecular entity diff --git a/graphviz/population_to_population_association.gv b/graphviz/population_to_population_association.gv index d06c8578f5..3cffb10eb4 100644 --- a/graphviz/population_to_population_association.gv +++ b/graphviz/population_to_population_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4748,283"]; + graph [bb="0,0,4563,283"]; node [label="\N"]; "population to population association" [height=0.5, label="population to population association", - pos="2468.4,265", + pos="2283.4,265", width=4.9648]; association [height=0.5, pos="62.394,178", width=1.7332]; "population to population association" -> association [label=is_a, lp="280.39,221.5", - pos="e,102.91,191.79 2290,263.46 1801.2,261.67 464.11,254.47 266.39,229 213.1,222.13 153.57,206.61 112.64,194.66"]; + pos="e,102.91,191.77 2105.2,263.18 1646,260.74 445.54,252.21 266.39,229 213.11,222.1 153.58,206.57 112.65,194.64"]; id [color=blue, height=0.5, label=string, @@ -18,8 +18,8 @@ digraph { width=1.0652]; "population to population association" -> id [color=blue, label=id, - lp="396.39,221.5", - pos="e,210.38,189.98 2290.7,262.91 1822,259.76 575.24,249.55 389.39,229 317.23,221.02 299.34,215.5 229.39,196 226.29,195.13 223.09,194.17 \ + lp="395.39,221.5", + pos="e,210.38,189.98 2106.1,262.61 1667.6,258.9 555.78,247.75 388.39,229 316.67,220.97 298.9,215.43 229.39,196 226.29,195.13 223.09,194.17 \ 219.89,193.15", style=solid]; iri [color=blue, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "population to population association" -> iri [color=blue, label=iri, - lp="509.39,221.5", - pos="e,315.3,190.2 2291,262.65 1840.6,258.97 676.07,247.76 501.39,229 426.6,220.97 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ -325.06,193.15", + lp="501.39,221.5", + pos="e,315.32,190.15 2104.6,264.74 1715.3,265.65 801.28,263.85 493.39,229 422.11,220.93 404.75,214.31 335.39,196 332.02,195.11 328.55,\ +194.13 325.07,193.11", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "population to population association" -> name [color=blue, label=name, - lp="616.39,221.5", - pos="e,439.35,191.54 2290.4,263.02 1855.2,260.29 760.93,251.28 596.39,229 545.26,222.08 488.24,206.51 449.14,194.57", + lp="604.39,221.5", + pos="e,437.98,191.87 2105.9,262.82 1700.8,259.75 731.58,250.29 584.39,229 537.02,222.15 484.46,206.96 447.86,195.11", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "population to population association" -> description [color=blue, label=description, - lp="736.89,221.5", - pos="e,585.45,194.14 2289.8,263.63 1871.1,262.3 849.91,256.29 696.39,229 661.33,222.77 623.33,209.4 595.03,198.06", + lp="717.89,221.5", + pos="e,581.77,194.62 2105,263.68 1715.7,262.46 813.94,256.65 677.39,229 647.36,222.92 615.28,210.09 591.01,198.95", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "population to population association" -> "has attribute" [color=blue, label="has attribute", - lp="882.39,221.5", - pos="e,725.98,192.82 2290,263.43 1896,261.69 975.02,254.89 835.39,229 800.43,222.52 762.57,208.39 735.2,196.8", + lp="852.39,221.5", + pos="e,721.33,194.01 2104.7,263.81 1738.9,262.84 928.68,257.46 805.39,229 778.89,222.88 751.04,209.98 730.13,198.82", style=solid]; negated [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=1.2999]; "population to population association" -> negated [color=blue, label=negated, - lp="1038.4,221.5", - pos="e,847.59,190.46 2289.6,264.31 1956.2,264.12 1251.6,259.91 1009.4,229 956.09,222.2 896.47,205.66 857.14,193.46", + lp="990.39,221.5", + pos="e,843.03,191.96 2106.7,262.26 1772.3,258.53 1070.9,248.49 961.39,229 923.37,222.23 881.85,207.52 852.5,195.8", style=solid]; qualifiers [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=2.1304]; "population to population association" -> qualifiers [color=blue, label=qualifiers, - lp="1178.9,221.5", - pos="e,996.68,193.07 2289.7,264.35 1981.1,264.09 1360.7,259.62 1145.4,229 1097.6,222.2 1044.5,207.74 1006.5,196.11", + lp="1101.9,221.5", + pos="e,982.4,194.93 2106,262.64 1793,259.68 1166.6,251.07 1068.4,229 1041.6,222.97 1013.3,210.59 991.57,199.66", style=solid]; publications [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=1.7332]; "population to population association" -> publications [color=blue, label=publications, - lp="1326.4,221.5", - pos="e,1148.1,192.71 2289.6,264.29 2007.2,263.81 1470.8,258.82 1282.4,229 1239.3,222.18 1191.8,207.69 1157.8,196.06", + lp="1202.4,221.5", + pos="e,1121.9,195.78 2107,262.04 1801.1,258.14 1200.7,248.1 1158.4,229 1146.3,223.57 1135.9,213.45 1128,203.73", style=solid]; "has evidence" [color=blue, height=0.5, @@ -100,276 +100,276 @@ digraph { width=2.0943]; "population to population association" -> "has evidence" [color=blue, label="has evidence", - lp="1480.9,221.5", - pos="e,1305.9,193.61 2290.2,263.48 2039.1,261.8 1593.7,255.1 1434.4,229 1393.5,222.3 1348.6,208.48 1315.7,197.06", + lp="1300.9,221.5", + pos="e,1255.9,195.88 2104.6,264.29 1817.7,263.86 1283.4,259 1254.4,229 1248.2,222.63 1248.8,213.73 1251.7,205.2", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1469.4,178", - width=3.015]; + label=string, + pos="1399.4,178", + width=1.0652]; "population to population association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1635.9,221.5", - pos="e,1495.5,195.59 2293.9,261.07 2052.6,256.44 1639.2,246.12 1571.4,229 1547.9,223.07 1523.5,211.31 1504.4,200.68", + lp="1419.9,221.5", + pos="e,1375.2,192.24 2105.2,263.56 1842.9,262.02 1380.9,255.53 1355.4,229 1345.9,219.09 1354.7,207.6 1366.9,198.13", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1704.4,178", - width=3.015]; + label=string, + pos="1494.4,178", + width=1.0652]; "population to population association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1807.4,221.5", - pos="e,1702.1,196.41 2292.9,261.41 2076.3,257.39 1733.7,248.07 1712.4,229 1706.1,223.34 1703.4,214.82 1702.5,206.41", + lp="1589.4,221.5", + pos="e,1489,196.04 2106.5,262.27 1880.4,259.17 1515.2,250.8 1494.4,229 1488.6,222.94 1487.2,214.32 1487.7,205.94", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1939.4,178", - width=3.015]; + label=string, + pos="1669.4,178", + width=1.0652]; "population to population association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2015.9,221.5", - pos="e,1918.7,195.97 2299.8,259 2140.1,253.41 1922.8,243.25 1909.4,229 1902.4,221.54 1905.6,212.18 1912,203.58", + lp="1809.9,221.5", + pos="e,1676.1,196.02 2108.3,261.19 1950.5,257.4 1738,248.68 1703.4,229 1693.8,223.55 1686.4,214.16 1680.9,204.98", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2121.4,178", + pos="1895.4,178", width=1.5346]; "population to population association" -> timepoint [color=blue, label=timepoint, - lp="2171.4,221.5", - pos="e,2121.9,196.47 2315.9,255.58 2235.6,249.79 2150.8,240.98 2136.4,229 2129.6,223.41 2125.9,214.91 2123.8,206.49", + lp="1972.4,221.5", + pos="e,1904.8,195.92 2115.3,258.82 2043.3,254.2 1968.6,245.48 1937.4,229 1926.7,223.32 1917.5,213.63 1910.6,204.28", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2233.4,178", + pos="2007.4,178", width=1.0652]; "population to population association" -> "original subject" [color=blue, label="original subject", - lp="2270.4,221.5", - pos="e,2219.6,194.92 2303.4,258.03 2263.1,252.96 2227.6,244.14 2214.4,229 2208.1,221.83 2209.9,212.39 2214.3,203.65", + lp="2076.4,221.5", + pos="e,2007.3,196.33 2122.3,257.17 2077.6,252.15 2036.9,243.58 2020.4,229 2013.9,223.25 2010.5,214.72 2008.7,206.31", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2347.4,178", + pos="2133.4,178", width=1.5887]; "population to population association" -> "original predicate" [color=blue, label="original predicate", - lp="2397.9,221.5", - pos="e,2336.3,195.76 2379.4,249.38 2358.7,244.13 2340.9,237.37 2334.4,229 2329.1,222.16 2329.6,213.39 2332.4,205.11", + lp="2207.9,221.5", + pos="e,2132.9,196.42 2194.8,249.34 2172.3,243.97 2152.3,237.17 2144.4,229 2138.6,222.99 2135.5,214.63 2134,206.47", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2461.4,178", + pos="2267.4,178", width=1.0652]; "population to population association" -> "original object" [color=blue, label="original object", - lp="2516.9,221.5", - pos="e,2462.8,196.18 2467,246.8 2466,235.16 2464.7,219.55 2463.6,206.24", + lp="2327.9,221.5", + pos="e,2270.6,196.18 2280.2,246.8 2278,235.16 2275,219.55 2272.5,206.24", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2594.4,178", + pos="2400.4,178", width=2.1304]; "population to population association" -> "subject category" [color=blue, label="subject category", - lp="2642.9,221.5", - pos="e,2590.6,196.4 2540.7,248.46 2552.2,243.62 2563.3,237.29 2572.4,229 2579.1,222.84 2583.9,214.24 2587.3,205.9", + lp="2452.9,221.5", + pos="e,2398.4,196.3 2354,248.46 2364.9,243.63 2375.2,237.3 2383.4,229 2389.5,222.8 2393.5,214.29 2396,206.04", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2765.4,178", + pos="2571.4,178", width=2.1304]; "population to population association" -> "object category" [color=blue, label="object category", - lp="2785.9,221.5", - pos="e,2750.6,195.73 2617.4,255.05 2647.8,249.69 2678.8,241.47 2706.4,229 2720,222.83 2733,212.54 2743.3,202.9", + lp="2593.9,221.5", + pos="e,2557.8,195.72 2432.1,254.99 2461,249.59 2490.3,241.37 2516.4,229 2529.3,222.88 2541.3,212.74 2550.8,203.17", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="2898.4,178", + pos="2704.4,178", width=1.0652]; "population to population association" -> "subject closure" [color=blue, label="subject closure", - lp="2921.9,221.5", - pos="e,2886,195.51 2596.1,252.38 2704.9,242.45 2843.9,229.66 2845.4,229 2858.3,223.16 2870.1,212.86 2879.2,203.11", + lp="2728.9,221.5", + pos="e,2692.6,195.5 2411.2,252.41 2517,242.73 2650.6,230.31 2653.4,229 2665.9,223.2 2677.1,213.04 2685.8,203.39", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="2998.4,178", + pos="2812.4,178", width=1.0652]; "population to population association" -> "object closure" [color=blue, label="object closure", - lp="3042.4,221.5", - pos="e,2997,196.23 2593.2,252.1 2614.3,250.27 2636,248.49 2656.4,247 2692.4,244.38 2951.5,250.54 2980.4,229 2987.7,223.53 2992.1,214.8 \ -2994.7,206.14", + lp="2851.4,221.5", + pos="e,2808.5,196.38 2408.5,252.1 2429.5,250.27 2451,248.5 2471.4,247 2506.5,244.42 2758,248.33 2787.4,229 2795.6,223.59 2801.2,214.63 \ +2805,205.78", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3131.4,178", + pos="2945.4,178", width=2.1304]; "population to population association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3200.9,221.5", - pos="e,3124.4,196.11 2592,251.95 2613.4,250.11 2635.5,248.37 2656.4,247 2705.2,243.8 3053.5,252.48 3096.4,229 3106.2,223.66 3113.8,214.29 \ -3119.4,205.09", + lp="3010.9,221.5", + pos="e,2936.8,196.16 2407,251.96 2428.4,250.12 2450.5,248.37 2471.4,247 2519.6,243.83 2862.3,250.8 2905.4,229 2916,223.62 2924.8,213.98 \ +2931.3,204.59", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3323.4,178", + pos="3138.4,178", width=2.1304]; "population to population association" -> "object category closure" [color=blue, label="object category closure", - lp="3390.9,221.5", - pos="e,3317.7,196.1 2590.7,251.84 2612.5,249.98 2635.1,248.26 2656.4,247 2691.7,244.91 3261.8,246.63 3292.4,229 3301.6,223.71 3308.4,\ -214.47 3313.3,205.37", + lp="3202.9,221.5", + pos="e,3131.1,196.17 2405.7,251.84 2427.5,249.98 2450.1,248.26 2471.4,247 2506.4,244.92 3071.4,245.43 3102.4,229 3112.4,223.68 3120.3,\ +214.19 3126.1,204.89", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3513.4,178", + pos="3328.4,178", width=1.0652]; "population to population association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3563.4,221.5", - pos="e,3506.4,196.19 2589.9,251.79 2612,249.92 2634.9,248.21 2656.4,247 2702,244.44 3438.1,250.54 3478.4,229 3488.2,223.75 3495.9,214.4 \ -3501.5,205.19", + lp="3375.4,221.5", + pos="e,3320.7,195.73 2404.9,251.79 2427,249.92 2449.9,248.21 2471.4,247 2516.8,244.45 3249.8,249.67 3290.4,229 3300.8,223.67 3309.2,213.99 \ +3315.4,204.55", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3672.4,178", + pos="3487.4,178", width=1.0652]; "population to population association" -> "object namespace" [color=blue, label="object namespace", - lp="3716.4,221.5", - pos="e,3665,195.73 2589.7,251.75 2611.8,249.87 2634.8,248.17 2656.4,247 2710.7,244.05 3587,253.93 3635.4,229 3645.7,223.67 3653.9,213.99 \ -3659.9,204.56", + lp="3529.4,221.5", + pos="e,3479.1,195.77 2404.7,251.75 2426.8,249.87 2449.8,248.17 2471.4,247 2525.5,244.06 3398.7,252.94 3447.4,229 3458.2,223.66 3467.1,\ +213.84 3473.7,204.31", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3823.4,178", + pos="3638.4,178", width=1.0652]; "population to population association" -> "subject label closure" [color=blue, label="subject label closure", - lp="3876.4,221.5", - pos="e,3815.4,195.77 2589.4,251.72 2611.7,249.85 2634.7,248.15 2656.4,247 2687.7,245.34 3756.3,242.97 3784.4,229 3795.1,223.66 3803.8,\ -213.84 3810.2,204.31", + lp="3689.4,221.5", + pos="e,3629.8,195.79 2404.4,251.72 2426.7,249.85 2449.7,248.15 2471.4,247 2502.6,245.34 3569.2,242.61 3597.4,229 3608.4,223.69 3617.4,\ +213.87 3624.2,204.34", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="3994.4,178", + pos="3809.4,178", width=1.0652]; "population to population association" -> "object label closure" [color=blue, label="object label closure", - lp="4041.9,221.5", - pos="e,3986.1,195.79 2589.2,251.71 2611.5,249.82 2634.6,248.13 2656.4,247 2692.4,245.12 3922,244.85 3954.4,229 3965.3,223.69 3974.1,213.87 \ -3980.7,204.33", + lp="3856.9,221.5", + pos="e,3800.5,195.81 2404.2,251.71 2426.5,249.83 2449.6,248.13 2471.4,247 2507.3,245.13 3734.9,244.43 3767.4,229 3778.5,223.72 3787.8,\ +213.9 3794.7,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4147.4,178", + pos="3962.4,178", width=2.347]; "population to population association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4200.9,221.5", - pos="e,4141.4,196.18 2588.9,251.7 2611.3,249.81 2634.5,248.12 2656.4,247 2696.9,244.92 4080,248.68 4115.4,229 4124.9,223.75 4131.9,214.39 \ -4137,205.18", + lp="4015.9,221.5", + pos="e,3956.4,196.18 2403.9,251.7 2426.3,249.81 2449.5,248.12 2471.4,247 2511.9,244.92 3895,248.68 3930.4,229 3939.9,223.75 3946.9,214.39 \ +3952,205.18", style=solid]; type [height=0.5, - pos="4281.4,178", + pos="4096.4,178", width=0.86659]; "population to population association" -> type [color=blue, label=type, - lp="4299.4,221.5", - pos="e,4284.1,195.98 2588.9,251.68 2611.3,249.79 2634.5,248.11 2656.4,247 2678.8,245.86 4257.5,243.84 4274.4,229 4280.9,223.32 4283.4,\ -214.65 4284.1,206.12", + lp="4114.4,221.5", + pos="e,4099.1,195.98 2403.9,251.68 2426.3,249.79 2449.5,248.11 2471.4,247 2493.8,245.86 4072.5,243.84 4089.4,229 4095.9,223.32 4098.4,\ +214.65 4099.1,206.12", style=solid]; category [height=0.5, - pos="4382.4,178", + pos="4197.4,178", width=1.4263]; "population to population association" -> category [color=blue, label=category, - lp="4377.9,221.5", - pos="e,4367.7,195.48 2588.9,251.68 2611.3,249.79 2634.5,248.1 2656.4,247 2702.5,244.67 4275.9,244.44 4319.4,229 4334.6,223.59 4349,212.83 \ -4360.1,202.68", + lp="4192.9,221.5", + pos="e,4182.7,195.48 2403.9,251.68 2426.3,249.79 2449.5,248.1 2471.4,247 2517.5,244.67 4090.9,244.44 4134.4,229 4149.6,223.59 4164,212.83 \ +4175.1,202.68", style=solid]; subject [height=0.5, - pos="4496.4,178", + pos="4311.4,178", width=1.2277]; "population to population association" -> subject [color=blue, label=subject, - lp="4473.4,221.5", - pos="e,4477.7,194.32 2588.9,251.66 2611.3,249.78 2634.5,248.1 2656.4,247 2753.9,242.1 4319.5,255.62 4413.4,229 4433.6,223.29 4453.7,211.3 \ -4469.2,200.49", + lp="4288.4,221.5", + pos="e,4292.7,194.32 2403.9,251.66 2426.3,249.78 2449.5,248.1 2471.4,247 2568.9,242.1 4134.5,255.62 4228.4,229 4248.6,223.29 4268.7,211.3 \ +4284.2,200.49", style=solid]; object [height=0.5, - pos="4539.4,91", + pos="4354.4,91", width=1.0832]; "population to population association" -> object [color=blue, label=object, - lp="4583.4,178", - pos="e,4552.8,108.09 2588.6,251.68 2611.1,249.78 2634.5,248.1 2656.4,247 2707.6,244.44 4454.6,244.95 4503.4,229 4527.3,221.18 4535.3,\ -216.87 4549.4,196 4563.2,175.52 4559.5,166.51 4562.4,142 4563.2,135.38 4564.3,133.39 4562.4,127 4561.4,123.55 4559.9,120.13 4558.1,\ + lp="4398.4,178", + pos="e,4367.8,108.09 2403.6,251.68 2426.1,249.78 2449.5,248.1 2471.4,247 2522.6,244.44 4269.6,244.95 4318.4,229 4342.3,221.18 4350.3,\ +216.87 4364.4,196 4378.2,175.52 4374.5,166.51 4377.4,142 4378.2,135.38 4379.3,133.39 4377.4,127 4376.4,123.55 4374.9,120.13 4373.1,\ 116.85", style=solid]; predicate [height=0.5, - pos="4693.4,178", + pos="4508.4,178", width=1.5165]; "population to population association" -> predicate [color=blue, label=predicate, - lp="4666.4,221.5", - pos="e,4669.6,194.35 2588.6,251.67 2611.1,249.78 2634.5,248.09 2656.4,247 2763.7,241.66 4485.8,253.56 4590.4,229 4615.3,223.16 4641.2,\ -210.56 4660.8,199.48", + lp="4480.4,221.5", + pos="e,4484.6,194.35 2403.6,251.67 2426.1,249.78 2449.5,248.09 2471.4,247 2578.7,241.66 4300.8,253.56 4405.4,229 4430.3,223.16 4456.2,\ +210.56 4475.8,199.48", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2703.4,265", + pos="2518.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2834.4,265", + pos="2649.4,265", width=2.0762]; subject -> object [label=relation, - lp="4534.4,134.5", - pos="e,4521.5,107.23 4497.5,159.55 4498.7,149.57 4501.2,137.07 4506.4,127 4508.6,122.68 4511.5,118.52 4514.7,114.66"]; + lp="4349.4,134.5", + pos="e,4336.5,107.23 4312.5,159.55 4313.7,149.57 4316.2,137.07 4321.4,127 4323.6,122.68 4326.5,118.52 4329.7,114.66"]; relation [height=0.5, - pos="4484.4,18", + pos="4299.4,18", width=1.2999]; - subject -> relation [pos="e,4485.7,36.188 4495.1,159.79 4493,132.48 4489,78.994 4486.5,46.38", + subject -> relation [pos="e,4300.7,36.188 4310.1,159.79 4308,132.48 4304,78.994 4301.5,46.38", style=dotted]; "population to population association_subject" [color=blue, height=0.5, label="population of individual organisms", - pos="3098.4,265", + pos="2913.4,265", width=4.7662]; - object -> relation [pos="e,4497.2,35.54 4526.9,73.889 4520,64.939 4511.2,53.617 4503.4,43.584", + object -> relation [pos="e,4312.2,35.54 4341.9,73.889 4335,64.939 4326.2,53.617 4318.4,43.584", style=dotted]; "population to population association_object" [color=blue, height=0.5, label="population of individual organisms", - pos="3459.4,265", + pos="3274.4,265", width=4.7662]; "population to population association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3727.4,265", + pos="3542.4,265", width=2.1665]; } diff --git a/graphviz/population_to_population_association.svg b/graphviz/population_to_population_association.svg index 279cea5d16..021711c791 100644 --- a/graphviz/population_to_population_association.svg +++ b/graphviz/population_to_population_association.svg @@ -4,16 +4,16 @@ - + %3 - + population to population association - -population to population association + +population to population association @@ -24,8 +24,8 @@ population to population association->association - - + + is_a @@ -37,9 +37,9 @@ population to population association->id - - -id + + +id @@ -50,9 +50,9 @@ population to population association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ population to population association->name - - -name + + +name @@ -76,9 +76,9 @@ population to population association->description - - -description + + +description @@ -89,9 +89,9 @@ population to population association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ population to population association->negated - - -negated + + +negated @@ -115,9 +115,9 @@ population to population association->qualifiers - - -qualifiers + + +qualifiers @@ -128,9 +128,9 @@ population to population association->publications - - -publications + + +publications @@ -141,363 +141,363 @@ population to population association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string population to population association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string population to population association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string population to population association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type population to population association->timepoint - - -timepoint + + +timepoint original subject - -string + +string population to population association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie population to population association->original predicate - - -original predicate + + +original predicate original object - -string + +string population to population association->original object - - -original object + + +original object subject category - -ontology class + +ontology class population to population association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class population to population association->object category - - -object category + + +object category subject closure - -string + +string population to population association->subject closure - - -subject closure + + +subject closure object closure - -string + +string population to population association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class population to population association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class population to population association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string population to population association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string population to population association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string population to population association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string population to population association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source population to population association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type population to population association->type - - -type + + +type category - -category + +category population to population association->category - - -category + + +category subject - -subject + +subject population to population association->subject - - -subject + + +subject object - -object + +object population to population association->object - - -object + + +object predicate - -predicate + +predicate population to population association->predicate - - -predicate + + +predicate association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + population to population association_subject - -population of individual organisms + +population of individual organisms object->relation - - + + population to population association_object - -population of individual organisms + +population of individual organisms population to population association_predicate - -predicate type + +predicate type diff --git a/graphviz/predicate_mapping.gv b/graphviz/predicate_mapping.gv index 657719f9a9..c07c8310c7 100644 --- a/graphviz/predicate_mapping.gv +++ b/graphviz/predicate_mapping.gv @@ -1,5 +1,5 @@ digraph { - graph [bb="0,0,3948.9,123"]; + graph [bb="0,0,3869.9,123"]; node [label="\N"]; "predicate mapping" [height=0.5, label="predicate mapping", @@ -148,72 +148,71 @@ digraph { "object context qualifier" [color=blue, height=0.5, label=string, - pos="2560.3,18", + pos="2642.3,18", width=1.0652]; "predicate mapping" -> "object context qualifier" [color=blue, label="object context qualifier", - lp="2723.3,61.5", - pos="e,2590.9,29.225 1955.2,103.16 2159.3,100.92 2613.2,93.234 2636.3,69 2641,64.181 2639.9,59.614 2636.3,54 2631.9,46.995 2616.2,39.253 \ -2600.2,32.836", + lp="2728.3,61.5", + pos="e,2645.4,36.327 1955,102.94 2158.6,100.28 2611.8,91.808 2636.3,69 2642.5,63.313 2644.9,54.898 2645.4,46.587", style=solid]; "causal mechanism qualifier" [color=blue, height=0.5, label=CausalMechanismQualifierEnum, - pos="2779.3,18", + pos="2861.3,18", width=4.5135]; "predicate mapping" -> "causal mechanism qualifier" [color=blue, label="causal mechanism qualifier", - lp="2912.8,61.5", - pos="e,2800.7,35.996 1955.7,104.02 2193.3,103.57 2781,99.396 2810.3,69 2817.5,61.568 2814.2,52.212 2807.5,43.609", + lp="2932.8,61.5", + pos="e,2850.8,36.238 1955.8,104.67 2184.6,105.64 2738.9,104.24 2815.3,69 2826.9,63.655 2837,53.886 2844.7,44.392", style=solid]; "anatomical context qualifier" [color=blue, height=0.5, - label=AnatomicalContextQualifierEnum, - pos="3126.3,18", - width=4.6218]; + label=string, + pos="3080.3,18", + width=1.0652]; "predicate mapping" -> "anatomical context qualifier" [color=blue, label="anatomical context qualifier", - lp="3159.3,61.5", - pos="e,3097,35.9 1955.3,103.21 2215.7,100.81 2912.7,92.265 3014.3,69 3040,63.122 3067,51.251 3088.1,40.551", + lp="3154.3,61.5", + pos="e,3070.2,35.776 1955.4,103.15 2229.3,100.51 2985.7,91.225 3034.3,69 3046.1,63.619 3056.3,53.652 3064,44.025", style=solid]; "species context qualifier" [color=blue, height=0.5, label="organism taxon", - pos="3394.3,18", + pos="3302.3,18", width=2.3109]; "predicate mapping" -> "species context qualifier" [color=blue, label="species context qualifier", - lp="3402.8,61.5", - pos="e,3362.4,34.708 1955.4,103.48 2253.4,101.63 3136.2,94.074 3263.3,69 3294.5,62.859 3327.9,50.009 3353.1,38.874", + lp="3364.8,61.5", + pos="e,3292.5,36.274 1955.5,103.7 2264.4,102.47 3199.5,96.484 3258.3,69 3269.7,63.7 3279.3,53.939 3286.6,44.438", style=solid]; "exact match" [color=blue, height=0.5, label="named thing", - pos="3565.3,18", + pos="3486.3,18", width=1.9318]; "predicate mapping" -> "exact match" [color=blue, label="exact match", - lp="3568.3,61.5", - pos="e,3548,35.692 1955.2,103.48 2297.1,101.47 3421.1,93.056 3494.3,69 3511.1,63.479 3527.5,52.52 3540.2,42.265", + lp="3515.3,61.5", + pos="e,3481,36.111 1955.5,104.45 2293.3,105.68 3391.4,106.73 3456.3,69 3465.4,63.718 3472.1,54.486 3476.8,45.382", style=solid]; "narrow match" [color=blue, height=0.5, label="named thing", - pos="3722.3,18", + pos="3643.3,18", width=1.9318]; "predicate mapping" -> "narrow match" [color=blue, label="narrow match", - lp="3709.3,61.5", - pos="e,3696.9,34.761 1955.5,104.44 2302,105.67 3454.9,106.85 3616.3,69 3641.6,63.079 3668,50.656 3688.1,39.676", + lp="3646.3,61.5", + pos="e,3623.8,35.47 1955.3,103.43 2306.6,101.2 3486.1,92.016 3563.3,69 3582.2,63.371 3601.1,51.98 3615.7,41.491", style=solid]; "broad match" [color=blue, height=0.5, label="named thing", - pos="3879.3,18", + pos="3800.3,18", width=1.9318]; "predicate mapping" -> "broad match" [color=blue, label="broad match", - lp="3854.8,61.5", - pos="e,3851.8,34.531 1955.7,104.42 2320.9,105.67 3586.5,107.19 3763.3,69 3791.1,63.006 3820.5,50.281 3842.7,39.17", + lp="3785.8,61.5", + pos="e,3776.1,35.01 1955.1,103.34 2324.1,100.69 3615.2,89.96 3700.3,69 3724,63.18 3748.5,51.054 3767.3,40.202", style=solid]; } diff --git a/graphviz/predicate_mapping.svg b/graphviz/predicate_mapping.svg index 6f10eaf2ac..671515f5e3 100644 --- a/graphviz/predicate_mapping.svg +++ b/graphviz/predicate_mapping.svg @@ -4,11 +4,11 @@ - + %3 - + predicate mapping @@ -200,93 +200,93 @@ object context qualifier - -string + +string predicate mapping->object context qualifier - - -object context qualifier + + +object context qualifier causal mechanism qualifier - -CausalMechanismQualifierEnum + +CausalMechanismQualifierEnum predicate mapping->causal mechanism qualifier - - -causal mechanism qualifier + + +causal mechanism qualifier anatomical context qualifier - -AnatomicalContextQualifierEnum + +string predicate mapping->anatomical context qualifier - - -anatomical context qualifier + + +anatomical context qualifier species context qualifier - -organism taxon + +organism taxon predicate mapping->species context qualifier - - -species context qualifier + + +species context qualifier exact match - -named thing + +named thing predicate mapping->exact match - - -exact match + + +exact match narrow match - -named thing + +named thing predicate mapping->narrow match - - -narrow match + + +narrow match broad match - -named thing + +named thing predicate mapping->broad match - - -broad match + + +broad match diff --git a/graphviz/reaction_to_catalyst_association.gv b/graphviz/reaction_to_catalyst_association.gv index 7ad0ab996b..e42f49c4b1 100644 --- a/graphviz/reaction_to_catalyst_association.gv +++ b/graphviz/reaction_to_catalyst_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,5574.6,283"]; + graph [bb="0,0,5356.6,283"]; node [label="\N"]; "reaction to catalyst association" [height=0.5, label="reaction to catalyst association", - pos="2919.6,265", + pos="2701.6,265", width=4.3149]; "reaction to participant association" [height=0.5, pos="169.63,178", width=4.7121]; "reaction to catalyst association" -> "reaction to participant association" [label=is_a, - lp="495.63,221.5", - pos="e,244.91,194.2 2765.2,263.08 2264.8,259.93 707.65,248.63 481.63,229 404.5,222.3 317.58,207.79 255.11,196.12"]; + lp="494.63,221.5", + pos="e,244.67,194.17 2546.3,264.46 2110.6,265.27 882.44,264.28 480.63,229 403.75,222.25 317.1,207.74 254.84,196.09"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "reaction to catalyst association" -> id [color=blue, label=id, - lp="612.63,221.5", - pos="e,424.62,190 2764.6,263.33 2280.7,260.99 818.46,252.08 605.63,229 532.58,221.08 514.44,215.65 443.63,196 440.53,195.14 437.33,194.17 \ -434.13,193.16", + lp="610.63,221.5", + pos="e,424.62,189.98 2546.8,263.09 2094.5,260.18 794.52,250.09 603.63,229 531.47,221.03 513.58,215.5 443.63,196 440.53,195.13 437.33,\ +194.17 434.13,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "reaction to catalyst association" -> iri [color=blue, label=iri, - lp="729.63,221.5", - pos="e,529.53,190.23 2765,263.09 2298.2,260.13 922.84,249.74 721.63,229 644.21,221.02 625.05,215.26 549.63,196 546.26,195.14 542.78,194.18 \ -539.29,193.17", + lp="723.63,221.5", + pos="e,529.54,190.2 2547,262.87 2111.6,259.45 895.27,248.28 715.63,229 640.84,220.97 622.46,214.85 549.63,196 546.26,195.13 542.78,194.16 \ +539.3,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "reaction to catalyst association" -> name [color=blue, label=name, - lp="840.63,221.5", - pos="e,654.44,191.28 2764.7,263.35 2312.1,261.19 1011.3,252.93 820.63,229 766.24,222.17 705.38,206.24 664.21,194.18", + lp="831.63,221.5", + pos="e,653.43,191.44 2547,263.18 2126.2,260.65 981.02,251.76 811.63,229 759.98,222.06 702.34,206.36 663.01,194.39", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "reaction to catalyst association" -> description [color=blue, label=description, - lp="968.13,221.5", - pos="e,802.89,193.79 2764.4,263.79 2327.4,262.83 1106.6,257.6 927.63,229 887.86,222.64 844.32,208.8 812.4,197.28", + lp="954.13,221.5", + pos="e,800.13,194.02 2546.5,263.68 2141.3,262.44 1071.8,256.58 913.63,229 877.63,222.72 838.52,209.2 809.55,197.79", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "reaction to catalyst association" -> "has attribute" [color=blue, label="has attribute", - lp="1123.6,221.5", - pos="e,943.71,191.9 2764.7,263.48 2350.9,261.76 1240.7,254.77 1076.6,229 1033.8,222.27 986.59,207.28 953.5,195.45", + lp="1101.6,221.5", + pos="e,941.06,192.7 2546.7,263.46 2164.7,261.74 1198.6,254.87 1054.6,229 1018.4,222.49 979.03,208.29 950.63,196.69", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "reaction to catalyst association" -> predicate [color=blue, label=predicate, - lp="1282.6,221.5", - pos="e,1101.1,193.25 2765.3,262.85 2380,259.67 1396,249.64 1248.6,229 1201.2,222.36 1148.6,207.95 1110.8,196.3", + lp="1245.6,221.5", + pos="e,1094.7,194.1 2547.2,262.93 2192.6,260.09 1340.3,251.05 1211.6,229 1174.5,222.63 1134,209.09 1104,197.71", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "reaction to catalyst association" -> negated [color=blue, label=negated, - lp="1424.6,221.5", - pos="e,1235.5,190.46 2764.2,264.57 2430.9,265.12 1656.5,262.58 1395.6,229 1343.1,222.23 1284.3,205.81 1245.4,193.62", + lp="1364.6,221.5", + pos="e,1229.6,192.55 2547.1,262.92 2214.6,260.17 1451.6,251.48 1335.6,229 1301.8,222.44 1265.2,208.27 1238.8,196.69", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "reaction to catalyst association" -> qualifiers [color=blue, label=qualifiers, - lp="1563.1,221.5", - pos="e,1384.4,193.2 2764.1,264.7 2452.9,265.34 1763.6,262.73 1529.6,229 1482.9,222.26 1431.2,207.87 1394,196.25", + lp="1468.1,221.5", + pos="e,1365.5,195.43 2546.5,263.76 2231.8,262.69 1539.2,257.12 1434.6,229 1413.1,223.21 1391.1,211.5 1374,200.86", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "reaction to catalyst association" -> publications [color=blue, label=publications, - lp="1708.6,221.5", - pos="e,1535.4,192.85 2764.2,264.82 2476.6,265.48 1871.6,262.63 1664.6,229 1623.3,222.28 1577.8,207.95 1545.1,196.35", + lp="1559.6,221.5", + pos="e,1500.3,196.25 2546.4,264.14 2234,263.77 1556.1,259.45 1515.6,229 1508.4,223.56 1504.4,214.83 1502.2,206.18", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,294 +110,295 @@ digraph { width=2.0943]; "reaction to catalyst association" -> "has evidence" [color=blue, label="has evidence", - lp="1867.1,221.5", - pos="e,1693.6,193.63 2764.4,264.06 2505.7,263.33 1997.4,258.08 1820.6,229 1780.2,222.35 1735.9,208.52 1703.3,197.09", + lp="1658.1,221.5", + pos="e,1627.5,194.88 2546.1,264.64 2252.7,265.07 1643.6,261.97 1611.6,229 1603,220.11 1609.3,209.91 1619.5,201.06", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1857.6,178", - width=3.015]; + label=string, + pos="1787.6,178", + width=1.0652]; "reaction to catalyst association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2022.1,221.5", - pos="e,1883.2,195.61 2766.4,261.99 2514.6,258.15 2033.6,248.39 1957.6,229 1934.5,223.1 1910.6,211.34 1891.9,200.71", + lp="1776.1,221.5", + pos="e,1757.1,189.23 2546.5,264.09 2275.1,263.47 1740.1,258.48 1711.6,229 1707,224.2 1708,219.61 1711.6,214 1716.1,207 1731.8,199.25 \ +1747.8,192.84", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2092.6,178", - width=3.015]; + label=string, + pos="1882.6,178", + width=1.0652]; "reaction to catalyst association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2193.6,221.5", - pos="e,2089.6,196.33 2765.6,262.52 2534.6,259.59 2122.7,251.25 2098.6,229 2092.5,223.32 2090.1,214.91 2089.5,206.59", + lp="1942.6,221.5", + pos="e,1862.1,193.24 2547,263.13 2307.4,261.02 1871.4,253.77 1847.6,229 1839.3,220.29 1845.3,209.43 1854.5,200.05", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2327.6,178", - width=3.015]; + label=string, + pos="2024.6,178", + width=1.0652]; "reaction to catalyst association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2402.1,221.5", - pos="e,2305.8,195.87 2768.5,260.67 2589,255.97 2311.7,245.99 2295.6,229 2288.5,221.43 2292,212.05 2298.8,203.46", + lp="2163.1,221.5", + pos="e,2030.7,196.02 2547.3,262.95 2369.9,260.6 2097.9,253.06 2056.6,229 2047.4,223.61 2040.4,214.35 2035.3,205.26", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2509.6,178", + pos="2251.6,178", width=1.5346]; "reaction to catalyst association" -> timepoint [color=blue, label=timepoint, - lp="2556.6,221.5", - pos="e,2509,196.43 2772.1,259.29 2666.9,254.54 2540.8,245.49 2521.6,229 2515.1,223.36 2511.8,214.85 2510.2,206.44", + lp="2325.6,221.5", + pos="e,2260.1,195.97 2546.8,263.52 2449.3,260.82 2333.9,252.46 2290.6,229 2280.4,223.43 2271.9,213.89 2265.5,204.63", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2621.6,178", + pos="2363.6,178", width=1.0652]; "reaction to catalyst association" -> "original subject" [color=blue, label="original subject", - lp="2654.6,221.5", - pos="e,2605.9,194.82 2779,257.26 2698.5,251.91 2611.2,242.98 2598.6,229 2592,221.56 2594.6,211.86 2600,202.98", + lp="2428.6,221.5", + pos="e,2361.9,196.27 2562.4,256.94 2479.2,251.38 2387,242.33 2372.6,229 2366.5,223.25 2363.6,214.83 2362.5,206.52", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2735.6,178", + pos="2488.6,178", width=1.5887]; "reaction to catalyst association" -> "original predicate" [color=blue, label="original predicate", - lp="2781.1,221.5", - pos="e,2721.8,195.8 2790.9,254.86 2757.7,249.7 2728.3,241.63 2717.6,229 2711.8,222.05 2713.1,213.06 2716.9,204.62", + lp="2559.1,221.5", + pos="e,2486.3,196.02 2574.5,254.63 2539.4,249.45 2507.7,241.43 2495.6,229 2489.8,222.99 2487.3,214.49 2486.6,206.2", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2849.6,178", + pos="2617.6,178", width=1.0652]; "reaction to catalyst association" -> "original object" [color=blue, label="original object", - lp="2905.1,221.5", - pos="e,2847.1,196.07 2874,247.64 2866,242.81 2858.7,236.69 2853.6,229 2849.2,222.32 2847.5,214 2847,206.08", + lp="2687.1,221.5", + pos="e,2620.6,196.35 2659.6,247.66 2650.8,242.72 2642.2,236.54 2635.6,229 2630,222.53 2626.1,214.18 2623.4,206.16", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2982.6,178", + pos="2750.6,178", width=2.1304]; "reaction to catalyst association" -> "subject category" [color=blue, label="subject category", - lp="3029.1,221.5", - pos="e,2977.2,196.22 2943.1,247.1 2949.3,241.81 2955.7,235.61 2960.6,229 2965.9,221.97 2970.2,213.49 2973.6,205.54", + lp="2808.1,221.5", + pos="e,2750.8,196.17 2727.1,247.12 2733.1,241.98 2738.8,235.86 2742.6,229 2746.5,222.15 2748.6,213.99 2749.8,206.26", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3153.6,178", + pos="2921.6,178", width=2.1304]; "reaction to catalyst association" -> "object category" [color=blue, label="object category", - lp="3172.1,221.5", - pos="e,3137.6,195.91 3023.4,251.53 3046.9,246.41 3071.2,239.18 3092.6,229 3106.2,222.54 3119.4,212.41 3130,202.94", + lp="2948.1,221.5", + pos="e,2909.1,195.95 2808.4,251.91 2830.1,246.76 2852.3,239.43 2871.6,229 2883.3,222.72 2894,212.86 2902.5,203.55", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3286.6,178", + pos="3054.6,178", width=1.0652]; "reaction to catalyst association" -> "subject closure" [color=blue, label="subject closure", - lp="3309.1,221.5", - pos="e,3273.6,195.42 3030.4,252.37 3118.2,243.03 3226.9,231.13 3231.6,229 3244.8,223.04 3257,212.72 3266.5,203", + lp="3082.1,221.5", + pos="e,3044,195.4 2812,252.26 2897.8,242.99 3003.1,231.26 3007.6,229 3019.3,223.13 3029.6,213.1 3037.6,203.55", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3386.6,178", + pos="3167.6,178", width=1.0652]; "reaction to catalyst association" -> "object closure" [color=blue, label="object closure", - lp="3429.6,221.5", - pos="e,3384.8,196.23 3028.7,252.15 3047.4,250.3 3066.6,248.51 3084.6,247 3116,244.38 3342.3,247.7 3367.6,229 3375,223.53 3379.6,214.8 \ -3382.3,206.14", + lp="3204.6,221.5", + pos="e,3163.2,195.9 2810.7,252.18 2829.4,250.33 2848.6,248.52 2866.6,247 2897,244.44 3115,245.48 3140.6,229 3149.2,223.52 3155.2,214.38 \ +3159.4,205.4", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3519.6,178", + pos="3300.6,178", width=2.1304]; "reaction to catalyst association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3588.1,221.5", - pos="e,3512.3,196.11 3027.4,252 3046.4,250.13 3066.1,248.37 3084.6,247 3128.9,243.72 3444.6,250.12 3483.6,229 3493.6,223.6 3501.5,214.09 \ -3507.3,204.8", + lp="3365.1,221.5", + pos="e,3291.3,196.16 2809.4,252.01 2828.4,250.14 2848.1,248.38 2866.6,247 2910.1,243.76 3219.5,248.32 3258.6,229 3269.5,223.62 3278.7,\ +213.98 3285.6,204.59", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3711.6,178", + pos="3493.6,178", width=2.1304]; "reaction to catalyst association" -> "object category closure" [color=blue, label="object category closure", - lp="3779.1,221.5", - pos="e,3705.6,196.11 3026.5,251.85 3045.8,249.98 3065.8,248.25 3084.6,247 3117.6,244.8 3650.9,245.31 3679.6,229 3689,223.66 3696.1,214.29 \ -3701.2,205.09", + lp="3557.1,221.5", + pos="e,3486,196.18 2808.5,251.85 2827.8,249.98 2847.8,248.25 2866.6,247 2899.4,244.82 3427.6,244.2 3456.6,229 3466.8,223.69 3474.9,214.19 \ +3480.9,204.89", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3901.6,178", + pos="3683.6,178", width=1.0652]; "reaction to catalyst association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3951.6,221.5", - pos="e,3894.6,196.18 3025.6,251.82 3045.2,249.93 3065.5,248.2 3084.6,247 3128,244.27 3828.3,249.51 3866.6,229 3876.4,223.75 3884.1,214.39 \ -3889.7,205.18", + lp="3730.6,221.5", + pos="e,3675.6,195.74 2807.6,251.82 2827.2,249.93 2847.5,248.2 2866.6,247 2909.8,244.28 3606,248.42 3644.6,229 3655.3,223.62 3664,213.8 \ +3670.4,204.27", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4060.6,178", + pos="3842.6,178", width=1.0652]; "reaction to catalyst association" -> "object namespace" [color=blue, label="object namespace", - lp="4104.6,221.5", - pos="e,4053.3,195.73 3025.6,251.76 3045.2,249.87 3065.5,248.17 3084.6,247 3136.7,243.82 3977.3,252.93 4023.6,229 4034,223.67 4042.1,213.99 \ -4048.2,204.55", + lp="3884.6,221.5", + pos="e,3834.3,195.77 2807.6,251.76 2827.2,249.87 2847.5,248.17 2866.6,247 2918.5,243.83 3756,251.98 3802.6,229 3813.5,223.66 3822.3,213.84 \ +3828.9,204.3", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4211.6,178", + pos="3993.6,178", width=1.0652]; "reaction to catalyst association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4264.6,221.5", - pos="e,4203.6,195.77 3025.2,251.76 3044.9,249.86 3065.4,248.15 3084.6,247 3145,243.4 4118.5,255.97 4172.6,229 4183.3,223.66 4192,213.84 \ -4198.4,204.3", + lp="4044.6,221.5", + pos="e,3985,195.79 2807.2,251.76 2826.9,249.86 2847.4,248.15 2866.6,247 2926.9,243.4 3898.3,255.26 3952.6,229 3963.6,223.69 3972.7,213.87 \ +3979.4,204.33", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4382.6,178", + pos="4164.6,178", width=1.0652]; "reaction to catalyst association" -> "object label closure" [color=blue, label="object label closure", - lp="4430.1,221.5", - pos="e,4374.3,195.79 3025.1,251.73 3044.9,249.83 3065.4,248.13 3084.6,247 3119.5,244.96 4311.2,244.36 4342.6,229 4353.5,223.69 4362.3,\ -213.87 4368.9,204.33", + lp="4212.1,221.5", + pos="e,4155.7,195.81 2807.1,251.73 2826.9,249.83 2847.4,248.13 2866.6,247 2901.5,244.96 4091.1,243.96 4122.6,229 4133.8,223.71 4143,213.9 \ +4150,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4526.6,178", + pos="4308.6,178", width=2.347]; "reaction to catalyst association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4586.1,221.5", - pos="e,4523.7,196.01 3025.1,251.7 3044.9,249.81 3065.4,248.11 3084.6,247 3124,244.73 4470.6,250.48 4503.6,229 4511.8,223.7 4517.1,214.72 \ -4520.5,205.82", + lp="4368.1,221.5", + pos="e,4305.7,196.01 2807.1,251.7 2826.9,249.81 2847.4,248.11 2866.6,247 2906,244.73 4252.6,250.48 4285.6,229 4293.8,223.7 4299.1,214.72 \ +4302.5,205.82", style=solid]; type [height=0.5, - pos="4660.6,178", + pos="4442.6,178", width=0.86659]; "reaction to catalyst association" -> type [color=blue, label=type, - lp="4682.6,221.5", - pos="e,4665.7,196.18 3024.7,251.73 3044.6,249.81 3065.2,248.11 3084.6,247 3106.5,245.75 4644.1,244.4 4659.6,229 4665.6,223.09 4667.2,\ -214.51 4666.9,206.12", + lp="4464.6,221.5", + pos="e,4447.7,196.18 2806.7,251.73 2826.6,249.81 2847.2,248.11 2866.6,247 2888.5,245.75 4426.1,244.4 4441.6,229 4447.6,223.09 4449.2,\ +214.51 4448.9,206.12", style=solid]; category [height=0.5, - pos="4761.6,178", + pos="4543.6,178", width=1.4263]; "reaction to catalyst association" -> category [color=blue, label=category, - lp="4760.1,221.5", - pos="e,4748,195.46 3024.7,251.72 3044.6,249.81 3065.2,248.11 3084.6,247 3129.5,244.44 4660.5,244.71 4702.6,229 4717.2,223.56 4730.7,212.8 \ -4741.1,202.65", + lp="4542.1,221.5", + pos="e,4530,195.46 2806.7,251.72 2826.6,249.81 2847.2,248.11 2866.6,247 2911.5,244.44 4442.5,244.71 4484.6,229 4499.2,223.56 4512.7,212.8 \ +4523.1,202.65", style=solid]; stoichiometry [color=blue, height=0.5, label=integer, - pos="4875.6,178", + pos="4657.6,178", width=1.2277]; "reaction to catalyst association" -> stoichiometry [color=blue, label=stoichiometry, - lp="4878.1,221.5", - pos="e,4857.4,194.55 3024.7,251.71 3044.6,249.8 3065.2,248.1 3084.6,247 3179.5,241.62 4704.4,255.69 4795.6,229 4815.1,223.31 4834.4,211.44 \ -4849.2,200.7", + lp="4660.1,221.5", + pos="e,4639.4,194.55 2806.7,251.71 2826.6,249.8 2847.2,248.1 2866.6,247 2961.5,241.62 4486.4,255.69 4577.6,229 4597.1,223.31 4616.4,211.44 \ +4631.2,200.7", style=solid]; "reaction direction" [color=blue, height=0.5, label=ReactionDirectionEnum, - pos="5059.6,178", + pos="4841.6,178", width=3.3761]; "reaction to catalyst association" -> "reaction direction" [color=blue, label="reaction direction", - lp="5046.1,221.5", - pos="e,5027.2,195.47 3024.7,251.7 3044.6,249.79 3065.2,248.09 3084.6,247 3187.1,241.24 4830.9,248.49 4931.6,229 4961.5,223.22 4993.4,\ -210.79 5017.9,199.76", + lp="4828.1,221.5", + pos="e,4809.2,195.47 2806.7,251.7 2826.6,249.79 2847.2,248.09 2866.6,247 2969.1,241.24 4612.9,248.49 4713.6,229 4743.5,223.22 4775.4,\ +210.79 4799.9,199.76", style=solid]; "reaction side" [color=blue, height=0.5, label=ReactionSideEnum, - pos="5297.6,178", + pos="5079.6,178", width=2.7442]; "reaction to catalyst association" -> "reaction side" [color=blue, label="reaction side", - lp="5232.1,221.5", - pos="e,5254.1,194.25 3024.7,251.68 3044.6,249.78 3065.2,248.08 3084.6,247 3309.7,234.43 4890.3,259.81 5113.6,229 5158.4,222.82 5207.8,\ -208.99 5244.2,197.44", + lp="5014.1,221.5", + pos="e,5036.1,194.25 2806.7,251.68 2826.6,249.78 2847.2,248.08 2866.6,247 3091.7,234.43 4672.3,259.81 4895.6,229 4940.4,222.82 4989.8,\ +208.99 5026.2,197.44", style=solid]; subject [height=0.5, - pos="5458.6,178", + pos="5240.6,178", width=1.2277]; "reaction to catalyst association" -> subject [color=blue, label=subject, - lp="5377.6,221.5", - pos="e,5427.4,190.79 3024.7,251.67 3044.6,249.77 3065.2,248.08 3084.6,247 3328.5,233.47 5040.6,261.91 5282.6,229 5330.1,222.54 5382.7,\ -206.34 5418,194.12", + lp="5159.6,221.5", + pos="e,5209.4,190.79 2806.7,251.67 2826.6,249.77 2847.2,248.08 2866.6,247 3110.5,233.47 4822.6,261.91 5064.6,229 5112.1,222.54 5164.7,\ +206.34 5200,194.12", style=solid]; object [height=0.5, - pos="5501.6,91", + pos="5283.6,91", width=1.0832]; "reaction to catalyst association" -> object [color=blue, label=object, - lp="5552.6,178", - pos="e,5515,108.09 3024.7,251.67 3044.6,249.76 3065.2,248.07 3084.6,247 3213.5,239.88 5280.2,249.24 5407.6,229 5455.5,221.39 5478.6,231.49 \ -5511.6,196 5532.9,173.16 5533.6,156.9 5524.6,127 5523.6,123.55 5522.1,120.13 5520.4,116.85", + lp="5334.6,178", + pos="e,5297,108.09 2806.7,251.67 2826.6,249.76 2847.2,248.07 2866.6,247 2995.5,239.88 5062.2,249.24 5189.6,229 5237.5,221.39 5260.6,231.49 \ +5293.6,196 5314.9,173.16 5315.6,156.9 5306.6,127 5305.6,123.55 5304.1,120.13 5302.4,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3131.6,265", + pos="2913.6,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3262.6,265", + pos="3044.6,265", width=2.0762]; subject -> object [label=relation, - lp="5496.6,134.5", - pos="e,5483.7,107.23 5459.7,159.55 5460.9,149.57 5463.4,137.07 5468.6,127 5470.9,122.68 5473.8,118.52 5477,114.66"]; + lp="5278.6,134.5", + pos="e,5265.7,107.23 5241.7,159.55 5242.9,149.57 5245.4,137.07 5250.6,127 5252.9,122.68 5255.8,118.52 5259,114.66"]; relation [height=0.5, - pos="5446.6,18", + pos="5228.6,18", width=1.2999]; - subject -> relation [pos="e,5447.9,36.188 5457.3,159.79 5455.3,132.48 5451.2,78.994 5448.7,46.38", + subject -> relation [pos="e,5229.9,36.188 5239.3,159.79 5237.3,132.48 5233.2,78.994 5230.7,46.38", style=dotted]; "reaction to participant association_subject" [color=blue, height=0.5, label="molecular entity", - pos="3442.6,265", + pos="3224.6,265", width=2.4192]; - object -> relation [pos="e,5459.4,35.54 5489.2,73.889 5482.2,64.939 5473.5,53.617 5465.7,43.584", + object -> relation [pos="e,5241.4,35.54 5271.2,73.889 5264.2,64.939 5255.5,53.617 5247.7,43.584", style=dotted]; "reaction to catalyst association_object" [color=blue, height=0.5, label="gene or gene product", - pos="3658.6,265", + pos="3440.6,265", width=3.0692]; } diff --git a/graphviz/reaction_to_catalyst_association.svg b/graphviz/reaction_to_catalyst_association.svg index 848c987da8..378408b513 100644 --- a/graphviz/reaction_to_catalyst_association.svg +++ b/graphviz/reaction_to_catalyst_association.svg @@ -4,16 +4,16 @@ - + %3 - + reaction to catalyst association - -reaction to catalyst association + +reaction to catalyst association @@ -24,9 +24,9 @@ reaction to catalyst association->reaction to participant association - - -is_a + + +is_a @@ -37,9 +37,9 @@ reaction to catalyst association->id - - -id + + +id @@ -50,9 +50,9 @@ reaction to catalyst association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ reaction to catalyst association->name - - -name + + +name @@ -76,9 +76,9 @@ reaction to catalyst association->description - - -description + + +description @@ -89,9 +89,9 @@ reaction to catalyst association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ reaction to catalyst association->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ reaction to catalyst association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ reaction to catalyst association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ reaction to catalyst association->publications - - -publications + + +publications @@ -154,383 +154,383 @@ reaction to catalyst association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string reaction to catalyst association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string reaction to catalyst association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string reaction to catalyst association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type reaction to catalyst association->timepoint - - -timepoint + + +timepoint original subject - -string + +string reaction to catalyst association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie reaction to catalyst association->original predicate - - -original predicate + + +original predicate original object - -string + +string reaction to catalyst association->original object - - -original object + + +original object subject category - -ontology class + +ontology class reaction to catalyst association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class reaction to catalyst association->object category - - -object category + + +object category subject closure - -string + +string reaction to catalyst association->subject closure - - -subject closure + + +subject closure object closure - -string + +string reaction to catalyst association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class reaction to catalyst association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class reaction to catalyst association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string reaction to catalyst association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string reaction to catalyst association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string reaction to catalyst association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string reaction to catalyst association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source reaction to catalyst association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type reaction to catalyst association->type - - -type + + +type category - -category + +category reaction to catalyst association->category - - -category + + +category stoichiometry - -integer + +integer reaction to catalyst association->stoichiometry - - -stoichiometry + + +stoichiometry reaction direction - -ReactionDirectionEnum + +ReactionDirectionEnum reaction to catalyst association->reaction direction - - -reaction direction + + +reaction direction reaction side - -ReactionSideEnum + +ReactionSideEnum reaction to catalyst association->reaction side - - -reaction side + + +reaction side subject - -subject + +subject reaction to catalyst association->subject - - -subject + + +subject object - -object + +object reaction to catalyst association->object - - -object + + +object association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + reaction to participant association_subject - -molecular entity + +molecular entity object->relation - - + + reaction to catalyst association_object - -gene or gene product + +gene or gene product diff --git a/graphviz/reaction_to_participant_association.gv b/graphviz/reaction_to_participant_association.gv index a719cc46fa..eff3d2945e 100644 --- a/graphviz/reaction_to_participant_association.gv +++ b/graphviz/reaction_to_participant_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,5567.7,283"]; + graph [bb="0,0,5349.7,283"]; node [label="\N"]; "reaction to participant association" [height=0.5, label="reaction to participant association", - pos="2905.5,265", + pos="2687.5,265", width=4.7121]; "chemical to chemical association" [height=0.5, pos="162.49,178", width=4.5135]; "reaction to participant association" -> "chemical to chemical association" [label=is_a, - lp="481.49,221.5", - pos="e,235.75,194.14 2736.7,263.03 2221.7,259.85 691.36,248.85 467.49,229 391.92,222.3 306.8,207.75 245.72,196.07"]; + lp="480.49,221.5", + pos="e,235.51,194.11 2517.8,264.56 2070.1,265.52 863.91,264.62 466.49,229 391.17,222.25 306.32,207.71 245.44,196.03"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "reaction to participant association" -> id [color=blue, label=id, - lp="598.49,221.5", - pos="e,410.47,190 2736.5,263.26 2239.2,260.82 802.31,251.87 591.49,229 518.44,221.08 500.29,215.65 429.49,196 426.38,195.14 423.18,194.17 \ -419.98,193.16", + lp="596.49,221.5", + pos="e,410.47,189.98 2518.8,263 2054.3,259.98 778.45,249.88 589.49,229 517.32,221.03 499.43,215.5 429.49,196 426.38,195.13 423.18,194.17 \ +419.98,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "reaction to participant association" -> iri [color=blue, label=iri, - lp="715.49,221.5", - pos="e,515.39,190.23 2736.5,263 2256.6,259.92 906.67,249.54 707.49,229 630.06,221.02 610.91,215.26 535.49,196 532.11,195.14 528.63,194.18 \ -525.14,193.17", + lp="709.49,221.5", + pos="e,515.39,190.2 2519,262.76 2072.2,259.22 879.25,248.08 701.49,229 626.69,220.97 608.31,214.85 535.49,196 532.11,195.13 528.63,194.16 \ +525.15,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "reaction to participant association" -> name [color=blue, label=name, - lp="826.49,221.5", - pos="e,640.29,191.28 2736.2,263.28 2271.1,261.01 995.15,252.68 806.49,229 752.09,222.17 691.23,206.24 650.06,194.18", + lp="817.49,221.5", + pos="e,639.28,191.44 2518.5,263.09 2086.7,260.45 964.99,251.51 797.49,229 745.83,222.06 688.19,206.36 648.86,194.39", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "reaction to participant association" -> description [color=blue, label=description, - lp="953.99,221.5", - pos="e,788.74,193.79 2735.9,263.75 2287.2,262.71 1090.5,257.29 913.49,229 873.71,222.64 830.17,208.8 798.25,197.28", + lp="939.99,221.5", + pos="e,785.98,194.02 2518.1,263.63 2102.7,262.3 1055.8,256.27 899.49,229 863.48,222.72 824.37,209.2 795.4,197.79", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "reaction to participant association" -> "has attribute" [color=blue, label="has attribute", - lp="1109.5,221.5", - pos="e,929.56,191.9 2736.4,263.42 2312.2,261.6 1224.8,254.48 1062.5,229 1019.6,222.27 972.44,207.28 939.35,195.45", + lp="1087.5,221.5", + pos="e,926.91,192.7 2518.3,263.4 2127.1,261.57 1182.7,254.55 1040.5,229 1004.3,222.49 964.88,208.29 936.48,196.69", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "reaction to participant association" -> predicate [color=blue, label=predicate, - lp="1268.5,221.5", - pos="e,1086.9,193.25 2736.8,262.73 2342,259.43 1380.1,249.38 1234.5,229 1187,222.36 1134.5,207.95 1096.7,196.3", + lp="1231.5,221.5", + pos="e,1080.5,194.1 2519,262.81 2156.4,259.85 1324.5,250.76 1197.5,229 1160.3,222.63 1119.8,209.09 1089.9,197.71", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "reaction to participant association" -> negated [color=blue, label=negated, - lp="1410.5,221.5", - pos="e,1221.3,190.46 2735.6,264.59 2394.9,265.04 1638.6,262.1 1381.5,229 1328.9,222.23 1270.2,205.81 1231.3,193.62", + lp="1350.5,221.5", + pos="e,1215.4,192.55 2519,262.8 2179.5,259.93 1435.9,251.17 1321.5,229 1287.6,222.44 1251,208.27 1224.7,196.69", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "reaction to participant association" -> qualifiers [color=blue, label=qualifiers, - lp="1549,221.5", - pos="e,1370.2,193.2 2735.6,264.73 2418.1,265.25 1745.9,262.23 1515.5,229 1468.8,222.26 1417,207.87 1379.8,196.25", + lp="1454,221.5", + pos="e,1351.4,195.43 2518.1,263.71 2197.1,262.52 1523.5,256.7 1420.5,229 1399,223.21 1376.9,211.5 1359.9,200.86", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "reaction to participant association" -> publications [color=blue, label=publications, - lp="1694.5,221.5", - pos="e,1521.2,192.85 2735.8,264.85 2442.9,265.38 1854.1,262.09 1650.5,229 1609.1,222.28 1563.6,207.95 1530.9,196.35", + lp="1545.5,221.5", + pos="e,1486.1,196.25 2518,264.12 2199.8,263.64 1541.3,259 1501.5,229 1494.3,223.56 1490.2,214.83 1488,206.18", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,294 +110,295 @@ digraph { width=2.0943]; "reaction to participant association" -> "has evidence" [color=blue, label="has evidence", - lp="1853,221.5", - pos="e,1679.5,193.63 2736,264.02 2473.4,263.13 1980.1,257.55 1806.5,229 1766.1,222.35 1721.7,208.52 1689.2,197.09", + lp="1644,221.5", + pos="e,1613.4,194.88 2517.9,264.66 2219.4,264.97 1628.9,261.45 1597.5,229 1588.9,220.11 1595.2,209.91 1605.4,201.06", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1843.5,178", - width=3.015]; + label=string, + pos="1773.5,178", + width=1.0652]; "reaction to participant association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2008,221.5", - pos="e,1869,195.61 2738.5,261.78 2483.3,257.8 2018,248.04 1943.5,229 1920.4,223.1 1896.4,211.34 1877.7,200.71", + lp="1762,221.5", + pos="e,1743,189.23 2518,264.05 2242.5,263.29 1725.5,257.97 1697.5,229 1692.9,224.2 1693.9,219.61 1697.5,214 1702,207 1717.7,199.25 1733.6,\ +192.84", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2078.5,178", - width=3.015]; + label=string, + pos="1868.5,178", + width=1.0652]; "reaction to participant association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2179.5,221.5", - pos="e,2075.5,196.33 2737.6,262.34 2504.4,259.25 2108,250.81 2084.5,229 2078.4,223.32 2076,214.91 2075.4,206.59", + lp="1928.5,221.5", + pos="e,1847.9,193.24 2518.5,263 2276.3,260.73 1856.8,253.29 1833.5,229 1825.1,220.29 1831.1,209.43 1840.4,200.05", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2313.5,178", - width=3.015]; + label=string, + pos="2010.5,178", + width=1.0652]; "reaction to participant association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2388,221.5", - pos="e,2291.7,195.87 2741.3,260.33 2561.8,255.49 2297.2,245.58 2281.5,229 2274.3,221.43 2277.8,212.05 2284.6,203.46", + lp="2149,221.5", + pos="e,2016.6,196.02 2518.9,262.75 2341.6,260.19 2082.7,252.42 2042.5,229 2033.2,223.61 2026.2,214.35 2021.2,205.26", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2495.5,178", + pos="2237.5,178", width=1.5346]; "reaction to participant association" -> timepoint [color=blue, label=timepoint, - lp="2542.5,221.5", - pos="e,2494.9,196.43 2746.3,258.74 2643.6,253.87 2525.9,244.88 2507.5,229 2500.9,223.36 2497.6,214.85 2496,206.44", + lp="2311.5,221.5", + pos="e,2245.9,195.97 2518.7,263.1 2424.4,259.99 2317.7,251.35 2276.5,229 2266.2,223.43 2257.8,213.89 2251.4,204.63", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2607.5,178", + pos="2349.5,178", width=1.0652]; "reaction to participant association" -> "original subject" [color=blue, label="original subject", - lp="2640.5,221.5", - pos="e,2591.7,194.82 2755.3,256.61 2677.7,251.21 2596.5,242.43 2584.5,229 2577.8,221.56 2580.4,211.86 2585.9,202.98", + lp="2414.5,221.5", + pos="e,2347.8,196.27 2538.6,256.28 2458.1,250.68 2372.3,241.81 2358.5,229 2352.3,223.25 2349.5,214.83 2348.4,206.52", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2721.5,178", + pos="2474.5,178", width=1.5887]; "reaction to participant association" -> "original predicate" [color=blue, label="original predicate", - lp="2767,221.5", - pos="e,2707.7,195.8 2771.2,253.96 2740.3,248.77 2713.5,240.91 2703.5,229 2697.6,222.05 2698.9,213.06 2702.8,204.62", + lp="2545,221.5", + pos="e,2472.2,196.02 2554.6,253.75 2521.9,248.56 2492.9,240.74 2481.5,229 2475.6,222.99 2473.2,214.49 2472.4,206.2", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2835.5,178", + pos="2603.5,178", width=1.0652]; "reaction to participant association" -> "original object" [color=blue, label="original object", - lp="2891,221.5", - pos="e,2832.9,196.07 2859.8,247.64 2851.9,242.81 2844.5,236.69 2839.5,229 2835.1,222.32 2833.3,214 2832.9,206.08", + lp="2673,221.5", + pos="e,2606.4,196.35 2645.1,247.47 2636.4,242.56 2627.9,236.45 2621.5,229 2615.9,222.53 2612,214.18 2609.3,206.16", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2968.5,178", + pos="2736.5,178", width=2.1304]; "reaction to participant association" -> "subject category" [color=blue, label="subject category", - lp="3015,221.5", - pos="e,2963.1,196.22 2928.9,247.1 2935.2,241.81 2941.6,235.61 2946.5,229 2951.7,221.97 2956,213.49 2959.4,205.54", + lp="2794,221.5", + pos="e,2736.6,196.17 2712.9,247.12 2718.9,241.98 2724.6,235.86 2728.5,229 2732.3,222.15 2734.5,213.99 2735.6,206.26", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3139.5,178", + pos="2907.5,178", width=2.1304]; "reaction to participant association" -> "object category" [color=blue, label="object category", - lp="3158,221.5", - pos="e,3123.4,195.91 3012,250.93 3034.6,245.84 3057.9,238.79 3078.5,229 3092.1,222.54 3105.3,212.41 3115.9,202.94", + lp="2934,221.5", + pos="e,2894.9,195.95 2797.3,251.16 2818.1,246.05 2839,238.93 2857.5,229 2869.1,222.72 2879.8,212.86 2888.3,203.55", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3272.5,178", + pos="3040.5,178", width=1.0652]; "reaction to participant association" -> "subject closure" [color=blue, label="subject closure", - lp="3295,221.5", - pos="e,3259.4,195.42 3025.5,252.26 3109.6,243.76 3208.5,233.07 3217.5,229 3230.7,223.04 3242.8,212.72 3252.4,203", + lp="3068,221.5", + pos="e,3029.8,195.4 2807.4,252.2 2889.5,243.81 2984.9,233.31 2993.5,229 3005.2,223.13 3015.5,213.1 3023.5,203.55", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3372.5,178", + pos="3153.5,178", width=1.0652]; "reaction to participant association" -> "object closure" [color=blue, label="object closure", - lp="3415.5,221.5", - pos="e,3370.7,196.22 3024.8,252.2 3044.7,250.36 3065.2,248.56 3084.5,247 3114.3,244.58 3329.4,246.82 3353.5,229 3360.9,223.52 3365.4,\ -214.78 3368.2,206.13", + lp="3190.5,221.5", + pos="e,3149,195.89 2807.3,252.19 2827.1,250.37 2847.4,248.57 2866.5,247 2895.3,244.63 3102.1,244.68 3126.5,229 3135,223.51 3141,214.36 \ +3145.2,205.38", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3505.5,178", + pos="3286.5,178", width=2.1304]; "reaction to participant association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3574,221.5", - pos="e,3498.1,196.1 3023.4,251.99 3043.7,250.15 3064.7,248.4 3084.5,247 3127.2,243.97 3431.8,249.41 3469.5,229 3479.5,223.59 3487.4,214.08 \ -3493.2,204.79", + lp="3351,221.5", + pos="e,3277.2,196.16 2805.4,252.01 2825.7,250.16 2846.7,248.41 2866.5,247 2908.4,244.01 3206.8,247.66 3244.5,229 3255.4,223.61 3264.5,\ +213.96 3271.4,204.58", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3697.5,178", + pos="3479.5,178", width=2.1304]; "reaction to participant association" -> "object category closure" [color=blue, label="object category closure", - lp="3765,221.5", - pos="e,3691.5,196.11 3021.9,251.86 3042.7,250 3064.2,248.27 3084.5,247 3116.7,244.97 3637.4,244.94 3665.5,229 3674.9,223.66 3682,214.29 \ -3687,205.09", + lp="3543,221.5", + pos="e,3471.8,196.17 2803.9,251.86 2824.7,250 2846.2,248.28 2866.5,247 2898.4,244.99 3414.1,243.85 3442.5,229 3452.6,223.68 3460.7,214.19 \ +3466.7,204.89", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3887.5,178", + pos="3669.5,178", width=1.0652]; "reaction to participant association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3937.5,221.5", - pos="e,3880.5,196.18 3021.4,251.77 3042.4,249.91 3064.1,248.21 3084.5,247 3127.1,244.48 3814.9,249.15 3852.5,229 3862.3,223.75 3869.9,\ -214.39 3875.6,205.18", + lp="3716.5,221.5", + pos="e,3661.5,195.74 2803.4,251.78 2824.4,249.91 2846.1,248.21 2866.5,247 2908.9,244.49 3592.6,248.07 3630.5,229 3641.2,223.62 3649.8,\ +213.79 3656.2,204.27", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4046.5,178", + pos="3828.5,178", width=1.0652]; "reaction to participant association" -> "object namespace" [color=blue, label="object namespace", - lp="4090.5,221.5", - pos="e,4039.1,195.73 3020.9,251.75 3042.1,249.87 3063.9,248.18 3084.5,247 3135.8,244.07 3963.8,252.58 4009.5,229 4019.8,223.67 4028,213.99 \ -4034,204.55", + lp="3870.5,221.5", + pos="e,3820.2,195.76 2802.9,251.75 2824.1,249.88 2845.9,248.18 2866.5,247 2917.6,244.08 3742.5,251.64 3788.5,229 3799.3,223.66 3808.2,\ +213.84 3814.8,204.3", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4197.5,178", + pos="3979.5,178", width=1.0652]; "reaction to participant association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4250.5,221.5", - pos="e,4189.5,195.76 3020.5,251.75 3041.7,249.86 3063.8,248.16 3084.5,247 3144.1,243.68 4105.1,255.63 4158.5,229 4169.2,223.66 4177.8,\ -213.84 4184.2,204.3", + lp="4030.5,221.5", + pos="e,3970.9,195.79 2802.5,251.75 2823.7,249.86 2845.8,248.16 2866.5,247 2926,243.68 3884.9,254.93 3938.5,229 3949.5,223.69 3958.5,213.87 \ +3965.3,204.33", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4368.5,178", + pos="4150.5,178", width=1.0652]; "reaction to participant association" -> "object label closure" [color=blue, label="object label closure", - lp="4416,221.5", - pos="e,4360.2,195.79 3020.5,251.71 3041.7,249.82 3063.8,248.13 3084.5,247 3119,245.11 4297.4,244.2 4328.5,229 4339.3,223.69 4348.2,213.87 \ -4354.8,204.33", + lp="4198,221.5", + pos="e,4141.6,195.81 2802.5,251.71 2823.7,249.82 2845.8,248.13 2866.5,247 2900.9,245.12 4077.3,243.8 4108.5,229 4119.6,223.71 4128.9,\ +213.9 4135.8,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4512.5,178", + pos="4294.5,178", width=2.347]; "reaction to participant association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4572,221.5", - pos="e,4509.5,196.01 3020.5,251.68 3041.7,249.8 3063.8,248.12 3084.5,247 3123.5,244.9 4456.8,250.27 4489.5,229 4497.6,223.7 4502.9,214.72 \ -4506.4,205.82", + lp="4354,221.5", + pos="e,4291.5,196.01 2802.5,251.68 2823.7,249.8 2845.8,248.12 2866.5,247 2905.5,244.9 4238.8,250.27 4271.5,229 4279.6,223.7 4284.9,214.72 \ +4288.4,205.82", style=solid]; type [height=0.5, - pos="4646.5,178", + pos="4428.5,178", width=0.86659]; "reaction to participant association" -> type [color=blue, label=type, - lp="4668.5,221.5", - pos="e,4651.6,196.18 3020,251.7 3041.4,249.8 3063.6,248.11 3084.5,247 3106.1,245.85 4630.1,244.27 4645.5,229 4651.4,223.09 4653,214.51 \ -4652.7,206.12", + lp="4450.5,221.5", + pos="e,4433.6,196.18 2802,251.7 2823.4,249.8 2845.6,248.11 2866.5,247 2888.1,245.85 4412.1,244.27 4427.5,229 4433.4,223.09 4435,214.51 \ +4434.7,206.12", style=solid]; category [height=0.5, - pos="4747.5,178", + pos="4529.5,178", width=1.4263]; "reaction to participant association" -> category [color=blue, label=category, - lp="4746,221.5", - pos="e,4733.9,195.46 3020,251.69 3041.4,249.8 3063.6,248.11 3084.5,247 3129,244.64 4646.7,244.58 4688.5,229 4703.1,223.56 4716.5,212.8 \ -4726.9,202.65", + lp="4528,221.5", + pos="e,4515.9,195.46 2802,251.69 2823.4,249.8 2845.6,248.11 2866.5,247 2911,244.64 4428.7,244.58 4470.5,229 4485.1,223.56 4498.5,212.8 \ +4508.9,202.65", style=solid]; object [height=0.5, - pos="5452.5,91", + pos="5234.5,91", width=1.0832]; "reaction to participant association" -> object [color=blue, label=object, - lp="4865.5,178", - pos="e,5413.6,92.765 3020,251.68 3041.4,249.79 3063.6,248.1 3084.5,247 3131.6,244.52 4738.5,248.42 4781.5,229 4819.1,212.01 4806.8,178.85 \ -4843.5,160 4941,109.84 5276.6,96.366 5403.4,93.024", + lp="4647.5,178", + pos="e,5195.6,92.765 2802,251.68 2823.4,249.79 2845.6,248.1 2866.5,247 2913.6,244.52 4520.5,248.42 4563.5,229 4601.1,212.01 4588.8,178.85 \ +4625.5,160 4723,109.84 5058.6,96.366 5185.4,93.024", style=solid]; stoichiometry [color=blue, height=0.5, label=integer, - pos="4940.5,178", + pos="4722.5,178", width=1.2277]; "reaction to participant association" -> stoichiometry [color=blue, label=stoichiometry, - lp="4936,221.5", - pos="e,4919.8,194.09 3020,251.68 3041.4,249.78 3063.6,248.1 3084.5,247 3182.4,241.86 4753.6,253.63 4848.5,229 4871,223.16 4893.9,210.7 \ -4911.3,199.68", + lp="4718,221.5", + pos="e,4701.8,194.09 2802,251.68 2823.4,249.78 2845.6,248.1 2866.5,247 2964.4,241.86 4535.6,253.63 4630.5,229 4653,223.16 4675.9,210.7 \ +4693.3,199.68", style=solid]; "reaction direction" [color=blue, height=0.5, label=ReactionDirectionEnum, - pos="5124.5,178", + pos="4906.5,178", width=3.3761]; "reaction to participant association" -> "reaction direction" [color=blue, label="reaction direction", - lp="5107,221.5", - pos="e,5090.5,195.35 3020,251.66 3041.4,249.77 3063.6,248.09 3084.5,247 3190.2,241.49 4885.4,248.16 4989.5,229 5021.2,223.16 5055.3,210.48 \ -5081.3,199.36", + lp="4889,221.5", + pos="e,4872.5,195.35 2802,251.66 2823.4,249.77 2845.6,248.09 2866.5,247 2972.2,241.49 4667.4,248.16 4771.5,229 4803.2,223.16 4837.3,210.48 \ +4863.3,199.36", style=solid]; "reaction side" [color=blue, height=0.5, label=ReactionSideEnum, - pos="5362.5,178", + pos="5144.5,178", width=2.7442]; "reaction to participant association" -> "reaction side" [color=blue, label="reaction side", - lp="5294,221.5", - pos="e,5318.3,194.13 3020,251.65 3041.4,249.76 3063.6,248.08 3084.5,247 3316.4,235.01 4944.3,260.09 5174.5,229 5220.6,222.77 5271.5,208.78 \ -5308.7,197.18", + lp="5076,221.5", + pos="e,5100.3,194.13 2802,251.65 2823.4,249.76 2845.6,248.08 2866.5,247 3098.4,235.01 4726.3,260.09 4956.5,229 5002.6,222.77 5053.5,208.78 \ +5090.7,197.18", style=solid]; subject [height=0.5, - pos="5523.5,178", + pos="5305.5,178", width=1.2277]; "reaction to participant association" -> subject [color=blue, label=subject, - lp="5439.5,221.5", - pos="e,5492,190.69 3020,251.64 3041.4,249.75 3063.6,248.07 3084.5,247 3335.3,234.12 5095.6,262.07 5344.5,229 5392.9,222.57 5446.6,206.28 \ -5482.4,194.03", + lp="5221.5,221.5", + pos="e,5274,190.69 2802,251.64 2823.4,249.75 2845.6,248.07 2866.5,247 3117.3,234.12 4877.6,262.07 5126.5,229 5174.9,222.57 5228.6,206.28 \ +5264.4,194.03", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3131.5,265", + pos="2913.5,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3262.5,265", + pos="3044.5,265", width=2.0762]; relation [height=0.5, - pos="5487.5,18", + pos="5269.5,18", width=1.2999]; - object -> relation [pos="e,5479,36.198 5460.8,73.174 5464.9,64.896 5469.9,54.723 5474.5,45.438", + object -> relation [pos="e,5261,36.198 5242.8,73.174 5246.9,64.896 5251.9,54.723 5256.5,45.438", style=dotted]; "chemical to chemical association_object" [color=blue, height=0.5, label="chemical entity", - pos="3437.5,265", + pos="3219.5,265", width=2.2748]; subject -> object [label=relation, - lp="5481.5,134.5", - pos="e,5448.7,109.01 5487.1,167.42 5474.3,162.12 5461.1,154.06 5453.5,142 5449.2,135.26 5447.9,126.93 5447.9,119.01"]; - subject -> relation [pos="e,5491.7,36.005 5519.8,160.05 5515.4,139.44 5507.6,103.63 5500.5,73 5498.4,64.183 5496.2,54.574 5494.1,45.938", + lp="5263.5,134.5", + pos="e,5230.7,109.01 5269.1,167.42 5256.3,162.12 5243.1,154.06 5235.5,142 5231.2,135.26 5229.9,126.93 5229.9,119.01"]; + subject -> relation [pos="e,5273.7,36.005 5301.8,160.05 5297.4,139.44 5289.6,103.63 5282.5,73 5280.4,64.183 5278.2,54.574 5276.1,45.938", style=dotted]; "reaction to participant association_subject" [color=blue, height=0.5, label="molecular entity", - pos="3624.5,265", + pos="3406.5,265", width=2.4192]; } diff --git a/graphviz/reaction_to_participant_association.svg b/graphviz/reaction_to_participant_association.svg index eb33d0efc8..965e06211e 100644 --- a/graphviz/reaction_to_participant_association.svg +++ b/graphviz/reaction_to_participant_association.svg @@ -4,16 +4,16 @@ - + %3 - + reaction to participant association - -reaction to participant association + +reaction to participant association @@ -24,9 +24,9 @@ reaction to participant association->chemical to chemical association - - -is_a + + +is_a @@ -37,9 +37,9 @@ reaction to participant association->id - - -id + + +id @@ -50,9 +50,9 @@ reaction to participant association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ reaction to participant association->name - - -name + + +name @@ -76,9 +76,9 @@ reaction to participant association->description - - -description + + +description @@ -89,9 +89,9 @@ reaction to participant association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ reaction to participant association->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ reaction to participant association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ reaction to participant association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ reaction to participant association->publications - - -publications + + +publications @@ -154,383 +154,383 @@ reaction to participant association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string reaction to participant association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string reaction to participant association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string reaction to participant association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type reaction to participant association->timepoint - - -timepoint + + +timepoint original subject - -string + +string reaction to participant association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie reaction to participant association->original predicate - - -original predicate + + +original predicate original object - -string + +string reaction to participant association->original object - - -original object + + +original object subject category - -ontology class + +ontology class reaction to participant association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class reaction to participant association->object category - - -object category + + +object category subject closure - -string + +string reaction to participant association->subject closure - - -subject closure + + +subject closure object closure - -string + +string reaction to participant association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class reaction to participant association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class reaction to participant association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string reaction to participant association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string reaction to participant association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string reaction to participant association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string reaction to participant association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source reaction to participant association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type reaction to participant association->type - - -type + + +type category - -category + +category reaction to participant association->category - - -category + + +category object - -object + +object reaction to participant association->object - - -object + + +object stoichiometry - -integer + +integer reaction to participant association->stoichiometry - - -stoichiometry + + +stoichiometry reaction direction - -ReactionDirectionEnum + +ReactionDirectionEnum reaction to participant association->reaction direction - - -reaction direction + + +reaction direction reaction side - -ReactionSideEnum + +ReactionSideEnum reaction to participant association->reaction side - - -reaction side + + +reaction side subject - -subject + +subject reaction to participant association->subject - - -subject + + +subject association_type - -string + +string association_category - -category type + +category type relation - -relation + +relation object->relation - - + + chemical to chemical association_object - -chemical entity + +chemical entity subject->object - - -relation + + +relation subject->relation - - + + reaction to participant association_subject - -molecular entity + +molecular entity diff --git a/graphviz/sequence_association.gv b/graphviz/sequence_association.gv index d8b505875f..a0157cc707 100644 --- a/graphviz/sequence_association.gv +++ b/graphviz/sequence_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4878.7,283"]; + graph [bb="0,0,4640.7,283"]; node [label="\N"]; "sequence association" [height=0.5, label="sequence association", - pos="2498.4,265", + pos="2260.4,265", width=3.015]; association [height=0.5, pos="62.394,178", width=1.7332]; "sequence association" -> association [label=is_a, lp="280.39,221.5", - pos="e,102.91,191.79 2389.9,263.73 1971.7,262.49 477.62,256.19 266.39,229 213.1,222.14 153.57,206.61 112.64,194.67"]; + pos="e,102.91,191.77 2152,263.51 1763.4,261.56 453.2,253.22 266.39,229 213.11,222.09 153.58,206.57 112.65,194.64"]; id [color=blue, height=0.5, label=string, @@ -19,7 +19,7 @@ digraph { "sequence association" -> id [color=blue, label=id, lp="396.39,221.5", - pos="e,210.38,189.98 2390.1,263.39 1987.2,260.95 588.45,250.98 389.39,229 317.23,221.03 299.34,215.5 229.39,196 226.29,195.13 223.09,\ + pos="e,210.38,189.98 2152.3,263.14 1780.1,260.03 564.05,248.48 389.39,229 317.23,220.95 299.34,215.5 229.39,196 226.29,195.13 223.09,\ 194.17 219.89,193.15", style=solid]; iri [color=blue, @@ -30,8 +30,8 @@ digraph { "sequence association" -> iri [color=blue, label=iri, lp="503.39,221.5", - pos="e,315.31,190.16 2390.2,263.29 2000.8,260.56 683.57,249.87 495.39,229 423.23,221 405.62,214.45 335.39,196 332.02,195.11 328.55,194.14 \ -325.06,193.12", + pos="e,315.31,190.16 2151.7,264.46 1819.2,265.44 818.63,265.23 495.39,229 423.24,220.91 405.62,214.45 335.39,196 332.02,195.11 328.55,\ +194.14 325.06,193.12", style=solid]; name [color=blue, height=0.5, @@ -41,7 +41,7 @@ digraph { "sequence association" -> name [color=blue, label=name, lp="607.39,221.5", - pos="e,438.25,191.77 2390,263.56 2011.9,261.81 765.43,254.17 587.39,229 538.92,222.15 485.05,206.78 447.81,194.87", + pos="e,438.25,191.75 2152.2,263.25 1806.3,260.66 741.22,250.95 587.39,229 538.93,222.08 485.06,206.72 447.82,194.84", style=solid]; description [color=blue, height=0.5, @@ -51,7 +51,7 @@ digraph { "sequence association" -> description [color=blue, label=description, lp="723.89,221.5", - pos="e,582.77,194.4 2390,264.07 2024.3,263.99 850.26,261.21 683.39,229 651.71,222.88 617.7,209.83 592.13,198.6", + pos="e,582.78,194.37 2151.9,263.72 1819.1,262.56 826.24,256.79 683.39,229 651.72,222.84 617.71,209.79 592.14,198.56", style=solid]; "has attribute" [color=blue, height=0.5, @@ -61,7 +61,7 @@ digraph { "sequence association" -> "has attribute" [color=blue, label="has attribute", lp="862.39,221.5", - pos="e,722.86,193.55 2389.7,264.11 2041.6,264.12 968.34,261.48 815.39,229 786.11,222.78 754.98,209.44 731.91,198.1", + pos="e,722.87,193.52 2151.9,263.7 1838.3,262.5 944.52,256.66 815.39,229 786.12,222.73 754.99,209.39 731.92,198.06", style=solid]; subject [color=blue, height=0.5, @@ -71,7 +71,7 @@ digraph { "sequence association" -> subject [color=blue, label=subject, lp="989.39,221.5", - pos="e,866.52,194.37 2389.9,263.73 2063.1,262.6 1101.8,256.91 963.39,229 932.94,222.86 900.37,209.9 875.84,198.71", + pos="e,866.53,194.33 2152.3,263.23 1861.7,260.87 1078.1,252.37 963.39,229 932.96,222.8 900.39,209.84 875.85,198.66", style=solid]; predicate [color=blue, height=0.5, @@ -81,7 +81,7 @@ digraph { "sequence association" -> predicate [color=blue, label=predicate, lp="1068.4,221.5", - pos="e,1008.4,196.14 2389.9,264.18 2060.9,264.37 1093.2,262.09 1034.4,229 1025,223.69 1017.9,214.33 1012.8,205.13", + pos="e,1008.4,196.12 2152.1,263.64 1861.3,262.33 1082.6,256.26 1034.4,229 1025,223.67 1017.9,214.3 1012.8,205.1", style=solid]; object [color=blue, height=0.5, @@ -91,8 +91,8 @@ digraph { "sequence association" -> object [color=blue, label=object, lp="1147.4,178", - pos="e,976.03,105.47 2390.9,262.4 2144.4,258.48 1543.9,247.3 1342.4,229 1245.2,220.17 1212.5,240.02 1125.4,196 1105.2,185.79 1108.1,172.77 \ -1089.4,160 1057.3,138.07 1017,120.64 985.5,108.92", + pos="e,976.03,105.47 2152.8,262.27 1936.6,258.43 1456.1,248.01 1292.4,229 1217.2,220.27 1192.1,231.62 1125.4,196 1105.4,185.35 1108.1,\ +172.77 1089.4,160 1057.3,138.07 1017,120.64 985.5,108.92", style=solid]; negated [color=blue, height=0.5, @@ -101,8 +101,8 @@ digraph { width=1.2999]; "sequence association" -> negated [color=blue, label=negated, - lp="1452.4,221.5", - pos="e,1260,190.37 2390.1,263.14 2155.7,260.86 1607.7,253.04 1423.4,229 1369.6,221.98 1309.4,205.49 1269.6,193.36", + lp="1371.4,221.5", + pos="e,1251,193.17 2151.5,264.8 1942.7,265.52 1493.3,262.91 1342.4,229 1313.5,222.52 1282.9,209.14 1260.2,197.85", style=solid]; qualifiers [color=blue, height=0.5, @@ -111,8 +111,8 @@ digraph { width=2.1304]; "sequence association" -> qualifiers [color=blue, label=qualifiers, - lp="1585.9,221.5", - pos="e,1408.3,193.18 2390.3,263.06 2177.4,260.71 1710.9,252.93 1552.4,229 1506.1,222.01 1454.8,207.72 1417.8,196.19", + lp="1461.9,221.5", + pos="e,1381.4,195.8 2152,263.21 1942,261.14 1494.3,253.84 1428.4,229 1413.6,223.43 1399.7,212.87 1388.8,202.88", style=solid]; publications [color=blue, height=0.5, @@ -121,8 +121,8 @@ digraph { width=1.7332]; "sequence association" -> publications [color=blue, label=publications, - lp="1723.4,221.5", - pos="e,1558,193.06 2390.4,262.96 2200.2,260.54 1812.7,252.76 1679.4,229 1640.7,222.11 1598.4,208.11 1567.6,196.67", + lp="1547.4,221.5", + pos="e,1508.5,195.6 2152.6,262.9 1948.8,260.28 1525.4,252.07 1503.4,229 1496.9,222.17 1498.6,212.96 1503.1,204.3", style=solid]; "has evidence" [color=blue, height=0.5, @@ -131,218 +131,220 @@ digraph { width=2.0943]; "sequence association" -> "has evidence" [color=blue, label="has evidence", - lp="1869.9,221.5", - pos="e,1713.8,194.06 2391.1,262.12 2228.8,258.64 1928.8,249.61 1823.4,229 1788.9,222.26 1751.4,209.05 1723.4,197.9", + lp="1645.9,221.5", + pos="e,1630.8,191.79 2153.2,262.13 1970.9,258.43 1618.1,248.74 1599.4,229 1586.5,215.4 1601.1,203.96 1621.2,195.48", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1881.4,178", - width=3.015]; + label=string, + pos="1811.4,178", + width=1.0652]; "sequence association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2009.9,221.5", - pos="e,1897.3,195.93 2389.8,264.68 2252.3,264.25 2023.9,258.82 1945.4,229 1930.4,223.32 1916.2,212.85 1904.9,202.96", + lp="1763.9,221.5", + pos="e,1782.1,189.74 2154.3,261.08 1995.9,256.21 1714.7,245.3 1699.4,229 1694.8,224.14 1695.4,219.31 1699.4,214 1717.2,190.45 1735.2,\ +204.94 1763.4,196 1766.3,195.07 1769.4,194.07 1772.4,193.05", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2116.4,178", - width=3.015]; + label=string, + pos="1906.4,178", + width=1.0652]; "sequence association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2176.4,221.5", - pos="e,2093.1,195.58 2391,262.38 2274.4,259.48 2102,251.41 2081.4,229 2074.1,221.04 2078.2,211.47 2085.7,202.85", + lp="1930.4,221.5", + pos="e,1877.1,189.79 2152.8,262.57 2034,259.84 1856.5,251.94 1835.4,229 1830.9,224.1 1831.9,219.66 1835.4,214 1839.4,207.54 1853.2,200.12 \ +1867.6,193.78", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2351.4,178", - width=3.015]; + label=string, + pos="2024.4,178", + width=1.0652]; "sequence association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2385.9,221.5", - pos="e,2303,194.15 2394,259.99 2345.3,255.69 2294.7,246.91 2279.4,229 2269.3,217.19 2278.7,206.86 2293.6,198.69", + lp="2144.9,221.5", + pos="e,2024.7,196.29 2158.9,258.53 2109.3,253.83 2056.5,245.11 2038.4,229 2031.9,223.21 2028.3,214.66 2026.3,206.26", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2533.4,178", + pos="2250.4,178", width=1.5346]; "sequence association" -> timepoint [color=blue, label=timepoint, - lp="2534.4,221.5", - pos="e,2513.1,194.83 2495.7,246.69 2494.9,236.76 2495.1,224.26 2499.4,214 2501.1,209.95 2503.5,206.11 2506.2,202.56", + lp="2291.4,221.5", + pos="e,2252.4,196.18 2258.4,246.8 2257,235.16 2255.2,219.55 2253.6,206.24", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2645.4,178", + pos="2362.4,178", width=1.0652]; "sequence association" -> "original subject" [color=blue, label="original subject", - lp="2647.4,221.5", - pos="e,2623.9,193.16 2533.2,247.93 2544.8,242.25 2557.8,235.62 2569.4,229 2570.6,228.29 2594.6,212.48 2615.4,198.82", + lp="2399.4,221.5", + pos="e,2354.5,195.95 2301.2,248.17 2311.5,243.03 2321.9,236.63 2330.4,229 2337.9,222.22 2344.4,213.26 2349.5,204.8", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2759.4,178", + pos="2488.4,178", width=1.5887]; "sequence association" -> "original predicate" [color=blue, label="original predicate", - lp="2789.9,221.5", - pos="e,2745.8,195.62 2578,252.67 2630.9,244.75 2692.8,234.63 2704.4,229 2717.2,222.76 2729.2,212.6 2738.7,203.05", + lp="2536.9,221.5", + pos="e,2482.8,196.02 2336.7,252.11 2390.6,243.46 2454.2,232.65 2459.4,229 2467.7,223.18 2474,214.13 2478.6,205.32", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2873.4,178", + pos="2622.4,178", width=1.0652]; "sequence association" -> "original object" [color=blue, label="original object", - lp="2917.9,221.5", - pos="e,2871.5,196.19 2575.1,252.18 2588.8,250.29 2603,248.47 2616.4,247 2642.8,244.11 2833.1,244.87 2854.4,229 2861.8,223.49 2866.3,214.74 \ -2869,206.09", + lp="2667.9,221.5", + pos="e,2620.9,196.15 2337.1,252.23 2350.8,250.33 2365,248.49 2378.4,247 2403.4,244.2 2584.4,244.29 2604.4,229 2611.7,223.44 2616,214.69 \ +2618.6,206.05", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3006.4,178", + pos="2755.4,178", width=2.1304]; "sequence association" -> "subject category" [color=blue, label="subject category", - lp="3048.9,221.5", - pos="e,3000,196.05 2574.1,252.03 2588.2,250.12 2602.7,248.33 2616.4,247 2655.9,243.16 2938.9,248.7 2973.4,229 2982.9,223.58 2990.1,214.2 \ -2995.4,205.01", + lp="2798.9,221.5", + pos="e,2749.3,196.03 2336.1,252.05 2350.2,250.13 2364.7,248.34 2378.4,247 2416.6,243.26 2690.2,248.3 2723.4,229 2732.7,223.62 2739.7,\ +214.37 2744.7,205.27", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3177.4,178", + pos="2926.4,178", width=2.1304]; "sequence association" -> "object category" [color=blue, label="object category", - lp="3195.9,221.5", - pos="e,3161.5,195.84 2573.5,251.96 2587.7,250.02 2602.5,248.25 2616.4,247 2671.3,242.06 3060.5,247.7 3112.4,229 3127.8,223.43 3142.6,\ -212.72 3154.1,202.64", + lp="2945.9,221.5", + pos="e,2910.8,195.83 2335.5,251.97 2349.7,250.03 2364.5,248.26 2378.4,247 2432,242.16 2811.8,247.46 2862.4,229 2877.5,223.47 2891.9,212.92 \ +2903.2,202.93", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3310.4,178", + pos="3059.4,178", width=1.0652]; "sequence association" -> "subject closure" [color=blue, label="subject closure", - lp="3333.9,221.5", - pos="e,3297.9,195.35 2573.2,251.91 2587.5,249.97 2602.4,248.2 2616.4,247 2687.2,240.93 3189.5,255.54 3255.4,229 3269.1,223.47 3281.6,\ -212.85 3291.2,202.81", + lp="3083.9,221.5", + pos="e,3047.2,195.34 2335.2,251.91 2349.5,249.97 2364.4,248.21 2378.4,247 2447.8,241.02 2940.9,255.36 3005.4,229 3018.8,223.51 3031,213.04 \ +3040.3,203.1", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3408.4,178", + pos="3167.4,178", width=1.0652]; "sequence association" -> "object closure" [color=blue, label="object closure", - lp="3450.4,221.5", - pos="e,3406.3,196.39 2572.8,251.9 2587.2,249.94 2602.3,248.18 2616.4,247 2659.1,243.43 3353.2,253.46 3388.4,229 3396.1,223.65 3400.8,\ -214.83 3403.7,206.06", + lp="3206.4,221.5", + pos="e,3163.7,196.01 2334.8,251.9 2349.2,249.95 2364.3,248.18 2378.4,247 2420.7,243.47 3106.5,251.74 3142.4,229 3150.8,223.65 3156.5,\ +214.54 3160.3,205.54", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3541.4,178", + pos="3300.4,178", width=2.1304]; "sequence association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3608.9,221.5", - pos="e,3533.8,196.22 2572.8,251.86 2587.2,249.91 2602.3,248.16 2616.4,247 2665.6,242.97 3460.6,251.65 3504.4,229 3514.6,223.74 3522.7,\ -214.25 3528.7,204.94", + lp="3365.9,221.5", + pos="e,3291.8,196.25 2334.8,251.86 2349.2,249.91 2364.3,248.16 2378.4,247 2427.2,243 3216.4,250.68 3260.4,229 3271.1,223.73 3279.8,214.11 \ +3286.4,204.7", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3731.4,178", + pos="3493.4,178", width=2.1304]; "sequence association" -> "object category closure" [color=blue, label="object category closure", - lp="3798.9,221.5", - pos="e,3725.7,196.15 2572.8,251.82 2587.2,249.87 2602.3,248.13 2616.4,247 2646.4,244.6 3674.2,243.86 3700.4,229 3709.6,223.76 3716.5,\ -214.54 3721.3,205.43", + lp="3557.9,221.5", + pos="e,3486.1,196.22 2334.8,251.82 2349.2,249.87 2364.3,248.13 2378.4,247 2438.2,242.22 3404.3,256.78 3457.4,229 3467.5,223.74 3475.4,\ +214.25 3481.2,204.95", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3921.4,178", + pos="3683.4,178", width=1.0652]; "sequence association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3971.4,221.5", - pos="e,3914.7,195.72 2572.5,251.83 2587,249.87 2602.2,248.12 2616.4,247 2651.6,244.23 3855.2,245.51 3886.4,229 3896.5,223.66 3904.3,213.98 \ -3909.9,204.54", + lp="3731.4,221.5", + pos="e,3675.7,195.76 2334.5,251.84 2349,249.87 2364.2,248.12 2378.4,247 2413.5,244.23 3614,244.86 3645.4,229 3655.9,223.71 3664.3,214.03 \ +3670.4,204.59", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4080.4,178", + pos="3842.4,178", width=1.0652]; "sequence association" -> "object namespace" [color=blue, label="object namespace", - lp="4124.4,221.5", - pos="e,4073,195.76 2572.5,251.82 2587,249.86 2602.2,248.11 2616.4,247 2655.9,243.92 4008.1,247.07 4043.4,229 4053.7,223.7 4061.9,214.03 \ -4067.9,204.59", + lp="3885.4,221.5", + pos="e,3834.4,195.78 2334.5,251.82 2349,249.86 2364.2,248.11 2378.4,247 2417.9,243.92 3767.9,246.59 3803.4,229 3814.1,223.68 3822.8,213.86 \ +3829.2,204.32", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4231.4,178", + pos="3993.4,178", width=1.0652]; "sequence association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4284.4,221.5", - pos="e,4223.4,195.79 2572.5,251.8 2587,249.85 2602.2,248.1 2616.4,247 2660,243.62 4153.2,248.43 4192.4,229 4203.1,223.69 4211.8,213.87 \ -4218.2,204.33", + lp="4046.4,221.5", + pos="e,3985.1,195.8 2334.5,251.8 2349,249.85 2364.2,248.1 2378.4,247 2422,243.62 3914.1,248.18 3953.4,229 3964.3,223.7 3973.1,213.89 \ +3979.7,204.35", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4402.4,178", + pos="4164.4,178", width=1.0652]; "sequence association" -> "object label closure" [color=blue, label="object label closure", - lp="4450.9,221.5", - pos="e,4394.1,195.8 2572.5,251.79 2587,249.83 2602.2,248.09 2616.4,247 2664.8,243.28 4318.8,250.24 4362.4,229 4373.3,223.71 4382.1,213.89 \ -4388.7,204.35", + lp="4212.9,221.5", + pos="e,4156.1,195.8 2334.5,251.79 2349,249.83 2364.2,248.09 2378.4,247 2426.8,243.28 4080.8,250.24 4124.4,229 4135.3,223.71 4144.1,213.89 \ +4150.7,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4564.4,178", + pos="4326.4,178", width=2.347]; "sequence association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4612.9,221.5", - pos="e,4555.8,196.3 2572.5,251.78 2587,249.82 2602.2,248.09 2616.4,247 2669.2,242.96 4476.7,252.19 4524.4,229 4535.1,223.79 4543.9,214.17 \ -4550.4,204.76", + lp="4374.9,221.5", + pos="e,4317.8,196.3 2334.5,251.78 2349,249.82 2364.2,248.09 2378.4,247 2431.2,242.96 4238.7,252.19 4286.4,229 4297.1,223.79 4305.9,214.17 \ +4312.4,204.76", style=solid]; type [height=0.5, - pos="4726.4,178", + pos="4488.4,178", width=0.86659]; "sequence association" -> type [color=blue, label=type, - lp="4721.4,221.5", - pos="e,4718.1,195.81 2572.5,251.77 2587,249.82 2602.2,248.08 2616.4,247 2673.7,242.64 4634.7,254.13 4686.4,229 4697.3,223.72 4706.1,213.9 \ -4712.7,204.36", + lp="4483.4,221.5", + pos="e,4480.1,195.81 2334.5,251.77 2349,249.82 2364.2,248.08 2378.4,247 2435.7,242.64 4396.7,254.13 4448.4,229 4459.3,223.72 4468.1,213.9 \ +4474.7,204.36", style=solid]; category [height=0.5, - pos="4827.4,178", + pos="4589.4,178", width=1.4263]; "sequence association" -> category [color=blue, label=category, - lp="4807.9,221.5", - pos="e,4807.2,194.82 2572.5,251.77 2587,249.81 2602.2,248.08 2616.4,247 2734.1,238.06 4627.5,260.21 4741.4,229 4762.1,223.34 4782.9,211.42 \ -4798.9,200.65", + lp="4569.9,221.5", + pos="e,4569.2,194.82 2334.5,251.77 2349,249.81 2364.2,248.08 2378.4,247 2496.1,238.06 4389.5,260.21 4503.4,229 4524.1,223.34 4544.9,211.42 \ +4560.9,200.65", style=solid]; subject -> object [label=relation, lp="919.39,134.5", @@ -357,11 +359,11 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="2663.4,265", + pos="2425.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2794.4,265", + pos="2556.4,265", width=2.0762]; } diff --git a/graphviz/sequence_association.svg b/graphviz/sequence_association.svg index e80f62661b..085a786a8f 100644 --- a/graphviz/sequence_association.svg +++ b/graphviz/sequence_association.svg @@ -4,16 +4,16 @@ - + %3 - + sequence association - -sequence association + +sequence association @@ -24,8 +24,8 @@ sequence association->association - - + + is_a @@ -37,7 +37,7 @@ sequence association->id - + id @@ -50,7 +50,7 @@ sequence association->iri - + iri @@ -63,8 +63,8 @@ sequence association->name - - + + name @@ -76,8 +76,8 @@ sequence association->description - - + + description @@ -89,8 +89,8 @@ sequence association->has attribute - - + + has attribute @@ -102,8 +102,8 @@ sequence association->subject - - + + subject @@ -115,8 +115,8 @@ sequence association->predicate - - + + predicate @@ -128,7 +128,7 @@ sequence association->object - + object @@ -141,9 +141,9 @@ sequence association->negated - - -negated + + +negated @@ -154,9 +154,9 @@ sequence association->qualifiers - - -qualifiers + + +qualifiers @@ -167,9 +167,9 @@ sequence association->publications - - -publications + + +publications @@ -180,269 +180,269 @@ sequence association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string sequence association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string sequence association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string sequence association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type sequence association->timepoint - - -timepoint + + +timepoint original subject - -string + +string sequence association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie sequence association->original predicate - - -original predicate + + +original predicate original object - -string + +string sequence association->original object - - -original object + + +original object subject category - -ontology class + +ontology class sequence association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class sequence association->object category - - -object category + + +object category subject closure - -string + +string sequence association->subject closure - - -subject closure + + +subject closure object closure - -string + +string sequence association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class sequence association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class sequence association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string sequence association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string sequence association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string sequence association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string sequence association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source sequence association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type sequence association->type - - -type + + +type category - -category + +category sequence association->category - - -category + + +category @@ -472,14 +472,14 @@ association_type - -string + +string association_category - -category type + +category type diff --git a/graphviz/sequence_feature_relationship.gv b/graphviz/sequence_feature_relationship.gv index a6f73fa988..9751941ccb 100644 --- a/graphviz/sequence_feature_relationship.gv +++ b/graphviz/sequence_feature_relationship.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4788.4,283"]; + graph [bb="0,0,4570.4,283"]; node [label="\N"]; "sequence feature relationship" [height=0.5, label="sequence feature relationship", - pos="2492.4,265", + pos="2274.4,265", width=4.1524]; association [height=0.5, pos="62.394,178", width=1.7332]; "sequence feature relationship" -> association [label=is_a, - lp="281.39,221.5", - pos="e,103.12,191.79 2343.2,263.59 1877.9,262.02 471.57,255.17 267.39,229 213.85,222.14 154.03,206.61 112.9,194.67"]; + lp="280.39,221.5", + pos="e,102.91,191.77 2125.4,263.32 1691.7,261.07 448.57,252.61 266.39,229 213.11,222.09 153.58,206.57 112.65,194.64"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "sequence feature relationship" -> id [color=blue, label=id, - lp="398.39,221.5", - pos="e,210.38,190 2343.4,263.11 1896,260.2 583.43,249.98 391.39,229 318.35,221.02 300.2,215.65 229.39,196 226.29,195.14 223.09,194.17 \ -219.89,193.16", + lp="396.39,221.5", + pos="e,210.38,189.98 2125.8,262.82 1710.9,259.31 559.57,247.96 389.39,229 317.23,220.96 299.34,215.5 229.39,196 226.29,195.13 223.09,\ +194.17 219.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "sequence feature relationship" -> iri [color=blue, label=iri, - lp="515.39,221.5", - pos="e,315.29,190.23 2343.7,262.85 1913.6,259.33 687.81,247.76 507.39,229 429.97,220.95 410.81,215.26 335.39,196 332.02,195.14 328.54,\ -194.18 325.05,193.17", + lp="509.39,221.5", + pos="e,315.3,190.2 2124.7,264.44 1756.4,264.98 813.98,262.89 501.39,229 426.61,220.89 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ +325.06,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "sequence feature relationship" -> name [color=blue, label=name, - lp="627.39,221.5", - pos="e,440.01,191.15 2343.8,263.06 1928.8,260.18 777.28,250.35 607.39,229 552.58,222.11 491.21,206.11 449.83,194.05", + lp="617.39,221.5", + pos="e,439.19,191.41 2125.9,262.83 1743.8,259.56 746.19,249.17 597.39,229 545.74,222 488.1,206.31 448.78,194.36", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "sequence feature relationship" -> description [color=blue, label=description, - lp="755.89,221.5", - pos="e,588.8,193.65 2343.3,263.42 1944.7,261.54 873.62,254.18 715.39,229 675.03,222.58 630.79,208.66 598.44,197.14", + lp="739.89,221.5", + pos="e,586.19,194.12 2125.5,263.26 1759.9,261.07 837.11,253.21 699.39,229 663.52,222.69 624.55,209.24 595.6,197.88", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "sequence feature relationship" -> "has attribute" [color=blue, label="has attribute", - lp="913.39,221.5", - pos="e,729.98,191.75 2343.6,263.04 1969.5,260.31 1009.7,251.21 866.39,229 822.26,222.16 773.51,207 739.58,195.15", + lp="887.39,221.5", + pos="e,726.83,192.67 2125.8,262.97 1784.4,260.24 964.06,251.41 840.39,229 804.17,222.43 764.8,208.24 736.39,196.65", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "sequence feature relationship" -> predicate [color=blue, label=predicate, - lp="1074.4,221.5", - pos="e,887.81,193.09 2342.8,264.67 2024.3,265.39 1288.2,263.15 1040.4,229 991.17,222.22 936.47,207.65 897.4,195.99", + lp="1031.4,221.5", + pos="e,880.43,194.06 2126.5,262.34 1813.9,258.49 1105.8,247.8 997.39,229 960.25,222.56 919.77,209.02 889.78,197.66", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "sequence feature relationship" -> negated [color=blue, label=negated, - lp="1220.4,221.5", - pos="e,1022.3,190.23 2343.2,263.57 2050.5,262.13 1410,255.9 1191.4,229 1135.6,222.13 1072.9,205.38 1032,193.16", + lp="1151.4,221.5", + pos="e,1015.6,192.51 2126.5,262.18 1837.6,258.22 1218.2,247.68 1122.4,229 1088.3,222.36 1051.5,208.2 1024.9,196.64", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "sequence feature relationship" -> qualifiers [color=blue, label=qualifiers, - lp="1356.9,221.5", - pos="e,1171.6,193.02 2343.3,263.64 2073.8,262.29 1515.8,256.2 1323.4,229 1274.6,222.11 1220.5,207.65 1181.6,196.05", + lp="1254.9,221.5", + pos="e,1151.6,195.39 2125.8,262.82 1856.1,260.11 1306.2,251.85 1221.4,229 1199.7,223.15 1177.4,211.43 1160.1,200.81", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "sequence feature relationship" -> publications [color=blue, label=publications, - lp="1499.4,221.5", - pos="e,1321.9,192.66 2343.2,263.59 2098.4,262.13 1621.7,255.82 1455.4,229 1412.5,222.09 1365.3,207.61 1331.5,196.01", + lp="1346.4,221.5", + pos="e,1286.4,196.26 2125.8,263.04 1861.6,260.73 1334.8,253.1 1302.4,229 1295.1,223.57 1290.9,214.84 1288.5,206.19", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,263 +110,264 @@ digraph { width=2.0943]; "sequence feature relationship" -> "has evidence" [color=blue, label="has evidence", - lp="1652.9,221.5", - pos="e,1479.4,193.55 2343.7,262.7 2129.3,260.04 1743.7,252.12 1606.4,229 1566,222.2 1521.6,208.38 1489.1,196.99", + lp="1444.9,221.5", + pos="e,1413.8,194.93 2125.1,263.35 1881.5,261.54 1423.1,254.72 1398.4,229 1390,220.25 1395.9,210.18 1405.7,201.37", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1643.4,178", - width=3.015]; + label=string, + pos="1573.4,178", + width=1.0652]; "sequence feature relationship" -> "knowledge source" [color=blue, label="knowledge source", - lp="1802.9,221.5", - pos="e,1667.9,195.78 2342.5,264.73 2155.9,264.3 1848.2,258.84 1738.4,229 1716.6,223.09 1694.2,211.61 1676.7,201.13", + lp="1562.9,221.5", + pos="e,1543.3,189.28 2126.3,262.52 1907.1,259.6 1519.7,251.3 1498.4,229 1493.8,224.18 1494.8,219.62 1498.4,214 1502.8,207.12 1518,199.47 \ +1533.6,193.08", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1878.4,178", - width=3.015]; + label=string, + pos="1668.4,178", + width=1.0652]; "sequence feature relationship" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1972.4,221.5", - pos="e,1872.6,196 2346.9,260.69 2170.1,255.94 1893.3,245.86 1877.4,229 1871.6,222.9 1870.4,214.27 1871,205.9", + lp="1729.4,221.5", + pos="e,1648.1,193.48 2128.5,261.03 1944.9,256.57 1651.2,246.7 1634.4,229 1626.3,220.46 1631.8,209.82 1640.6,200.55", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2113.4,178", - width=3.015]; + label=string, + pos="1810.4,178", + width=1.0652]; "sequence feature relationship" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2180.9,221.5", - pos="e,2087.6,195.53 2346,261.3 2233,257.65 2092.9,249.08 2074.4,229 2066.7,220.62 2071.6,210.86 2080.1,202.2", + lp="1949.9,221.5", + pos="e,1816.9,195.93 2134.1,258.7 2018,253.31 1868.2,243.66 1843.4,229 1834,223.44 1826.8,214.03 1821.5,204.86", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2295.4,178", + pos="2037.4,178", width=1.5346]; "sequence feature relationship" -> timepoint [color=blue, label=timepoint, - lp="2332.4,221.5", - pos="e,2291.1,196.26 2370.8,254.5 2337.7,249.32 2308.1,241.32 2297.4,229 2292,222.83 2290.3,214.43 2290.3,206.27", + lp="2112.4,221.5", + pos="e,2046.6,196.08 2169.7,252.12 2131.5,246.38 2093.6,238.62 2077.4,229 2067.4,223.06 2058.9,213.63 2052.3,204.55", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2407.4,178", + pos="2149.4,178", width=1.0652]; "sequence feature relationship" -> "original subject" [color=blue, label="original subject", - lp="2430.4,221.5", - pos="e,2387.4,193.75 2401.4,250.57 2390.9,245.4 2381.4,238.42 2374.4,229 2367.7,220.01 2372.5,209.73 2380.3,200.83", + lp="2214.4,221.5", + pos="e,2148.2,196.23 2188.7,250.18 2177.3,245.12 2166.7,238.27 2158.4,229 2152.9,222.8 2150.2,214.39 2149,206.23", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2521.4,178", + pos="2274.4,178", width=1.5887]; "sequence feature relationship" -> "original predicate" [color=blue, label="original predicate", - lp="2556.9,221.5", - pos="e,2504.6,195.4 2490.1,246.84 2489.4,236.95 2489.6,224.45 2493.4,214 2494.7,210.42 2496.5,206.94 2498.6,203.64", + lp="2337.9,221.5", + pos="e,2274.4,196.18 2274.4,246.8 2274.4,235.16 2274.4,219.55 2274.4,206.24", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2635.4,178", + pos="2403.4,178", width=1.0652]; "sequence feature relationship" -> "original object" [color=blue, label="original object", - lp="2681.9,221.5", - pos="e,2634.3,196.46 2585.2,250.84 2598.2,245.7 2610.5,238.65 2620.4,229 2626.5,223.04 2630.2,214.69 2632.3,206.52", + lp="2459.9,221.5", + pos="e,2407.8,195.99 2355.6,249.87 2376.9,244.45 2395.8,237.5 2402.4,229 2407.4,222.62 2408.9,214.26 2408.7,206.21", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2768.4,178", + pos="2536.4,178", width=2.1304]; "sequence feature relationship" -> "subject category" [color=blue, label="subject category", - lp="2811.9,221.5", - pos="e,2762.2,196.16 2601.8,252.66 2661.5,245.72 2725.6,236.71 2737.4,229 2746.2,223.28 2752.9,214.13 2757.8,205.22", + lp="2586.9,221.5", + pos="e,2533.7,196.01 2385.2,252.91 2443.3,246.2 2504.6,237.36 2515.4,229 2522.8,223.28 2527.6,214.49 2530.7,205.86", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2939.4,178", + pos="2707.4,178", width=2.1304]; "sequence feature relationship" -> "object category" [color=blue, label="object category", - lp="2956.9,221.5", - pos="e,2923.5,195.83 2598.4,252.27 2616.1,250.43 2634.3,248.6 2651.4,247 2701.1,242.35 2828.9,247.14 2875.4,229 2890.3,223.19 2904.6,\ -212.71 2915.8,202.84", + lp="2728.9,221.5", + pos="e,2693.3,196.06 2380.8,252.27 2398.4,250.43 2416.4,248.61 2433.4,247 2481.6,242.43 2605.9,247.91 2650.4,229 2663.9,223.26 2676.5,\ +213.03 2686.3,203.31", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3072.4,178", + pos="2840.4,178", width=1.0652]; "sequence feature relationship" -> "subject closure" [color=blue, label="subject closure", - lp="3093.9,221.5", - pos="e,3059.6,195.25 2596.2,252.03 2614.6,250.16 2633.5,248.39 2651.4,247 2691.9,243.84 2978.8,244.4 3016.4,229 3030.2,223.33 3042.9,\ -212.69 3052.7,202.69", + lp="2864.9,221.5", + pos="e,2828.7,195.23 2378.7,252.01 2396.9,250.15 2415.7,248.39 2433.4,247 2472.8,243.9 2752.1,244.68 2788.4,229 2801.5,223.35 2813.2,\ +212.87 2822.2,202.95", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3172.4,178", + pos="2953.4,178", width=1.0652]; "sequence feature relationship" -> "object closure" [color=blue, label="object closure", - lp="3214.4,221.5", - pos="e,3170.3,196.34 2595.4,251.92 2614,250.04 2633.3,248.29 2651.4,247 2679.2,245.02 3129.6,245.03 3152.4,229 3160.1,223.61 3164.8,214.77 \ -3167.7,206.01", + lp="2988.4,221.5", + pos="e,2948,196.05 2377.4,251.93 2396,250.05 2415.3,248.3 2433.4,247 2460.6,245.05 2899.9,242.85 2923.4,229 2932.5,223.65 2939.1,214.41 \ +2943.8,205.31", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3305.4,178", + pos="3086.4,178", width=2.1304]; "sequence feature relationship" -> "subject category closure" [color=blue, label="subject category closure", - lp="3372.9,221.5", - pos="e,3297.7,196.18 2594.9,251.86 2613.7,249.97 2633.1,248.24 2651.4,247 2685.6,244.68 3238,244.88 3268.4,229 3278.5,223.69 3286.6,214.2 \ -3292.6,204.9", + lp="3148.9,221.5", + pos="e,3076.5,196.25 2376.9,251.87 2395.7,249.98 2415.1,248.25 2433.4,247 2467.2,244.7 3011.8,243.4 3042.4,229 3053.7,223.67 3063.3,213.91 \ +3070.7,204.41", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3497.4,178", + pos="3279.4,178", width=2.1304]; "sequence feature relationship" -> "object category closure" [color=blue, label="object category closure", - lp="3563.9,221.5", - pos="e,3491.1,196.16 2594.5,251.8 2613.4,249.9 2633,248.19 2651.4,247 2696.5,244.1 3424.9,250.85 3464.4,229 3474,223.72 3481.2,214.36 \ -3486.5,205.15", + lp="3341.9,221.5", + pos="e,3271.1,196.23 2376.5,251.8 2395.4,249.91 2415,248.19 2433.4,247 2478.1,244.11 3200.3,249.12 3240.4,229 3250.8,223.76 3259.3,214.27 \ +3265.7,204.96", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3687.4,178", + pos="3469.4,178", width=1.0652]; "sequence feature relationship" -> "subject namespace" [color=blue, label="subject namespace", - lp="3736.4,221.5", - pos="e,3680.3,195.72 2594.1,251.78 2613.1,249.87 2632.8,248.16 2651.4,247 2706.9,243.54 3602.2,254.78 3651.4,229 3661.6,223.66 3669.6,\ -213.98 3675.4,204.54", + lp="3515.4,221.5", + pos="e,3461.1,195.77 2376.1,251.78 2395.1,249.87 2414.8,248.16 2433.4,247 2488.6,243.55 3379.7,253.42 3429.4,229 3440.2,223.67 3449.1,\ +213.85 3455.7,204.31", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3846.4,178", + pos="3628.4,178", width=1.0652]; "sequence feature relationship" -> "object namespace" [color=blue, label="object namespace", - lp="3890.4,221.5", - pos="e,3838.7,195.76 2594.1,251.74 2613.1,249.84 2632.8,248.13 2651.4,247 2683.5,245.04 3779.7,243.51 3808.4,229 3818.9,223.7 3827.2,\ -214.03 3833.4,204.59", + lp="3669.4,221.5", + pos="e,3619.8,195.79 2376.1,251.74 2395.1,249.84 2414.8,248.13 2433.4,247 2465.4,245.04 3558.5,242.94 3587.4,229 3598.4,223.69 3607.4,\ +213.88 3614.2,204.34", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3997.4,178", + pos="3779.4,178", width=1.0652]; "sequence feature relationship" -> "subject label closure" [color=blue, label="subject label closure", - lp="4050.4,221.5", - pos="e,3989.4,195.78 2593.6,251.75 2612.8,249.84 2632.7,248.13 2651.4,247 2687.6,244.82 3925.9,245.15 3958.4,229 3969.1,223.68 3977.8,\ -213.86 3984.2,204.32", + lp="3831.4,221.5", + pos="e,3770.5,195.81 2375.6,251.75 2394.8,249.84 2414.7,248.13 2433.4,247 2469.6,244.82 3704.7,244.53 3737.4,229 3748.5,223.72 3757.8,\ +213.9 3764.7,204.36", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4168.4,178", + pos="3950.4,178", width=1.0652]; "sequence feature relationship" -> "object label closure" [color=blue, label="object label closure", - lp="4215.9,221.5", - pos="e,4160.1,195.8 2593.6,251.73 2612.8,249.82 2632.7,248.11 2651.4,247 2692.4,244.57 4091.5,247 4128.4,229 4139.3,223.7 4148.1,213.88 \ -4154.7,204.34", + lp="3998.9,221.5", + pos="e,3941.8,195.81 2375.6,251.73 2394.8,249.82 2414.7,248.11 2433.4,247 2474.3,244.57 3872.4,246.76 3909.4,229 3920.4,223.71 3929.4,\ +213.9 3936.2,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4330.4,178", + pos="4112.4,178", width=2.347]; "sequence feature relationship" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4378.9,221.5", - pos="e,4321.5,196.31 2593.6,251.71 2612.8,249.8 2632.7,248.1 2651.4,247 2696.8,244.33 4248.4,248.69 4289.4,229 4300.2,223.79 4309.2,214.18 \ -4315.9,204.77", + lp="4160.9,221.5", + pos="e,4103.8,196.29 2375.6,251.71 2394.8,249.8 2414.7,248.1 2433.4,247 2478.8,244.33 4031.5,248.95 4072.4,229 4083.1,223.78 4091.9,214.17 \ +4098.4,204.75", style=solid]; type [height=0.5, - pos="4464.4,178", + pos="4246.4,178", width=0.86659]; "sequence feature relationship" -> type [color=blue, label=type, - lp="4478.4,221.5", - pos="e,4465.2,196.18 2593.6,251.7 2612.8,249.79 2632.7,248.09 2651.4,247 2676.4,245.54 4432.8,244.59 4452.4,229 4459.2,223.54 4462.6,\ -214.93 4464.1,206.37", + lp="4260.4,221.5", + pos="e,4247.2,196.18 2375.6,251.7 2394.8,249.79 2414.7,248.09 2433.4,247 2458.4,245.54 4214.8,244.59 4234.4,229 4241.2,223.54 4244.6,\ +214.93 4246.1,206.37", style=solid]; category [height=0.5, - pos="4565.4,178", + pos="4347.4,178", width=1.4263]; "sequence feature relationship" -> category [color=blue, label=category, - lp="4558.9,221.5", - pos="e,4549.8,195.25 2593.6,251.69 2612.8,249.79 2632.7,248.09 2651.4,247 2702.6,244.02 4449.8,245.4 4498.4,229 4514.6,223.53 4530.1,\ -212.51 4542.1,202.2", + lp="4340.9,221.5", + pos="e,4331.8,195.25 2375.6,251.69 2394.8,249.79 2414.7,248.09 2433.4,247 2484.6,244.02 4231.8,245.4 4280.4,229 4296.6,223.53 4312.1,\ +212.51 4324.1,202.2", style=solid]; subject [height=0.5, - pos="4679.4,178", + pos="4461.4,178", width=1.2277]; "sequence feature relationship" -> subject [color=blue, label=subject, - lp="4655.4,221.5", - pos="e,4660.1,194.33 2593.6,251.69 2612.8,249.78 2632.7,248.08 2651.4,247 2759.2,240.75 4490.4,257.84 4594.4,229 4615.1,223.25 4636,211.09 \ -4651.9,200.2", + lp="4437.4,221.5", + pos="e,4442.1,194.33 2375.6,251.69 2394.8,249.78 2414.7,248.08 2433.4,247 2541.2,240.75 4272.4,257.84 4376.4,229 4397.1,223.25 4418,211.09 \ +4433.9,200.2", style=solid]; object [height=0.5, - pos="4722.4,91", + pos="4504.4,91", width=1.0832]; "sequence feature relationship" -> object [color=blue, label=object, - lp="4766.4,178", - pos="e,4735.8,108.09 2593.6,251.68 2612.8,249.77 2632.7,248.08 2651.4,247 2707.8,243.74 4631.6,246.26 4685.4,229 4709.7,221.2 4718,217.1 \ -4732.4,196 4746.3,175.59 4742.5,166.51 4745.4,142 4746.2,135.38 4747.3,133.39 4745.4,127 4744.4,123.55 4742.9,120.13 4741.1,116.85", + lp="4548.4,178", + pos="e,4517.8,108.09 2375.6,251.68 2394.8,249.77 2414.7,248.08 2433.4,247 2489.8,243.74 4413.6,246.26 4467.4,229 4491.7,221.2 4500,217.1 \ +4514.4,196 4528.3,175.59 4524.5,166.51 4527.4,142 4528.2,135.38 4529.3,133.39 4527.4,127 4526.4,123.55 4524.9,120.13 4523.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2698.4,265", + pos="2480.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2829.4,265", + pos="2611.4,265", width=2.0762]; subject -> object [label=relation, - lp="4717.4,134.5", - pos="e,4704.5,107.23 4680.5,159.55 4681.7,149.57 4684.2,137.07 4689.4,127 4691.6,122.68 4694.5,118.52 4697.7,114.66"]; + lp="4499.4,134.5", + pos="e,4486.5,107.23 4462.5,159.55 4463.7,149.57 4466.2,137.07 4471.4,127 4473.6,122.68 4476.5,118.52 4479.7,114.66"]; relation [height=0.5, - pos="4667.4,18", + pos="4449.4,18", width=1.2999]; - subject -> relation [pos="e,4668.7,36.188 4678.1,159.79 4676,132.48 4672,78.994 4669.5,46.38", + subject -> relation [pos="e,4450.7,36.188 4460.1,159.79 4458,132.48 4454,78.994 4451.5,46.38", style=dotted]; "sequence feature relationship_subject" [color=blue, height=0.5, label="nucleic acid entity", - pos="3017.4,265", + pos="2799.4,265", width=2.6539]; - object -> relation [pos="e,4680.2,35.54 4709.9,73.889 4703,64.939 4694.2,53.617 4686.4,43.584", + object -> relation [pos="e,4462.2,35.54 4491.9,73.889 4485,64.939 4476.2,53.617 4468.4,43.584", style=dotted]; "sequence feature relationship_object" [color=blue, height=0.5, label="nucleic acid entity", - pos="3226.4,265", + pos="3008.4,265", width=2.6539]; } diff --git a/graphviz/sequence_feature_relationship.svg b/graphviz/sequence_feature_relationship.svg index 03e2525206..70daa8c5a8 100644 --- a/graphviz/sequence_feature_relationship.svg +++ b/graphviz/sequence_feature_relationship.svg @@ -4,16 +4,16 @@ - + %3 - + sequence feature relationship - -sequence feature relationship + +sequence feature relationship @@ -24,9 +24,9 @@ sequence feature relationship->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ sequence feature relationship->id - - -id + + +id @@ -50,9 +50,9 @@ sequence feature relationship->iri - - -iri + + +iri @@ -63,9 +63,9 @@ sequence feature relationship->name - - -name + + +name @@ -76,9 +76,9 @@ sequence feature relationship->description - - -description + + +description @@ -89,9 +89,9 @@ sequence feature relationship->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ sequence feature relationship->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ sequence feature relationship->negated - - -negated + + +negated @@ -128,9 +128,9 @@ sequence feature relationship->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ sequence feature relationship->publications - - -publications + + +publications @@ -154,344 +154,344 @@ sequence feature relationship->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string sequence feature relationship->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string sequence feature relationship->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string sequence feature relationship->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type sequence feature relationship->timepoint - - -timepoint + + +timepoint original subject - -string + +string sequence feature relationship->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie sequence feature relationship->original predicate - - -original predicate + + +original predicate original object - -string + +string sequence feature relationship->original object - - -original object + + +original object subject category - -ontology class + +ontology class sequence feature relationship->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class sequence feature relationship->object category - - -object category + + +object category subject closure - -string + +string sequence feature relationship->subject closure - - -subject closure + + +subject closure object closure - -string + +string sequence feature relationship->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class sequence feature relationship->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class sequence feature relationship->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string sequence feature relationship->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string sequence feature relationship->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string sequence feature relationship->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string sequence feature relationship->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source sequence feature relationship->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type sequence feature relationship->type - - -type + + +type category - -category + +category sequence feature relationship->category - - -category + + +category subject - -subject + +subject sequence feature relationship->subject - - -subject + + +subject object - -object + +object sequence feature relationship->object - - -object + + +object association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + sequence feature relationship_subject - -nucleic acid entity + +nucleic acid entity object->relation - - + + sequence feature relationship_object - -nucleic acid entity + +nucleic acid entity diff --git a/graphviz/sequence_variant_modulates_treatment_association.gv b/graphviz/sequence_variant_modulates_treatment_association.gv index bbf3f6011a..9f18258670 100644 --- a/graphviz/sequence_variant_modulates_treatment_association.gv +++ b/graphviz/sequence_variant_modulates_treatment_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4788.4,283"]; + graph [bb="0,0,4570.4,283"]; node [label="\N"]; "sequence variant modulates treatment association" [height=0.5, label="sequence variant modulates treatment association", - pos="2492.4,265", + pos="2274.4,265", width=6.8244]; association [height=0.5, pos="62.394,178", width=1.7332]; "sequence variant modulates treatment association" -> association [label=is_a, - lp="281.39,221.5", - pos="e,103.12,191.79 2247.8,263.24 1710.4,261.11 459.08,253.57 267.39,229 213.85,222.14 154.03,206.61 112.9,194.67"]; + lp="280.39,221.5", + pos="e,102.91,191.77 2030.2,262.79 1533.3,259.89 436.63,251.07 266.39,229 213.11,222.09 153.58,206.57 112.65,194.64"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "sequence variant modulates treatment association" -> id [color=blue, label=id, - lp="398.39,221.5", - pos="e,210.38,190 2248.8,262.47 1734.7,258.87 571.3,248.65 391.39,229 318.35,221.02 300.2,215.65 229.39,196 226.29,195.14 223.09,194.17 \ -219.89,193.16", + lp="396.39,221.5", + pos="e,210.38,189.98 2031.8,262 1559.3,257.74 548.03,246.68 389.39,229 317.23,220.96 299.34,215.5 229.39,196 226.29,195.13 223.09,194.17 \ +219.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "sequence variant modulates treatment association" -> iri [color=blue, label=iri, - lp="515.39,221.5", - pos="e,315.29,190.23 2249.7,262.06 1757.9,257.79 676.02,246.53 507.39,229 429.97,220.95 410.81,215.26 335.39,196 332.02,195.14 328.54,\ -194.18 325.05,193.17", + lp="509.39,221.5", + pos="e,315.3,190.2 2028.5,264.51 1613.2,264.46 789.59,260.24 501.39,229 426.61,220.89 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ +325.06,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "sequence variant modulates treatment association" -> name [color=blue, label=name, - lp="627.39,221.5", - pos="e,440.01,191.15 2249.3,262.37 1776.5,258.79 765.71,248.9 607.39,229 552.58,222.11 491.21,206.11 449.83,194.05", + lp="617.39,221.5", + pos="e,439.19,191.41 2032,261.99 1601.4,257.97 735.23,247.68 597.39,229 545.74,222 488.1,206.31 448.78,194.36", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "sequence variant modulates treatment association" -> description [color=blue, label=description, - lp="755.89,221.5", - pos="e,588.8,193.65 2248.3,262.93 1796.6,260.4 862.33,252.38 715.39,229 675.03,222.58 630.79,208.66 598.44,197.14", + lp="739.89,221.5", + pos="e,586.19,194.12 2030.5,262.64 1620.8,259.75 826.38,251.32 699.39,229 663.52,222.69 624.55,209.24 595.6,197.88", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "sequence variant modulates treatment association" -> "has attribute" [color=blue, label="has attribute", - lp="913.39,221.5", - pos="e,729.98,191.75 2249.1,262.31 1828.8,258.85 998.8,249.52 866.39,229 822.26,222.16 773.51,207 739.58,195.15", + lp="887.39,221.5", + pos="e,726.83,192.67 2031.6,262.16 1653.1,258.68 953.8,249.55 840.39,229 804.17,222.43 764.8,208.24 736.39,196.65", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "sequence variant modulates treatment association" -> predicate [color=blue, label=predicate, - lp="1074.4,221.5", - pos="e,887.81,193.09 2246.5,264.77 1894.8,264.72 1265.8,260.05 1040.4,229 991.17,222.22 936.47,207.65 897.4,195.99", + lp="1031.4,221.5", + pos="e,880.43,194.06 2034.2,261.15 1692.5,256.52 1096.2,246.12 997.39,229 960.25,222.56 919.77,209.02 889.78,197.66", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "sequence variant modulates treatment association" -> negated [color=blue, label=negated, - lp="1220.4,221.5", - pos="e,1022.3,190.23 2248.1,262.99 1929.3,260.71 1388.7,253.27 1191.4,229 1135.6,222.13 1072.9,205.38 1032,193.16", + lp="1151.4,221.5", + pos="e,1015.6,192.51 2035.2,260.86 1723.8,256.13 1209.1,245.89 1122.4,229 1088.3,222.36 1051.5,208.2 1024.9,196.64", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "sequence variant modulates treatment association" -> qualifiers [color=blue, label=qualifiers, - lp="1356.9,221.5", - pos="e,1171.6,193.02 2248.2,263.03 1959.1,260.76 1495.3,253.31 1323.4,229 1274.6,222.11 1220.5,207.65 1181.6,196.05", + lp="1254.9,221.5", + pos="e,1151.6,195.39 2032.6,261.77 1745.9,258.22 1297.3,249.45 1221.4,229 1199.7,223.15 1177.4,211.43 1160.1,200.81", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "sequence variant modulates treatment association" -> publications [color=blue, label=publications, - lp="1499.4,221.5", - pos="e,1321.9,192.66 2248.4,262.85 1990.8,260.37 1602.2,252.67 1455.4,229 1412.5,222.09 1365.3,207.61 1331.5,196.01", + lp="1346.4,221.5", + pos="e,1286.4,196.26 2031.8,262.09 1753.5,258.88 1331.3,250.49 1302.4,229 1295.1,223.57 1290.9,214.84 1288.5,206.19", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,261 +110,262 @@ digraph { width=2.0943]; "sequence variant modulates treatment association" -> "has evidence" [color=blue, label="has evidence", - lp="1652.9,221.5", - pos="e,1479.4,193.55 2251.6,261.36 2032.5,257.71 1725.7,249.09 1606.4,229 1566,222.2 1521.6,208.38 1489.1,196.99", + lp="1444.9,221.5", + pos="e,1413.8,194.93 2031,262.48 1779.4,259.67 1420.2,251.69 1398.4,229 1390,220.25 1395.9,210.18 1405.7,201.37", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1643.4,178", - width=3.015]; + label=string, + pos="1573.4,178", + width=1.0652]; "sequence variant modulates treatment association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1802.9,221.5", - pos="e,1667.9,195.78 2246.9,264.08 2064.2,261.99 1830.9,254.16 1738.4,229 1716.6,223.09 1694.2,211.61 1676.7,201.13", + lp="1562.9,221.5", + pos="e,1543.3,189.28 2034.4,261.11 1813.4,257.23 1517,248.43 1498.4,229 1493.8,224.18 1494.8,219.62 1498.4,214 1502.8,207.12 1518,199.47 \ +1533.6,193.08", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1878.4,178", - width=3.015]; + label=string, + pos="1668.4,178", + width=1.0652]; "sequence variant modulates treatment association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1972.4,221.5", - pos="e,1872.6,196 2264.5,258.27 2095.1,252.86 1891,243.41 1877.4,229 1871.6,222.9 1870.4,214.27 1871,205.9", + lp="1729.4,221.5", + pos="e,1648.1,193.48 2043.5,258.76 1866,253.56 1648.7,244.15 1634.4,229 1626.3,220.46 1631.8,209.82 1640.6,200.55", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2113.4,178", - width=3.015]; + label=string, + pos="1810.4,178", + width=1.0652]; "sequence variant modulates treatment association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2180.9,221.5", - pos="e,2087.6,195.53 2266,257.95 2175.3,253.13 2088.6,244.49 2074.4,229 2066.7,220.62 2071.6,210.86 2080.1,202.2", + lp="1949.9,221.5", + pos="e,1816.9,195.93 2067.5,255.29 1967,249.59 1863.6,240.96 1843.4,229 1834,223.44 1826.8,214.03 1821.5,204.86", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2295.4,178", + pos="2037.4,178", width=1.5346]; "sequence variant modulates treatment association" -> timepoint [color=blue, label=timepoint, - lp="2332.4,221.5", - pos="e,2291.1,196.26 2348.1,250.32 2324.8,245.29 2305.6,238.4 2297.4,229 2292,222.83 2290.3,214.43 2290.3,206.27", + lp="2112.4,221.5", + pos="e,2046.6,196.08 2152.4,249.36 2120.4,243.97 2091.1,237.16 2077.4,229 2067.4,223.06 2058.9,213.63 2052.3,204.55", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2407.4,178", + pos="2149.4,178", width=1.0652]; "sequence variant modulates treatment association" -> "original subject" [color=blue, label="original subject", - lp="2430.4,221.5", - pos="e,2387.4,193.75 2397.2,248.35 2388.3,243.45 2380.5,237.13 2374.4,229 2367.7,220.01 2372.5,209.73 2380.3,200.83", + lp="2214.4,221.5", + pos="e,2148.2,196.23 2184.4,248.16 2174.6,243.34 2165.6,237.09 2158.4,229 2152.9,222.8 2150.2,214.39 2149,206.23", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2521.4,178", + pos="2274.4,178", width=1.5887]; "sequence variant modulates treatment association" -> "original predicate" [color=blue, label="original predicate", - lp="2556.9,221.5", - pos="e,2504.6,195.4 2490.1,246.84 2489.4,236.95 2489.6,224.45 2493.4,214 2494.7,210.42 2496.5,206.94 2498.6,203.64", + lp="2337.9,221.5", + pos="e,2274.4,196.18 2274.4,246.8 2274.4,235.16 2274.4,219.55 2274.4,206.24", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2635.4,178", + pos="2403.4,178", width=1.0652]; "sequence variant modulates treatment association" -> "original object" [color=blue, label="original object", - lp="2681.9,221.5", - pos="e,2634.3,196.46 2591,248.4 2601.8,243.53 2612,237.21 2620.4,229 2626.5,223.04 2630.2,214.69 2632.3,206.52", + lp="2459.9,221.5", + pos="e,2407.8,195.99 2362,248.17 2380.6,243.02 2396.4,236.63 2402.4,229 2407.4,222.62 2408.9,214.26 2408.7,206.21", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2768.4,178", + pos="2536.4,178", width=2.1304]; "sequence variant modulates treatment association" -> "subject category" [color=blue, label="subject category", - lp="2811.9,221.5", - pos="e,2762.2,196.16 2653.8,251.39 2690,246.2 2722.1,238.99 2737.4,229 2746.2,223.28 2752.9,214.13 2757.8,205.22", + lp="2586.9,221.5", + pos="e,2533.7,196.01 2440.8,251.75 2473.6,246.61 2502.1,239.32 2515.4,229 2522.8,223.28 2527.6,214.49 2530.7,205.86", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2939.4,178", + pos="2707.4,178", width=2.1304]; "sequence variant modulates treatment association" -> "object category" [color=blue, label="object category", - lp="2956.9,221.5", - pos="e,2923.4,195.77 2668.5,252.44 2759.4,245.65 2855.5,236.88 2875.4,229 2890.3,223.11 2904.5,212.62 2915.8,202.76", + lp="2728.9,221.5", + pos="e,2693.3,196.01 2451.1,252.48 2539.3,245.84 2631.4,237.2 2650.4,229 2663.9,223.19 2676.4,212.95 2686.3,203.24", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3072.4,178", + pos="2840.4,178", width=1.0652]; "sequence variant modulates treatment association" -> "subject closure" [color=blue, label="subject closure", - lp="3093.9,221.5", - pos="e,3059.6,195.16 2667.2,252.32 2819.6,242.14 3016.4,229 3016.4,229 3030.2,223.21 3042.9,212.56 3052.7,202.58", + lp="2864.9,221.5", + pos="e,2828.3,195.63 2448.7,252.3 2597.4,242.3 2787.4,229.44 2788.4,229 2801.2,223.32 2812.8,213.03 2821.7,203.26", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3172.4,178", + pos="2953.4,178", width=1.0652]; "sequence variant modulates treatment association" -> "object closure" [color=blue, label="object closure", - lp="3214.4,221.5", - pos="e,3170.3,196.32 2663.5,252.07 2691.5,250.27 2720.3,248.51 2747.4,247 2769.9,245.75 3134,242.04 3152.4,229 3160,223.63 3164.7,214.92 \ -3167.6,206.26", + lp="2988.4,221.5", + pos="e,2948,196.02 2445.8,252.08 2473.7,250.28 2502.4,248.52 2529.4,247 2573.1,244.54 2885.8,251.46 2923.4,229 2932.4,223.61 2939.1,214.36 \ +2943.8,205.27", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3305.4,178", + pos="3086.4,178", width=2.1304]; "sequence variant modulates treatment association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3372.9,221.5", - pos="e,3297.7,196.16 2661.7,251.95 2690.3,250.13 2719.7,248.4 2747.4,247 2776.3,245.54 3242.8,242.48 3268.4,229 3278.5,223.67 3286.6,\ -214.17 3292.6,204.87", + lp="3148.9,221.5", + pos="e,3076.5,196.23 2443.8,251.96 2472.3,250.14 2501.7,248.41 2529.4,247 2586.4,244.1 2990.8,253.4 3042.4,229 3053.7,223.64 3063.3,213.87 \ +3070.7,204.38", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3497.4,178", + pos="3279.4,178", width=2.1304]; "sequence variant modulates treatment association" -> "object category closure" [color=blue, label="object category closure", - lp="3563.9,221.5", - pos="e,3491.1,196.15 2660,251.83 2689.1,250 2719.1,248.3 2747.4,247 2787.2,245.17 3429.5,248.32 3464.4,229 3473.9,223.7 3481.2,214.34 \ -3486.5,205.14", + lp="3341.9,221.5", + pos="e,3271.1,196.22 2442,251.84 2471.1,250.01 2501.1,248.3 2529.4,247 2568.9,245.19 3205.1,246.78 3240.4,229 3250.8,223.74 3259.3,214.26 \ +3265.7,204.95", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3687.4,178", + pos="3469.4,178", width=1.0652]; "sequence variant modulates treatment association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3736.4,221.5", - pos="e,3680.3,195.72 2659,251.77 2688.4,249.93 2718.8,248.24 2747.4,247 2797.6,244.83 3606.9,252.34 3651.4,229 3661.6,223.65 3669.6,213.96 \ -3675.4,204.53", + lp="3515.4,221.5", + pos="e,3461.1,195.76 2441.3,251.75 2470.7,249.92 2500.9,248.23 2529.4,247 2579.4,244.84 3384.5,251.11 3429.4,229 3440.2,223.66 3449.1,\ +213.83 3455.7,204.3", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3846.4,178", + pos="3628.4,178", width=1.0652]; "sequence variant modulates treatment association" -> "object namespace" [color=blue, label="object namespace", - lp="3890.4,221.5", - pos="e,3838.7,195.75 2658.6,251.72 2688.2,249.88 2718.7,248.2 2747.4,247 2776.8,245.77 3782.1,242.32 3808.4,229 3818.9,223.7 3827.2,214.02 \ -3833.4,204.58", + lp="3669.4,221.5", + pos="e,3619.8,195.79 2440.6,251.72 2470.2,249.88 2500.7,248.2 2529.4,247 2588.1,244.54 3534.5,254.6 3587.4,229 3598.4,223.69 3607.4,213.87 \ +3614.2,204.33", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3997.4,178", + pos="3779.4,178", width=1.0652]; "sequence variant modulates treatment association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4050.4,221.5", - pos="e,3989.4,195.77 2658.3,251.69 2688,249.85 2718.6,248.17 2747.4,247 2781,245.63 3928.3,243.98 3958.4,229 3969.1,223.67 3977.8,213.85 \ -3984.2,204.31", + lp="3831.4,221.5", + pos="e,3770.5,195.81 2440.3,251.69 2470,249.85 2500.6,248.17 2529.4,247 2562.9,245.63 3707.1,243.4 3737.4,229 3748.5,223.71 3757.8,213.9 \ +3764.7,204.35", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4168.4,178", + pos="3950.4,178", width=1.0652]; "sequence variant modulates treatment association" -> "object label closure" [color=blue, label="object label closure", - lp="4215.9,221.5", - pos="e,4160.1,195.79 2658,251.67 2687.7,249.82 2718.5,248.15 2747.4,247 2785.7,245.47 4093.9,245.84 4128.4,229 4139.3,223.69 4148.1,213.88 \ -4154.7,204.34", + lp="3998.9,221.5", + pos="e,3941.8,195.8 2440,251.67 2469.7,249.82 2500.5,248.15 2529.4,247 2567.7,245.47 3874.8,245.62 3909.4,229 3920.4,223.71 3929.4,213.89 \ +3936.2,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4330.4,178", + pos="4112.4,178", width=2.347]; "sequence variant modulates treatment association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4378.9,221.5", - pos="e,4321.5,196.3 2657.6,251.66 2687.5,249.8 2718.4,248.14 2747.4,247 2790.2,245.32 4250.8,247.55 4289.4,229 4300.2,223.79 4309.2,214.18 \ -4315.9,204.76", + lp="4160.9,221.5", + pos="e,4103.8,196.29 2439.6,251.66 2469.5,249.8 2500.4,248.14 2529.4,247 2572.2,245.32 4033.9,247.79 4072.4,229 4083.1,223.78 4091.9,\ +214.16 4098.4,204.75", style=solid]; type [height=0.5, - pos="4464.4,178", + pos="4246.4,178", width=0.86659]; "sequence variant modulates treatment association" -> type [color=blue, label=type, - lp="4478.4,221.5", - pos="e,4465.2,196.18 2657.3,251.65 2687.2,249.79 2718.2,248.12 2747.4,247 2771.1,246.09 4433.9,243.76 4452.4,229 4459.2,223.54 4462.6,\ -214.92 4464.1,206.37", + lp="4260.4,221.5", + pos="e,4247.2,196.18 2439.3,251.65 2469.2,249.79 2500.2,248.12 2529.4,247 2553.1,246.09 4215.9,243.76 4234.4,229 4241.2,223.54 4244.6,\ +214.92 4246.1,206.37", style=solid]; category [height=0.5, - pos="4565.4,178", + pos="4347.4,178", width=1.4263]; "sequence variant modulates treatment association" -> category [color=blue, label=category, - lp="4558.9,221.5", - pos="e,4549.8,195.25 2657.3,251.64 2687.2,249.79 2718.2,248.12 2747.4,247 2796,245.13 4452.3,244.56 4498.4,229 4514.6,223.53 4530.1,212.5 \ -4542.1,202.2", + lp="4340.9,221.5", + pos="e,4331.8,195.25 2439.3,251.64 2469.2,249.79 2500.2,248.12 2529.4,247 2578,245.13 4234.3,244.56 4280.4,229 4296.6,223.53 4312.1,212.5 \ +4324.1,202.2", style=solid]; subject [height=0.5, - pos="4679.4,178", + pos="4461.4,178", width=1.2277]; "sequence variant modulates treatment association" -> subject [color=blue, label=subject, - lp="4655.4,221.5", - pos="e,4660.1,194.33 2657.3,251.63 2687.2,249.78 2718.2,248.11 2747.4,247 2849.9,243.09 4495.5,256.44 4594.4,229 4615.1,223.24 4636,211.08 \ -4651.9,200.2", + lp="4437.4,221.5", + pos="e,4442.1,194.33 2439.3,251.63 2469.2,249.78 2500.2,248.11 2529.4,247 2631.9,243.09 4277.5,256.44 4376.4,229 4397.1,223.24 4418,211.08 \ +4433.9,200.2", style=solid]; object [height=0.5, - pos="4722.4,91", + pos="4504.4,91", width=1.0832]; "sequence variant modulates treatment association" -> object [color=blue, label=object, - lp="4766.4,178", - pos="e,4735.8,108.09 2657.3,251.62 2687.2,249.77 2718.2,248.11 2747.4,247 2801.2,244.96 4634.1,245.46 4685.4,229 4709.7,221.2 4718,217.1 \ -4732.4,196 4746.3,175.59 4742.5,166.51 4745.4,142 4746.2,135.38 4747.3,133.39 4745.4,127 4744.4,123.55 4742.9,120.13 4741.1,116.85", + lp="4548.4,178", + pos="e,4517.8,108.09 2439.3,251.62 2469.2,249.77 2500.2,248.11 2529.4,247 2583.2,244.96 4416.1,245.46 4467.4,229 4491.7,221.2 4500,217.1 \ +4514.4,196 4528.3,175.59 4524.5,166.51 4527.4,142 4528.2,135.38 4529.3,133.39 4527.4,127 4526.4,123.55 4524.9,120.13 4523.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2794.4,265", + pos="2576.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2925.4,265", + pos="2707.4,265", width=2.0762]; subject -> object [label=relation, - lp="4717.4,134.5", - pos="e,4704.5,107.23 4680.5,159.55 4681.7,149.57 4684.2,137.07 4689.4,127 4691.6,122.68 4694.5,118.52 4697.7,114.66"]; + lp="4499.4,134.5", + pos="e,4486.5,107.23 4462.5,159.55 4463.7,149.57 4466.2,137.07 4471.4,127 4473.6,122.68 4476.5,118.52 4479.7,114.66"]; relation [height=0.5, - pos="4667.4,18", + pos="4449.4,18", width=1.2999]; - subject -> relation [pos="e,4668.7,36.188 4678.1,159.79 4676,132.48 4672,78.994 4669.5,46.38", + subject -> relation [pos="e,4450.7,36.188 4460.1,159.79 4458,132.48 4454,78.994 4451.5,46.38", style=dotted]; "sequence variant modulates treatment association_subject" [color=blue, height=0.5, label="sequence variant", - pos="3108.4,265", + pos="2890.4,265", width=2.5095]; - object -> relation [pos="e,4680.2,35.54 4709.9,73.889 4703,64.939 4694.2,53.617 4686.4,43.584", + object -> relation [pos="e,4462.2,35.54 4491.9,73.889 4485,64.939 4476.2,53.617 4468.4,43.584", style=dotted]; "sequence variant modulates treatment association_object" [color=blue, height=0.5, label=treatment, - pos="3274.4,265", + pos="3056.4,265", width=1.6068]; } diff --git a/graphviz/sequence_variant_modulates_treatment_association.svg b/graphviz/sequence_variant_modulates_treatment_association.svg index 82165947a2..633ce616ac 100644 --- a/graphviz/sequence_variant_modulates_treatment_association.svg +++ b/graphviz/sequence_variant_modulates_treatment_association.svg @@ -4,16 +4,16 @@ - + %3 - + sequence variant modulates treatment association - -sequence variant modulates treatment association + +sequence variant modulates treatment association @@ -24,9 +24,9 @@ sequence variant modulates treatment association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ sequence variant modulates treatment association->id - - -id + + +id @@ -50,9 +50,9 @@ sequence variant modulates treatment association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ sequence variant modulates treatment association->name - - -name + + +name @@ -76,9 +76,9 @@ sequence variant modulates treatment association->description - - -description + + +description @@ -89,9 +89,9 @@ sequence variant modulates treatment association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ sequence variant modulates treatment association->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ sequence variant modulates treatment association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ sequence variant modulates treatment association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ sequence variant modulates treatment association->publications - - -publications + + +publications @@ -154,344 +154,344 @@ sequence variant modulates treatment association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string sequence variant modulates treatment association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string sequence variant modulates treatment association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string sequence variant modulates treatment association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type sequence variant modulates treatment association->timepoint - - -timepoint + + +timepoint original subject - -string + +string sequence variant modulates treatment association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie sequence variant modulates treatment association->original predicate - - -original predicate + + +original predicate original object - -string + +string sequence variant modulates treatment association->original object - - -original object + + +original object subject category - -ontology class + +ontology class sequence variant modulates treatment association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class sequence variant modulates treatment association->object category - - -object category + + +object category subject closure - -string + +string sequence variant modulates treatment association->subject closure - - -subject closure + + +subject closure object closure - -string + +string sequence variant modulates treatment association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class sequence variant modulates treatment association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class sequence variant modulates treatment association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string sequence variant modulates treatment association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string sequence variant modulates treatment association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string sequence variant modulates treatment association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string sequence variant modulates treatment association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source sequence variant modulates treatment association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type sequence variant modulates treatment association->type - - -type + + +type category - -category + +category sequence variant modulates treatment association->category - - -category + + +category subject - -subject + +subject sequence variant modulates treatment association->subject - - -subject + + +subject object - -object + +object sequence variant modulates treatment association->object - - -object + + +object association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + sequence variant modulates treatment association_subject - -sequence variant + +sequence variant object->relation - - + + sequence variant modulates treatment association_object - -treatment + +treatment diff --git a/graphviz/taxon_to_taxon_association.gv b/graphviz/taxon_to_taxon_association.gv index ea2af3caff..5f6b6e13c4 100644 --- a/graphviz/taxon_to_taxon_association.gv +++ b/graphviz/taxon_to_taxon_association.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4788.4,283"]; + graph [bb="0,0,4570.4,283"]; node [label="\N"]; "taxon to taxon association" [height=0.5, label="taxon to taxon association", - pos="2492.4,265", + pos="2274.4,265", width=3.665]; association [height=0.5, pos="62.394,178", width=1.7332]; "taxon to taxon association" -> association [label=is_a, - lp="281.39,221.5", - pos="e,103.12,191.79 2360.8,263.64 1914.4,262.2 474.2,255.51 267.39,229 213.85,222.14 154.03,206.61 112.9,194.67"]; + lp="280.39,221.5", + pos="e,102.91,191.77 2142.7,263.41 1725.8,261.3 451.06,252.93 266.39,229 213.11,222.09 153.58,206.57 112.65,194.64"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "taxon to taxon association" -> id [color=blue, label=id, - lp="398.39,221.5", - pos="e,210.38,190 2360.7,263.22 1931,260.47 585.98,250.26 391.39,229 318.35,221.02 300.2,215.65 229.39,196 226.29,195.14 223.09,194.17 \ -219.89,193.16", + lp="396.39,221.5", + pos="e,210.38,189.98 2143.2,262.97 1744.2,259.63 562.01,248.24 389.39,229 317.23,220.96 299.34,215.5 229.39,196 226.29,195.13 223.09,\ +194.17 219.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "taxon to taxon association" -> iri [color=blue, label=iri, - lp="515.39,221.5", - pos="e,315.29,190.23 2361.2,263 1948,259.65 690.32,248.02 507.39,229 429.97,220.95 410.81,215.26 335.39,196 332.02,195.14 328.54,194.18 \ -325.05,193.17", + lp="509.39,221.5", + pos="e,315.3,190.2 2142.4,264.41 1787.7,265.04 819.14,263.45 501.39,229 426.61,220.89 408.22,214.85 335.39,196 332.02,195.13 328.54,194.16 \ +325.06,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "taxon to taxon association" -> name [color=blue, label=name, - lp="627.39,221.5", - pos="e,440.01,191.15 2360.8,263.18 1961.4,260.46 779.67,250.65 607.39,229 552.58,222.11 491.21,206.11 449.83,194.05", + lp="617.39,221.5", + pos="e,439.19,191.41 2143.1,262.98 1774.8,259.88 748.49,249.48 597.39,229 545.74,222 488.1,206.31 448.78,194.36", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "taxon to taxon association" -> description [color=blue, label=description, - lp="755.89,221.5", - pos="e,588.8,193.65 2360.9,263.5 1977.1,261.76 876,254.56 715.39,229 675.03,222.58 630.79,208.66 598.44,197.14", + lp="739.89,221.5", + pos="e,586.19,194.12 2142.9,263.36 1790,261.33 839.34,253.6 699.39,229 663.52,222.69 624.55,209.24 595.6,197.88", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "taxon to taxon association" -> "has attribute" [color=blue, label="has attribute", - lp="913.39,221.5", - pos="e,729.98,191.75 2360.9,263.17 2000.1,260.59 1011.9,251.56 866.39,229 822.26,222.16 773.51,207 739.58,195.15", + lp="887.39,221.5", + pos="e,726.83,192.67 2143.1,263.11 1813.1,260.54 966.21,251.8 840.39,229 804.17,222.43 764.8,208.24 736.39,196.65", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "taxon to taxon association" -> predicate [color=blue, label=predicate, - lp="1074.4,221.5", - pos="e,887.81,193.09 2360.4,264.62 2052.3,265.46 1292.9,263.8 1040.4,229 991.17,222.22 936.47,207.65 897.4,195.99", + lp="1031.4,221.5", + pos="e,880.43,194.06 2143.5,262.55 1840.4,258.88 1107.9,248.15 997.39,229 960.25,222.56 919.77,209.02 889.78,197.66", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "taxon to taxon association" -> negated [color=blue, label=negated, - lp="1220.4,221.5", - pos="e,1022.3,190.23 2360.8,263.65 2076.9,262.38 1414.5,256.46 1191.4,229 1135.6,222.13 1072.9,205.38 1032,193.16", + lp="1151.4,221.5", + pos="e,1015.6,192.51 2143.8,262.41 1863.2,258.65 1220.2,248.07 1122.4,229 1088.3,222.36 1051.5,208.2 1024.9,196.64", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "taxon to taxon association" -> qualifiers [color=blue, label=qualifiers, - lp="1356.9,221.5", - pos="e,1171.6,193.02 2360.6,263.72 2098.4,262.55 1520,256.8 1323.4,229 1274.6,222.11 1220.5,207.65 1181.6,196.05", + lp="1254.9,221.5", + pos="e,1151.6,195.39 2143.2,262.99 1880.7,260.47 1308,252.35 1221.4,229 1199.7,223.15 1177.4,211.43 1160.1,200.81", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "taxon to taxon association" -> publications [color=blue, label=publications, - lp="1499.4,221.5", - pos="e,1321.9,192.66 2360.5,263.68 2121.5,262.42 1625.7,256.46 1455.4,229 1412.5,222.09 1365.3,207.61 1331.5,196.01", + lp="1346.4,221.5", + pos="e,1286.4,196.26 2142.7,263.19 1884.9,261.05 1335.5,253.63 1302.4,229 1295.1,223.57 1290.9,214.84 1288.5,206.19", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,263 +110,264 @@ digraph { width=2.0943]; "taxon to taxon association" -> "has evidence" [color=blue, label="has evidence", - lp="1652.9,221.5", - pos="e,1479.4,193.55 2361.1,262.91 2150.8,260.47 1747.5,252.76 1606.4,229 1566,222.2 1521.6,208.38 1489.1,196.99", + lp="1444.9,221.5", + pos="e,1413.8,194.93 2142.7,263.47 1904.4,261.87 1423.7,255.36 1398.4,229 1390,220.25 1395.9,210.18 1405.7,201.37", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1643.4,178", - width=3.015]; + label=string, + pos="1573.4,178", + width=1.0652]; "taxon to taxon association" -> "knowledge source" [color=blue, label="knowledge source", - lp="1802.9,221.5", - pos="e,1667.9,195.78 2360.3,264.76 2176,264.63 1851.7,259.81 1738.4,229 1716.6,223.09 1694.2,211.61 1676.7,201.13", + lp="1562.9,221.5", + pos="e,1543.3,189.28 2143.4,262.75 1928,260.04 1520.3,251.89 1498.4,229 1493.8,224.18 1494.8,219.62 1498.4,214 1502.8,207.12 1518,199.47 \ +1533.6,193.08", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1878.4,178", - width=3.015]; + label=string, + pos="1668.4,178", + width=1.0652]; "taxon to taxon association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="1972.4,221.5", - pos="e,1872.6,196 2363.4,261.13 2188,256.58 1893.8,246.39 1877.4,229 1871.6,222.9 1870.4,214.27 1871,205.9", + lp="1729.4,221.5", + pos="e,1648.1,193.48 2144.7,261.42 1962.7,257.15 1651.7,247.23 1634.4,229 1626.3,220.46 1631.8,209.82 1640.6,200.55", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2113.4,178", - width=3.015]; + label=string, + pos="1810.4,178", + width=1.0652]; "taxon to taxon association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2180.9,221.5", - pos="e,2087.6,195.53 2362.4,261.8 2247.1,258.46 2093.8,250.07 2074.4,229 2066.7,220.62 2071.6,210.86 2080.1,202.2", + lp="1949.9,221.5", + pos="e,1816.9,195.93 2148.9,259.38 2031.1,254.14 1869.2,244.29 1843.4,229 1834,223.44 1826.8,214.03 1821.5,204.86", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2295.4,178", + pos="2037.4,178", width=1.5346]; "taxon to taxon association" -> timepoint [color=blue, label=timepoint, - lp="2332.4,221.5", - pos="e,2291.1,196.26 2379.2,255.75 2342.9,250.63 2309,242.36 2297.4,229 2292,222.83 2290.3,214.43 2290.3,206.27", + lp="2112.4,221.5", + pos="e,2046.6,196.08 2175.8,253.01 2135.5,247.19 2094.5,239.13 2077.4,229 2067.4,223.06 2058.9,213.63 2052.3,204.55", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2407.4,178", + pos="2149.4,178", width=1.0652]; "taxon to taxon association" -> "original subject" [color=blue, label="original subject", - lp="2430.4,221.5", - pos="e,2387.4,193.75 2403.7,251.67 2392.3,246.41 2381.9,239.1 2374.4,229 2367.7,220.01 2372.5,209.73 2380.3,200.83", + lp="2214.4,221.5", + pos="e,2148.2,196.23 2190.8,251.06 2178.5,245.92 2167.1,238.82 2158.4,229 2152.9,222.8 2150.2,214.39 2149,206.23", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2521.4,178", + pos="2274.4,178", width=1.5887]; "taxon to taxon association" -> "original predicate" [color=blue, label="original predicate", - lp="2556.9,221.5", - pos="e,2504.6,195.4 2490.1,246.84 2489.4,236.95 2489.6,224.45 2493.4,214 2494.7,210.42 2496.5,206.94 2498.6,203.64", + lp="2337.9,221.5", + pos="e,2274.4,196.18 2274.4,246.8 2274.4,235.16 2274.4,219.55 2274.4,206.24", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2635.4,178", + pos="2403.4,178", width=1.0652]; "taxon to taxon association" -> "original object" [color=blue, label="original object", - lp="2681.9,221.5", - pos="e,2634.3,196.46 2582.6,251.85 2596.6,246.63 2609.8,239.3 2620.4,229 2626.5,223.04 2630.2,214.69 2632.3,206.52", + lp="2459.9,221.5", + pos="e,2407.8,195.99 2353.2,250.47 2375.5,244.97 2395.5,237.81 2402.4,229 2407.4,222.62 2408.9,214.26 2408.7,206.21", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2768.4,178", + pos="2536.4,178", width=2.1304]; "taxon to taxon association" -> "subject category" [color=blue, label="subject category", - lp="2811.9,221.5", - pos="e,2762.2,196.16 2587,252.37 2653.1,243.92 2730.9,233.26 2737.4,229 2746.2,223.28 2752.9,214.13 2757.8,205.22", + lp="2586.9,221.5", + pos="e,2533.7,196.01 2369,252.44 2433.9,244.15 2509.4,233.66 2515.4,229 2522.8,223.28 2527.6,214.49 2530.7,205.86", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="2939.4,178", + pos="2707.4,178", width=2.1304]; "taxon to taxon association" -> "object category" [color=blue, label="object category", - lp="2956.9,221.5", - pos="e,2923.7,195.62 2585.2,252.19 2601.3,250.33 2617.8,248.52 2633.4,247 2687.1,241.77 2825.1,248.44 2875.4,229 2890.4,223.19 2904.8,\ -212.61 2916.1,202.67", + lp="2728.9,221.5", + pos="e,2693.4,196.09 2367.6,252.18 2383.5,250.33 2399.9,248.52 2415.4,247 2467.5,241.86 2602.1,249.31 2650.4,229 2663.9,223.3 2676.5,\ +213.08 2686.4,203.35", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3072.4,178", + pos="2840.4,178", width=1.0652]; "taxon to taxon association" -> "subject closure" [color=blue, label="subject closure", - lp="3093.9,221.5", - pos="e,3059.6,195.26 2584.1,251.96 2600.5,250.09 2617.4,248.34 2633.4,247 2675.8,243.45 2977,245.11 3016.4,229 3030.2,223.34 3042.9,212.71 \ -3052.7,202.7", + lp="2864.9,221.5", + pos="e,2828.8,195.24 2366.1,251.98 2382.5,250.1 2399.4,248.35 2415.4,247 2456.7,243.51 2750.3,245.43 2788.4,229 2801.5,223.37 2813.2,\ +212.88 2822.2,202.97", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3172.4,178", + pos="2953.4,178", width=1.0652]; "taxon to taxon association" -> "object closure" [color=blue, label="object closure", - lp="3214.4,221.5", - pos="e,3170.3,196.35 2583.3,251.88 2599.9,250 2617.2,248.26 2633.4,247 2662.2,244.77 3128.8,245.59 3152.4,229 3160.1,223.61 3164.8,214.77 \ -3167.7,206.02", + lp="2988.4,221.5", + pos="e,2948,196.06 2365.3,251.89 2381.9,250.01 2399.2,248.26 2415.4,247 2443.5,244.81 2899.1,243.35 2923.4,229 2932.5,223.66 2939.1,214.41 \ +2943.8,205.32", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3305.4,178", + pos="3086.4,178", width=2.1304]; "taxon to taxon association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3372.9,221.5", - pos="e,3297.7,196.19 2582.9,251.84 2599.7,249.95 2617,248.21 2633.4,247 2668.6,244.39 3237.1,245.33 3268.4,229 3278.6,223.7 3286.6,214.2 \ -3292.6,204.9", + lp="3148.9,221.5", + pos="e,3076.5,196.26 2364.9,251.85 2381.7,249.95 2399,248.22 2415.4,247 2450.1,244.41 3010.8,243.81 3042.4,229 3053.7,223.68 3063.3,213.91 \ +3070.7,204.42", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3497.4,178", + pos="3279.4,178", width=2.1304]; "taxon to taxon association" -> "object category closure" [color=blue, label="object category closure", - lp="3563.9,221.5", - pos="e,3491.1,196.16 2582.5,251.8 2599.4,249.89 2616.9,248.17 2633.4,247 2679.5,243.73 3424,251.32 3464.4,229 3474,223.72 3481.2,214.36 \ -3486.5,205.16", + lp="3341.9,221.5", + pos="e,3271.1,196.24 2364.5,251.8 2381.4,249.89 2398.9,248.17 2415.4,247 2461.1,243.75 3199.4,249.56 3240.4,229 3250.8,223.76 3259.3,\ +214.28 3265.7,204.97", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3687.4,178", + pos="3469.4,178", width=1.0652]; "taxon to taxon association" -> "subject namespace" [color=blue, label="subject namespace", - lp="3736.4,221.5", - pos="e,3680.3,195.72 2582.1,251.78 2599.1,249.87 2616.8,248.14 2633.4,247 2689.8,243.11 3601.3,255.23 3651.4,229 3661.6,223.66 3669.6,\ -213.98 3675.4,204.54", + lp="3515.4,221.5", + pos="e,3461.1,195.77 2364.1,251.79 2381.1,249.87 2398.8,248.15 2415.4,247 2471.6,243.12 3378.8,253.86 3429.4,229 3440.2,223.67 3449.1,\ +213.85 3455.7,204.31", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="3846.4,178", + pos="3628.4,178", width=1.0652]; "taxon to taxon association" -> "object namespace" [color=blue, label="object namespace", - lp="3890.4,221.5", - pos="e,3838.7,195.76 2582.1,251.75 2599.1,249.84 2616.8,248.13 2633.4,247 2666,244.79 3779.3,243.73 3808.4,229 3818.9,223.71 3827.2,214.03 \ -3833.4,204.59", + lp="3669.4,221.5", + pos="e,3619.8,195.79 2364.1,251.75 2381.1,249.84 2398.8,248.13 2415.4,247 2447.9,244.8 3558.1,243.15 3587.4,229 3598.4,223.7 3607.4,213.88 \ +3614.2,204.34", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="3997.4,178", + pos="3779.4,178", width=1.0652]; "taxon to taxon association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4050.4,221.5", - pos="e,3989.4,195.78 2582.1,251.73 2599.1,249.82 2616.8,248.11 2633.4,247 2670.1,244.54 3925.4,245.37 3958.4,229 3969.1,223.68 3977.8,\ -213.86 3984.2,204.32", + lp="3831.4,221.5", + pos="e,3770.5,195.81 2364.1,251.73 2381.1,249.82 2398.8,248.11 2415.4,247 2452,244.55 3704.2,244.74 3737.4,229 3748.5,223.72 3757.8,213.9 \ +3764.7,204.36", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4168.4,178", + pos="3950.4,178", width=1.0652]; "taxon to taxon association" -> "object label closure" [color=blue, label="object label closure", - lp="4215.9,221.5", - pos="e,4160.1,195.8 2581.8,251.75 2598.9,249.82 2616.7,248.11 2633.4,247 2674.8,244.26 4091.1,247.22 4128.4,229 4139.3,223.7 4148.1,213.88 \ -4154.7,204.34", + lp="3998.9,221.5", + pos="e,3941.8,195.81 2363.8,251.75 2380.9,249.82 2398.7,248.11 2415.4,247 2456.8,244.26 3872,246.98 3909.4,229 3920.4,223.71 3929.4,213.9 \ +3936.2,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4330.4,178", + pos="4112.4,178", width=2.347]; "taxon to taxon association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4378.9,221.5", - pos="e,4321.5,196.31 2581.8,251.73 2598.9,249.81 2616.7,248.1 2633.4,247 2679.3,243.99 4247.9,248.9 4289.4,229 4300.2,223.79 4309.2,214.18 \ -4315.9,204.77", + lp="4160.9,221.5", + pos="e,4103.8,196.3 2363.8,251.73 2380.9,249.81 2398.7,248.1 2415.4,247 2461.3,243.99 4031,249.16 4072.4,229 4083.1,223.78 4091.9,214.17 \ +4098.4,204.75", style=solid]; type [height=0.5, - pos="4464.4,178", + pos="4246.4,178", width=0.86659]; "taxon to taxon association" -> type [color=blue, label=type, - lp="4478.4,221.5", - pos="e,4465.2,196.18 2581.8,251.72 2598.9,249.8 2616.7,248.09 2633.4,247 2658.6,245.36 4432.6,244.74 4452.4,229 4459.2,223.54 4462.6,\ -214.93 4464.1,206.37", + lp="4260.4,221.5", + pos="e,4247.2,196.18 2363.8,251.72 2380.9,249.8 2398.7,248.09 2415.4,247 2440.6,245.36 4214.6,244.74 4234.4,229 4241.2,223.54 4244.6,\ +214.93 4246.1,206.37", style=solid]; category [height=0.5, - pos="4565.4,178", + pos="4347.4,178", width=1.4263]; "taxon to taxon association" -> category [color=blue, label=category, - lp="4558.9,221.5", - pos="e,4549.8,195.25 2581.8,251.72 2598.9,249.79 2616.7,248.09 2633.4,247 2685.1,243.64 4449.3,245.56 4498.4,229 4514.6,223.53 4530.1,\ -212.51 4542.1,202.2", + lp="4340.9,221.5", + pos="e,4331.8,195.25 2363.8,251.72 2380.9,249.79 2398.7,248.09 2415.4,247 2467.1,243.64 4231.3,245.56 4280.4,229 4296.6,223.53 4312.1,\ +212.51 4324.1,202.2", style=solid]; subject [height=0.5, - pos="4679.4,178", + pos="4461.4,178", width=1.2277]; "taxon to taxon association" -> subject [color=blue, label=subject, - lp="4655.4,221.5", - pos="e,4660.1,194.33 2581.8,251.71 2598.9,249.79 2616.7,248.08 2633.4,247 2742.1,239.97 4489.4,258.11 4594.4,229 4615.1,223.25 4636,211.09 \ -4651.9,200.2", + lp="4437.4,221.5", + pos="e,4442.1,194.33 2363.8,251.71 2380.9,249.79 2398.7,248.08 2415.4,247 2524.1,239.97 4271.4,258.11 4376.4,229 4397.1,223.25 4418,211.09 \ +4433.9,200.2", style=solid]; object [height=0.5, - pos="4722.4,91", + pos="4504.4,91", width=1.0832]; "taxon to taxon association" -> object [color=blue, label=object, - lp="4766.4,178", - pos="e,4735.8,108.09 2581.8,251.71 2598.9,249.78 2616.7,248.08 2633.4,247 2690.3,243.33 4631.1,246.41 4685.4,229 4709.7,221.2 4718,217.1 \ -4732.4,196 4746.3,175.59 4742.5,166.51 4745.4,142 4746.2,135.38 4747.3,133.39 4745.4,127 4744.4,123.55 4742.9,120.13 4741.1,116.85", + lp="4548.4,178", + pos="e,4517.8,108.09 2363.8,251.71 2380.9,249.78 2398.7,248.08 2415.4,247 2472.3,243.33 4413.1,246.41 4467.4,229 4491.7,221.2 4500,217.1 \ +4514.4,196 4528.3,175.59 4524.5,166.51 4527.4,142 4528.2,135.38 4529.3,133.39 4527.4,127 4526.4,123.55 4524.9,120.13 4523.1,116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2680.4,265", + pos="2462.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="2811.4,265", + pos="2593.4,265", width=2.0762]; subject -> object [label=relation, - lp="4717.4,134.5", - pos="e,4704.5,107.23 4680.5,159.55 4681.7,149.57 4684.2,137.07 4689.4,127 4691.6,122.68 4694.5,118.52 4697.7,114.66"]; + lp="4499.4,134.5", + pos="e,4486.5,107.23 4462.5,159.55 4463.7,149.57 4466.2,137.07 4471.4,127 4473.6,122.68 4476.5,118.52 4479.7,114.66"]; relation [height=0.5, - pos="4667.4,18", + pos="4449.4,18", width=1.2999]; - subject -> relation [pos="e,4668.7,36.188 4678.1,159.79 4676,132.48 4672,78.994 4669.5,46.38", + subject -> relation [pos="e,4450.7,36.188 4460.1,159.79 4458,132.48 4454,78.994 4451.5,46.38", style=dotted]; "taxon to taxon association_subject" [color=blue, height=0.5, label="organism taxon", - pos="2987.4,265", + pos="2769.4,265", width=2.3109]; - object -> relation [pos="e,4680.2,35.54 4709.9,73.889 4703,64.939 4694.2,53.617 4686.4,43.584", + object -> relation [pos="e,4462.2,35.54 4491.9,73.889 4485,64.939 4476.2,53.617 4468.4,43.584", style=dotted]; "taxon to taxon association_object" [color=blue, height=0.5, label="organism taxon", - pos="3171.4,265", + pos="2953.4,265", width=2.3109]; } diff --git a/graphviz/taxon_to_taxon_association.svg b/graphviz/taxon_to_taxon_association.svg index b2865df1be..93bf2ae522 100644 --- a/graphviz/taxon_to_taxon_association.svg +++ b/graphviz/taxon_to_taxon_association.svg @@ -4,16 +4,16 @@ - + %3 - + taxon to taxon association - -taxon to taxon association + +taxon to taxon association @@ -24,9 +24,9 @@ taxon to taxon association->association - - -is_a + + +is_a @@ -37,9 +37,9 @@ taxon to taxon association->id - - -id + + +id @@ -50,9 +50,9 @@ taxon to taxon association->iri - - -iri + + +iri @@ -63,9 +63,9 @@ taxon to taxon association->name - - -name + + +name @@ -76,9 +76,9 @@ taxon to taxon association->description - - -description + + +description @@ -89,9 +89,9 @@ taxon to taxon association->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ taxon to taxon association->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ taxon to taxon association->negated - - -negated + + +negated @@ -128,9 +128,9 @@ taxon to taxon association->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ taxon to taxon association->publications - - -publications + + +publications @@ -154,344 +154,344 @@ taxon to taxon association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string taxon to taxon association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string taxon to taxon association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string taxon to taxon association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type taxon to taxon association->timepoint - - -timepoint + + +timepoint original subject - -string + +string taxon to taxon association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie taxon to taxon association->original predicate - - -original predicate + + +original predicate original object - -string + +string taxon to taxon association->original object - - -original object + + +original object subject category - -ontology class + +ontology class taxon to taxon association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class taxon to taxon association->object category - - -object category + + +object category subject closure - -string + +string taxon to taxon association->subject closure - - -subject closure + + +subject closure object closure - -string + +string taxon to taxon association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class taxon to taxon association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class taxon to taxon association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string taxon to taxon association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string taxon to taxon association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string taxon to taxon association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string taxon to taxon association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source taxon to taxon association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type taxon to taxon association->type - - -type + + +type category - -category + +category taxon to taxon association->category - - -category + + +category subject - -subject + +subject taxon to taxon association->subject - - -subject + + +subject object - -object + +object taxon to taxon association->object - - -object + + +object association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + taxon to taxon association_subject - -organism taxon + +organism taxon object->relation - - + + taxon to taxon association_object - -organism taxon + +organism taxon diff --git a/graphviz/transcript_to_gene_relationship.gv b/graphviz/transcript_to_gene_relationship.gv index b13a425a40..93b0e5f560 100644 --- a/graphviz/transcript_to_gene_relationship.gv +++ b/graphviz/transcript_to_gene_relationship.gv @@ -1,16 +1,16 @@ digraph { - graph [bb="0,0,4962.5,283"]; + graph [bb="0,0,4744.5,283"]; node [label="\N"]; "transcript to gene relationship" [height=0.5, label="transcript to gene relationship", - pos="2666.5,265", + pos="2448.5,265", width=4.2607]; "sequence feature relationship" [height=0.5, pos="149.49,178", width=4.1524]; "transcript to gene relationship" -> "sequence feature relationship" [label=is_a, - lp="455.49,221.5", - pos="e,219,194.01 2513.7,262.96 2044.9,259.58 645.91,248 441.49,229 368.99,222.26 287.38,207.69 228.91,196"]; + lp="454.49,221.5", + pos="e,218.76,193.97 2295.1,264.36 1890.2,264.82 799.66,262.79 440.49,229 368.24,222.2 286.91,207.63 228.64,195.97"]; id [color=blue, height=0.5, label=string, @@ -18,9 +18,9 @@ digraph { width=1.0652]; "transcript to gene relationship" -> id [color=blue, label=id, - lp="572.49,221.5", - pos="e,384.47,190 2513.9,263.08 2063.1,260.15 757.01,249.92 565.49,229 492.44,221.02 474.29,215.65 403.49,196 400.38,195.14 397.18,194.17 \ -393.98,193.16", + lp="570.49,221.5", + pos="e,384.47,189.98 2296.1,262.79 1878.2,259.24 733.15,247.91 563.49,229 491.33,220.96 473.43,215.5 403.49,196 400.38,195.13 397.18,\ +194.17 393.98,193.15", style=solid]; iri [color=blue, height=0.5, @@ -29,9 +29,9 @@ digraph { width=1.2277]; "transcript to gene relationship" -> iri [color=blue, label=iri, - lp="689.49,221.5", - pos="e,489.39,190.23 2513.9,262.82 2080.4,259.26 861.36,247.7 681.49,229 604.07,220.95 584.91,215.26 509.49,196 506.11,195.14 502.63,\ -194.18 499.14,193.17", + lp="683.49,221.5", + pos="e,489.4,190.2 2295,264.45 1924.2,264.97 987.02,262.77 675.49,229 600.7,220.89 582.31,214.85 509.49,196 506.11,195.13 502.63,194.16 \ +499.15,193.15", style=solid]; name [color=blue, height=0.5, @@ -40,8 +40,8 @@ digraph { width=1.5707]; "transcript to gene relationship" -> name [color=blue, label=name, - lp="801.49,221.5", - pos="e,614.11,191.15 2513.7,263.03 2095.4,260.12 950.82,250.28 781.49,229 726.67,222.11 665.3,206.11 623.92,194.05", + lp="791.49,221.5", + pos="e,613.28,191.41 2296.1,262.8 1911.2,259.49 919.78,249.1 771.49,229 719.84,222 662.19,206.31 622.87,194.36", style=solid]; description [color=blue, height=0.5, @@ -50,8 +50,8 @@ digraph { width=2.0943]; "transcript to gene relationship" -> description [color=blue, label=description, - lp="929.99,221.5", - pos="e,762.9,193.65 2513.4,263.4 2111.7,261.49 1047.2,254.1 889.49,229 849.13,222.58 804.89,208.66 772.54,197.14", + lp="913.99,221.5", + pos="e,760.28,194.12 2295.6,263.24 1927.2,261.02 1010.7,253.12 873.49,229 837.61,222.69 798.64,209.24 769.7,197.88", style=solid]; "has attribute" [color=blue, height=0.5, @@ -60,8 +60,8 @@ digraph { width=1.4443]; "transcript to gene relationship" -> "has attribute" [color=blue, label="has attribute", - lp="1087.5,221.5", - pos="e,904.07,191.75 2513.9,263.01 2137.2,260.25 1183.3,251.13 1040.5,229 996.35,222.16 947.61,207 913.67,195.15", + lp="1061.5,221.5", + pos="e,900.92,192.67 2296,262.94 1952.4,260.18 1137.7,251.33 1014.5,229 978.27,222.43 938.89,208.24 910.49,196.65", style=solid]; predicate [color=blue, height=0.5, @@ -70,8 +70,8 @@ digraph { width=2.1665]; "transcript to gene relationship" -> predicate [color=blue, label=predicate, - lp="1248.5,221.5", - pos="e,1061.9,193.09 2512.9,264.68 2192.4,265.37 1461.3,263.01 1214.5,229 1165.3,222.22 1110.6,207.65 1071.5,195.99", + lp="1205.5,221.5", + pos="e,1054.5,194.06 2296.7,262.29 1982.2,258.4 1279.5,247.72 1171.5,229 1134.3,222.56 1093.9,209.02 1063.9,197.66", style=solid]; negated [color=blue, height=0.5, @@ -80,8 +80,8 @@ digraph { width=1.2999]; "transcript to gene relationship" -> negated [color=blue, label=negated, - lp="1394.5,221.5", - pos="e,1196.4,190.23 2513.4,263.55 2218.8,262.07 1583.2,255.78 1365.5,229 1309.6,222.13 1247,205.38 1206.1,193.16", + lp="1325.5,221.5", + pos="e,1189.7,192.51 2297,262.13 2006.6,258.14 1391.9,247.61 1296.5,229 1262.4,222.36 1225.6,208.2 1199,196.64", style=solid]; qualifiers [color=blue, height=0.5, @@ -90,8 +90,8 @@ digraph { width=2.1304]; "transcript to gene relationship" -> qualifiers [color=blue, label=qualifiers, - lp="1531,221.5", - pos="e,1345.7,193.02 2513.4,263.62 2242.4,262.23 1688.9,256.07 1497.5,229 1448.7,222.11 1394.6,207.65 1355.7,196.05", + lp="1429,221.5", + pos="e,1325.7,195.39 2296.1,262.78 2025.2,260.04 1479.9,251.74 1395.5,229 1373.8,223.15 1351.5,211.43 1334.2,200.81", style=solid]; publications [color=blue, height=0.5, @@ -100,8 +100,8 @@ digraph { width=1.7332]; "transcript to gene relationship" -> publications [color=blue, label=publications, - lp="1673.5,221.5", - pos="e,1496,192.66 2513.4,263.56 2267.4,262.06 1794.9,255.67 1629.5,229 1586.6,222.09 1539.4,207.61 1505.6,196.01", + lp="1520.5,221.5", + pos="e,1460.5,196.26 2296,263.01 2030.6,260.65 1508.7,252.98 1476.5,229 1469.2,223.57 1465,214.84 1462.6,206.19", style=solid]; "has evidence" [color=blue, height=0.5, @@ -110,264 +110,265 @@ digraph { width=2.0943]; "transcript to gene relationship" -> "has evidence" [color=blue, label="has evidence", - lp="1827,221.5", - pos="e,1653.5,193.55 2514.3,262.66 2299.1,259.95 1917,251.99 1780.5,229 1740.1,222.2 1695.7,208.38 1663.2,196.99", + lp="1619,221.5", + pos="e,1587.9,194.93 2295.3,263.32 2050.8,261.47 1597.1,254.59 1572.5,229 1564.1,220.25 1570,210.18 1579.8,201.37", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1817.5,178", - width=3.015]; + label=string, + pos="1747.5,178", + width=1.0652]; "transcript to gene relationship" -> "knowledge source" [color=blue, label="knowledge source", - lp="1977,221.5", - pos="e,1842,195.78 2513,264.72 2326,264.23 2021.6,258.65 1912.5,229 1890.7,223.09 1868.3,211.61 1850.8,201.13", + lp="1737,221.5", + pos="e,1717.4,189.28 2296.3,262.47 2076.4,259.5 1693.7,251.16 1672.5,229 1667.9,224.18 1668.9,219.62 1672.5,214 1676.9,207.12 1692.1,\ +199.47 1707.7,193.08", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2052.5,178", - width=3.015]; + label=string, + pos="1842.5,178", + width=1.0652]; "transcript to gene relationship" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2146.5,221.5", - pos="e,2046.7,196 2517.6,260.6 2340.7,255.81 2067.3,245.75 2051.5,229 2045.7,222.9 2044.5,214.27 2045.1,205.9", + lp="1903.5,221.5", + pos="e,1822.2,193.48 2298.7,260.94 2114.8,256.43 1825.1,246.57 1808.5,229 1800.4,220.46 1805.9,209.82 1814.7,200.55", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2287.5,178", - width=3.015]; + label=string, + pos="1984.5,178", + width=1.0652]; "transcript to gene relationship" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2355,221.5", - pos="e,2261.7,195.53 2516.4,261.18 2404,257.46 2266.8,248.87 2248.5,229 2240.8,220.62 2245.7,210.86 2254.2,202.2", + lp="2124,221.5", + pos="e,1991,195.93 2305,258.56 2189.4,253.14 2042,243.53 2017.5,229 2008.1,223.44 2000.8,214.03 1995.6,204.86", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2469.5,178", + pos="2210.5,178", width=1.5346]; "transcript to gene relationship" -> timepoint [color=blue, label=timepoint, - lp="2506.5,221.5", - pos="e,2465.2,196.26 2543.3,254.25 2510.9,249.06 2482,241.12 2471.5,229 2466.1,222.83 2464.4,214.43 2464.4,206.27", + lp="2286.5,221.5", + pos="e,2220.1,196.09 2321.1,254.94 2296.9,249.53 2272.5,241.33 2251.5,229 2241.4,223.07 2232.7,213.64 2225.9,204.56", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2581.5,178", + pos="2322.5,178", width=1.0652]; "transcript to gene relationship" -> "original subject" [color=blue, label="original subject", - lp="2604.5,221.5", - pos="e,2561.4,193.75 2575.2,250.43 2564.8,245.28 2555.5,238.33 2548.5,229 2541.8,220.01 2546.6,209.73 2554.4,200.83", + lp="2388.5,221.5", + pos="e,2321.7,196.26 2363,250.04 2351.5,245 2340.8,238.19 2332.5,229 2326.9,222.83 2324,214.43 2322.7,206.27", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2695.5,178", + pos="2448.5,178", width=1.5887]; "transcript to gene relationship" -> "original predicate" [color=blue, label="original predicate", - lp="2731,221.5", - pos="e,2678.7,195.4 2664.1,246.84 2663.5,236.95 2663.7,224.45 2667.5,214 2668.8,210.42 2670.6,206.94 2672.7,203.64", + lp="2512,221.5", + pos="e,2448.5,196.18 2448.5,246.8 2448.5,235.16 2448.5,219.55 2448.5,206.24", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2809.5,178", + pos="2577.5,178", width=1.0652]; "transcript to gene relationship" -> "original object" [color=blue, label="original object", - lp="2856,221.5", - pos="e,2808.4,196.46 2759.9,250.58 2772.7,245.47 2784.8,238.49 2794.5,229 2800.6,223.04 2804.2,214.69 2806.4,206.52", + lp="2634,221.5", + pos="e,2581.9,195.99 2530.4,249.69 2551.4,244.31 2569.9,237.4 2576.5,229 2581.5,222.62 2582.9,214.26 2582.8,206.21", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="2942.5,178", + pos="2710.5,178", width=2.1304]; "transcript to gene relationship" -> "subject category" [color=blue, label="subject category", - lp="2986,221.5", - pos="e,2936.3,196.16 2777.3,252.5 2836.6,245.58 2899.8,236.65 2911.5,229 2920.2,223.28 2927,214.13 2931.9,205.22", + lp="2761,221.5", + pos="e,2707.8,196.01 2561,252.71 2618.5,246.03 2678.8,237.28 2689.5,229 2696.9,223.28 2701.7,214.49 2704.8,205.86", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3113.5,178", + pos="2881.5,178", width=2.1304]; "transcript to gene relationship" -> "object category" [color=blue, label="object category", - lp="3131,221.5", - pos="e,3097.6,195.83 2775.6,252.28 2793.6,250.44 2812.1,248.62 2829.5,247 2878.3,242.46 3003.8,246.85 3049.5,229 3064.4,223.18 3078.7,\ -212.7 3089.9,202.83", + lp="2903,221.5", + pos="e,2867.4,196.05 2557.6,252.32 2575.6,250.48 2594.1,248.64 2611.5,247 2658.8,242.54 2780.8,247.59 2824.5,229 2838,223.25 2850.6,213.02 \ +2860.4,203.3", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3246.5,178", + pos="3014.5,178", width=1.0652]; "transcript to gene relationship" -> "subject closure" [color=blue, label="subject closure", - lp="3268,221.5", - pos="e,3233.7,195.25 2773.4,252.02 2792.1,250.16 2811.3,248.4 2829.5,247 2869.5,243.92 3153.3,244.24 3190.5,229 3204.3,223.32 3217,212.69 \ -3226.8,202.68", + lp="3039,221.5", + pos="e,3002.8,195.22 2555.4,252.04 2574.1,250.18 2593.3,248.41 2611.5,247 2650.4,243.97 2926.6,244.51 2962.5,229 2975.5,223.35 2987.3,\ +212.86 2996.2,202.95", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3346.5,178", + pos="3127.5,178", width=1.0652]; "transcript to gene relationship" -> "object closure" [color=blue, label="object closure", - lp="3388.5,221.5", - pos="e,3344.4,196.34 2772.1,251.94 2791.1,250.05 2810.9,248.3 2829.5,247 2857,245.07 3303.9,244.9 3326.5,229 3334.2,223.6 3338.9,214.77 \ -3341.8,206.01", + lp="3162.5,221.5", + pos="e,3122.1,196.05 2554.5,251.91 2573.5,250.04 2593,248.3 2611.5,247 2665.4,243.2 3051,256.49 3097.5,229 3106.5,223.65 3113.2,214.4 \ +3117.9,205.31", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3479.5,178", + pos="3260.5,178", width=2.1304]; "transcript to gene relationship" -> "subject category closure" [color=blue, label="subject category closure", - lp="3547,221.5", - pos="e,3471.8,196.18 2771.6,251.87 2790.8,249.99 2810.8,248.25 2829.5,247 2863.5,244.73 3412.3,244.78 3442.5,229 3452.6,223.69 3460.7,\ -214.2 3466.7,204.9", + lp="3323,221.5", + pos="e,3250.6,196.25 2553.6,251.88 2572.8,249.99 2592.8,248.25 2611.5,247 2645,244.75 3186.1,243.31 3216.5,229 3227.8,223.67 3237.4,213.91 \ +3244.8,204.41", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3671.5,178", + pos="3453.5,178", width=2.1304]; "transcript to gene relationship" -> "object category closure" [color=blue, label="object category closure", - lp="3738,221.5", - pos="e,3665.2,196.16 2771.2,251.81 2790.5,249.91 2810.6,248.19 2829.5,247 2874.4,244.17 3599.1,250.74 3638.5,229 3648,223.72 3655.3,214.36 \ -3660.6,205.15", + lp="3516,221.5", + pos="e,3445.2,196.23 2553.2,251.81 2572.5,249.92 2592.6,248.19 2611.5,247 2656,244.18 3374.6,249.03 3414.5,229 3424.9,223.76 3433.4,214.27 \ +3439.8,204.96", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="3861.5,178", + pos="3643.5,178", width=1.0652]; "transcript to gene relationship" -> "subject namespace" [color=blue, label="subject namespace", - lp="3910.5,221.5", - pos="e,3854.4,195.72 2770.7,251.78 2790.2,249.88 2810.5,248.16 2829.5,247 2884.7,243.63 3776.5,254.67 3825.5,229 3835.7,223.66 3843.7,\ -213.97 3849.5,204.54", + lp="3689.5,221.5", + pos="e,3635.2,195.77 2552.7,251.79 2572.2,249.88 2592.5,248.16 2611.5,247 2666.5,243.64 3554,253.33 3603.5,229 3614.3,223.67 3623.2,213.84 \ +3629.8,204.31", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4020.5,178", + pos="3802.5,178", width=1.0652]; "transcript to gene relationship" -> "object namespace" [color=blue, label="object namespace", - lp="4064.5,221.5", - pos="e,4012.8,195.76 2770.7,251.75 2790.2,249.85 2810.5,248.14 2829.5,247 2861.5,245.09 3953.9,243.46 3982.5,229 3993,223.7 4001.3,214.03 \ -4007.5,204.59", + lp="3843.5,221.5", + pos="e,3793.9,195.79 2552.7,251.75 2572.2,249.85 2592.5,248.14 2611.5,247 2643.4,245.09 3732.7,242.89 3761.5,229 3772.5,223.69 3781.5,\ +213.88 3788.3,204.34", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4171.5,178", + pos="3953.5,178", width=1.0652]; "transcript to gene relationship" -> "subject label closure" [color=blue, label="subject label closure", - lp="4224.5,221.5", - pos="e,4163.5,195.78 2770.7,251.72 2790.2,249.82 2810.5,248.12 2829.5,247 2865.6,244.87 4100.1,245.11 4132.5,229 4143.2,223.67 4151.9,\ -213.85 4158.3,204.32", + lp="4005.5,221.5", + pos="e,3944.6,195.81 2552.7,251.72 2572.2,249.82 2592.5,248.12 2611.5,247 2647.5,244.87 3878.9,244.48 3911.5,229 3922.6,223.72 3931.9,\ +213.9 3938.8,204.36", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4342.5,178", + pos="4124.5,178", width=1.0652]; "transcript to gene relationship" -> "object label closure" [color=blue, label="object label closure", - lp="4390,221.5", - pos="e,4334.2,195.8 2770.3,251.74 2789.9,249.82 2810.3,248.11 2829.5,247 2870.3,244.63 4265.7,246.95 4302.5,229 4313.3,223.7 4322.2,213.88 \ -4328.8,204.34", + lp="4173,221.5", + pos="e,4115.9,195.81 2552.3,251.74 2571.9,249.82 2592.3,248.11 2611.5,247 2652.3,244.63 4046.6,246.72 4083.5,229 4094.5,223.71 4103.5,\ +213.9 4110.3,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4504.5,178", + pos="4286.5,178", width=2.347]; "transcript to gene relationship" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4553,221.5", - pos="e,4495.6,196.31 2770.3,251.72 2789.9,249.81 2810.3,248.1 2829.5,247 2874.8,244.39 4422.6,248.64 4463.5,229 4474.3,223.79 4483.3,\ -214.18 4490,204.77", + lp="4335,221.5", + pos="e,4277.9,196.29 2552.3,251.72 2571.9,249.81 2592.3,248.1 2611.5,247 2656.8,244.39 4205.7,248.9 4246.5,229 4257.2,223.78 4266,214.16 \ +4272.5,204.75", style=solid]; type [height=0.5, - pos="4638.5,178", + pos="4420.5,178", width=0.86659]; "transcript to gene relationship" -> type [color=blue, label=type, - lp="4652.5,221.5", - pos="e,4639.3,196.18 2770.3,251.7 2789.9,249.79 2810.3,248.09 2829.5,247 2854.4,245.58 4607,244.55 4626.5,229 4633.3,223.54 4636.7,214.93 \ -4638.2,206.37", + lp="4434.5,221.5", + pos="e,4421.3,196.18 2552.3,251.7 2571.9,249.79 2592.3,248.09 2611.5,247 2636.4,245.58 4389,244.55 4408.5,229 4415.3,223.54 4418.7,214.93 \ +4420.2,206.37", style=solid]; category [height=0.5, - pos="4739.5,178", + pos="4521.5,178", width=1.4263]; "transcript to gene relationship" -> category [color=blue, label=category, - lp="4733,221.5", - pos="e,4723.9,195.25 2770.3,251.7 2789.9,249.79 2810.3,248.09 2829.5,247 2880.6,244.09 4624,245.37 4672.5,229 4688.7,223.53 4704.2,212.51 \ -4716.2,202.2", + lp="4515,221.5", + pos="e,4505.9,195.25 2552.3,251.7 2571.9,249.79 2592.3,248.09 2611.5,247 2662.6,244.09 4406,245.37 4454.5,229 4470.7,223.53 4486.2,212.51 \ +4498.2,202.2", style=solid]; subject [height=0.5, - pos="4853.5,178", + pos="4635.5,178", width=1.2277]; "transcript to gene relationship" -> subject [color=blue, label=subject, - lp="4829.5,221.5", - pos="e,4834.2,194.33 2770.3,251.69 2789.9,249.78 2810.3,248.09 2829.5,247 2937,240.91 4664.7,257.79 4768.5,229 4789.2,223.25 4810.1,211.09 \ -4826,200.2", + lp="4611.5,221.5", + pos="e,4616.2,194.33 2552.3,251.69 2571.9,249.78 2592.3,248.09 2611.5,247 2719,240.91 4446.7,257.79 4550.5,229 4571.2,223.25 4592.1,211.09 \ +4608,200.2", style=solid]; object [height=0.5, - pos="4896.5,91", + pos="4678.5,91", width=1.0832]; "transcript to gene relationship" -> object [color=blue, label=object, - lp="4940.5,178", - pos="e,4909.9,108.09 2770.3,251.68 2789.9,249.78 2810.3,248.08 2829.5,247 2885.8,243.82 4805.8,246.23 4859.5,229 4883.8,221.2 4892.1,\ -217.1 4906.5,196 4920.4,175.59 4916.6,166.51 4919.5,142 4920.3,135.38 4921.4,133.39 4919.5,127 4918.5,123.55 4917,120.13 4915.2,\ + lp="4722.5,178", + pos="e,4691.9,108.09 2552.3,251.68 2571.9,249.78 2592.3,248.08 2611.5,247 2667.8,243.82 4587.8,246.23 4641.5,229 4665.8,221.2 4674.1,\ +217.1 4688.5,196 4702.4,175.59 4698.6,166.51 4701.5,142 4702.3,135.38 4703.4,133.39 4701.5,127 4700.5,123.55 4699,120.13 4697.2,\ 116.85", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="2876.5,265", + pos="2658.5,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3007.5,265", + pos="2789.5,265", width=2.0762]; subject -> object [label=relation, - lp="4891.5,134.5", - pos="e,4878.6,107.23 4854.6,159.55 4855.8,149.57 4858.3,137.07 4863.5,127 4865.7,122.68 4868.6,118.52 4871.8,114.66"]; + lp="4673.5,134.5", + pos="e,4660.6,107.23 4636.6,159.55 4637.8,149.57 4640.3,137.07 4645.5,127 4647.7,122.68 4650.6,118.52 4653.8,114.66"]; relation [height=0.5, - pos="4841.5,18", + pos="4623.5,18", width=1.2999]; - subject -> relation [pos="e,4842.8,36.188 4852.2,159.79 4850.1,132.48 4846,78.994 4843.6,46.38", + subject -> relation [pos="e,4624.8,36.188 4634.2,159.79 4632.1,132.48 4628,78.994 4625.6,46.38", style=dotted]; "transcript to gene relationship_subject" [color=blue, height=0.5, label=transcript, - pos="3157.5,265", + pos="2939.5,265", width=1.5887]; - object -> relation [pos="e,4854.3,35.54 4884,73.889 4877.1,64.939 4868.3,53.617 4860.5,43.584", + object -> relation [pos="e,4636.3,35.54 4666,73.889 4659.1,64.939 4650.3,53.617 4642.5,43.584", style=dotted]; "transcript to gene relationship_object" [color=blue, height=0.5, label=gene, - pos="3265.5,265", + pos="3047.5,265", width=0.92075]; } diff --git a/graphviz/transcript_to_gene_relationship.svg b/graphviz/transcript_to_gene_relationship.svg index b8e3373a35..b1eaf1c077 100644 --- a/graphviz/transcript_to_gene_relationship.svg +++ b/graphviz/transcript_to_gene_relationship.svg @@ -4,16 +4,16 @@ - + %3 - + transcript to gene relationship - -transcript to gene relationship + +transcript to gene relationship @@ -24,9 +24,9 @@ transcript to gene relationship->sequence feature relationship - - -is_a + + +is_a @@ -37,9 +37,9 @@ transcript to gene relationship->id - - -id + + +id @@ -50,9 +50,9 @@ transcript to gene relationship->iri - - -iri + + +iri @@ -63,9 +63,9 @@ transcript to gene relationship->name - - -name + + +name @@ -76,9 +76,9 @@ transcript to gene relationship->description - - -description + + +description @@ -89,9 +89,9 @@ transcript to gene relationship->has attribute - - -has attribute + + +has attribute @@ -102,9 +102,9 @@ transcript to gene relationship->predicate - - -predicate + + +predicate @@ -115,9 +115,9 @@ transcript to gene relationship->negated - - -negated + + +negated @@ -128,9 +128,9 @@ transcript to gene relationship->qualifiers - - -qualifiers + + +qualifiers @@ -141,9 +141,9 @@ transcript to gene relationship->publications - - -publications + + +publications @@ -154,344 +154,344 @@ transcript to gene relationship->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string transcript to gene relationship->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string transcript to gene relationship->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string transcript to gene relationship->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type transcript to gene relationship->timepoint - - -timepoint + + +timepoint original subject - -string + +string transcript to gene relationship->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie transcript to gene relationship->original predicate - - -original predicate + + +original predicate original object - -string + +string transcript to gene relationship->original object - - -original object + + +original object subject category - -ontology class + +ontology class transcript to gene relationship->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class transcript to gene relationship->object category - - -object category + + +object category subject closure - -string + +string transcript to gene relationship->subject closure - - -subject closure + + +subject closure object closure - -string + +string transcript to gene relationship->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class transcript to gene relationship->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class transcript to gene relationship->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string transcript to gene relationship->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string transcript to gene relationship->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string transcript to gene relationship->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string transcript to gene relationship->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source transcript to gene relationship->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type transcript to gene relationship->type - - -type + + +type category - -category + +category transcript to gene relationship->category - - -category + + +category subject - -subject + +subject transcript to gene relationship->subject - - -subject + + +subject object - -object + +object transcript to gene relationship->object - - -object + + +object association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + transcript to gene relationship_subject - -transcript + +transcript object->relation - - + + transcript to gene relationship_object - -gene + +gene diff --git a/graphviz/variant_as_a_model_of_disease_association.gv b/graphviz/variant_as_a_model_of_disease_association.gv index 17afe69b65..0e282786a0 100644 --- a/graphviz/variant_as_a_model_of_disease_association.gv +++ b/graphviz/variant_as_a_model_of_disease_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,6090.4,283"]; + graph [bb="0,0,5872.4,283"]; node [label="\N"]; "variant as a model of disease association" [height=0.5, label="variant as a model of disease association", - pos="3424.2,265", + pos="3206.2,265", width=5.5606]; "variant to disease association" [height=0.5, pos="148.19,178", width=4.1163]; "variant as a model of disease association" -> "variant to disease association" [label=is_a, - lp="798.19,221.5", - pos="e,252.43,190.86 3225.1,262.79 2695.2,259.36 1258.8,248.48 784.19,229 570.97,220.25 517.75,214.82 305.19,196 291.45,194.78 277.05,\ + lp="797.19,221.5", + pos="e,252.43,190.86 3005.8,264.79 2590.9,265.63 1607.6,263.39 783.19,229 570.42,220.13 517.31,214.8 305.19,196 291.45,194.78 277.05,\ 193.39 262.78,191.93"]; "model to disease association mixin" [height=0.5, pos="486.19,178", width=4.7843]; "variant as a model of disease association" -> "model to disease association mixin" [label=uses, - lp="1015.7,221.5", - pos="e,593.58,192.08 3224.7,263.25 2725.1,261.03 1430,253.06 999.19,229 863.22,221.41 707.62,205.17 603.78,193.25"]; + lp="1014.7,221.5", + pos="e,593.87,192.09 3007.1,262.92 2540.3,260.07 1385.5,250.94 998.19,229 862.7,221.32 707.69,205.15 604.05,193.26"]; "entity to disease association mixin" [height=0.5, pos="847.19,178", width=4.7482]; "variant as a model of disease association" -> "entity to disease association mixin" [label=uses, - lp="1170.7,221.5", - pos="e,921.56,194.24 3223.8,264.66 2746.6,265.64 1552.7,264.33 1154.2,229 1078.4,222.28 993.03,207.81 931.59,196.16"]; + lp="1169.7,221.5", + pos="e,921.63,194.27 3005.8,264.28 2562.2,264.31 1508.3,260.87 1153.2,229 1077.8,222.23 992.84,207.8 931.63,196.18"]; id [color=blue, height=0.5, label=string, @@ -31,9 +31,9 @@ digraph { width=1.0652]; "variant as a model of disease association" -> id [color=blue, label=id, - lp="1288.2,221.5", - pos="e,1103.2,189.98 3225,262.89 2730.1,259.82 1470.7,250.02 1281.2,229 1209.5,221.04 1191.7,215.43 1122.2,196 1119.1,195.13 1115.9,194.17 \ -1112.7,193.15", + lp="1287.2,221.5", + pos="e,1103.2,189.97 3007.7,262.51 2550.2,258.76 1448,247.88 1280.2,229 1208.9,220.98 1191.3,215.35 1122.2,196 1119.1,195.13 1115.9,194.16 \ +1112.7,193.14", style=solid]; iri [color=blue, height=0.5, @@ -42,9 +42,9 @@ digraph { width=1.2277]; "variant as a model of disease association" -> iri [color=blue, label=iri, - lp="1401.2,221.5", - pos="e,1208.1,190.19 3225.5,262.61 2749.7,259 1571.6,248.22 1393.2,229 1318.8,220.99 1300.6,214.78 1228.2,196 1224.8,195.12 1221.3,194.16 \ -1217.8,193.14", + lp="1392.2,221.5", + pos="e,1208.1,190.13 3008.2,262.31 2569.5,258.27 1541.7,247.01 1384.2,229 1313.8,220.95 1296.7,214.18 1228.2,196 1224.8,195.11 1221.3,\ +194.12 1217.9,193.1", style=solid]; name [color=blue, height=0.5, @@ -53,8 +53,8 @@ digraph { width=1.5707]; "variant as a model of disease association" -> name [color=blue, label=name, - lp="1508.2,221.5", - pos="e,1331.9,191.54 3225,263.04 2765.2,260.45 1656.5,251.88 1488.2,229 1437.4,222.09 1380.8,206.58 1341.9,194.65", + lp="1494.2,221.5", + pos="e,1330.5,191.99 3007.3,262.78 2584.3,259.79 1622,250.68 1474.2,229 1427.7,222.18 1376.2,207.07 1340.2,195.23", style=solid]; description [color=blue, height=0.5, @@ -63,8 +63,8 @@ digraph { width=2.0943]; "variant as a model of disease association" -> description [color=blue, label=description, - lp="1628.7,221.5", - pos="e,1478,194.15 3224.5,263.74 2782,262.64 1745.5,257.07 1588.2,229 1553.3,222.78 1515.6,209.42 1487.5,198.07", + lp="1605.7,221.5", + pos="e,1473.5,194.75 3006.4,263.87 2599.7,262.99 1702.5,257.78 1565.2,229 1536.4,222.98 1505.9,210.3 1482.7,199.22", style=solid]; "has attribute" [color=blue, height=0.5, @@ -73,8 +73,8 @@ digraph { width=1.4443]; "variant as a model of disease association" -> "has attribute" [color=blue, label="has attribute", - lp="1774.2,221.5", - pos="e,1618.8,192.95 3224.4,263.54 2807.3,262.04 1870.6,255.7 1727.2,229 1692.7,222.58 1655.4,208.62 1628.3,197.07", + lp="1737.2,221.5", + pos="e,1612.5,194.25 3006.2,264.21 2623.4,263.9 1814.4,259.57 1690.2,229 1665.7,222.98 1640.4,210.39 1621.2,199.35", style=solid]; negated [color=blue, height=0.5, @@ -83,8 +83,8 @@ digraph { width=1.2999]; "variant as a model of disease association" -> negated [color=blue, label=negated, - lp="1929.2,221.5", - pos="e,1740,190.46 3224,264.62 2870.6,264.84 2150,261.15 1900.2,229 1847.6,222.23 1788.9,205.81 1750,193.62", + lp="1869.2,221.5", + pos="e,1734.1,192.55 3007.9,262.54 2656.6,259.42 1951.4,250.54 1840.2,229 1806.3,222.44 1769.7,208.27 1743.4,196.69", style=solid]; qualifiers [color=blue, height=0.5, @@ -93,8 +93,8 @@ digraph { width=2.1304]; "variant as a model of disease association" -> qualifiers [color=blue, label=qualifiers, - lp="2067.7,221.5", - pos="e,1888.9,193.2 3223.7,264.76 2895.4,265.04 2257.4,261.19 2034.2,229 1987.5,222.26 1935.7,207.87 1898.5,196.25", + lp="1972.7,221.5", + pos="e,1870.1,195.43 3006.3,263.59 2675.1,262.14 2039,255.85 1939.2,229 1917.7,223.21 1895.6,211.5 1878.6,200.86", style=solid]; publications [color=blue, height=0.5, @@ -103,8 +103,8 @@ digraph { width=1.7332]; "variant as a model of disease association" -> publications [color=blue, label=publications, - lp="2213.2,221.5", - pos="e,2039.9,192.85 3224,264.89 2922.4,265.12 2366,260.97 2169.2,229 2127.8,222.28 2082.3,207.95 2049.6,196.35", + lp="2064.2,221.5", + pos="e,2004.8,196.25 3006.2,264.06 2678.3,263.33 2058.8,258.07 2020.2,229 2013,223.56 2008.9,214.83 2006.7,206.18", style=solid]; "has evidence" [color=blue, height=0.5, @@ -113,308 +113,309 @@ digraph { width=2.0943]; "variant as a model of disease association" -> "has evidence" [color=blue, label="has evidence", - lp="2371.7,221.5", - pos="e,2198.2,193.63 3224.1,263.9 2955.4,262.68 2492.2,256.48 2325.2,229 2284.8,222.35 2240.4,208.52 2207.9,197.09", + lp="2162.7,221.5", + pos="e,2132.1,194.88 3006,264.67 2699.7,264.7 2146.6,260.38 2116.2,229 2107.6,220.11 2113.9,209.91 2124.1,201.06", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2362.2,178", - width=3.015]; + label=string, + pos="2292.2,178", + width=1.0652]; "variant as a model of disease association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2526.7,221.5", - pos="e,2387.7,195.61 3228,261.31 2968.1,257.07 2534,247.34 2462.2,229 2439.1,223.1 2415.1,211.34 2396.4,200.71", + lp="2280.7,221.5", + pos="e,2261.7,189.23 3006.3,263.95 2724.9,262.88 2243.2,256.94 2216.2,229 2211.6,224.2 2212.6,219.61 2216.2,214 2220.7,207 2236.4,199.25 \ +2252.3,192.84", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2597.2,178", - width=3.015]; + label=string, + pos="2387.2,178", + width=1.0652]; "variant as a model of disease association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2698.2,221.5", - pos="e,2594.2,196.33 3226.8,261.94 2991.2,258.54 2625.8,249.92 2603.2,229 2597.1,223.32 2594.7,214.91 2594.1,206.59", + lp="2447.2,221.5", + pos="e,2366.6,193.24 3007.4,262.71 2762.1,260.11 2374.6,252.32 2352.2,229 2343.8,220.29 2349.8,209.43 2359.1,200.05", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2832.2,178", - width=3.015]; + label=string, + pos="2529.2,178", + width=1.0652]; "variant as a model of disease association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2906.7,221.5", - pos="e,2810.4,195.87 3233,259.58 3055.1,254.5 2815.1,244.77 2800.2,229 2793,221.43 2796.5,212.05 2803.3,203.46", + lp="2667.7,221.5", + pos="e,2535.3,196.02 3008.1,262.29 2832.8,259.3 2599.2,251.15 2561.2,229 2551.9,223.61 2544.9,214.35 2539.9,205.26", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="3014.2,178", + pos="2756.2,178", width=1.5346]; "variant as a model of disease association" -> timepoint [color=blue, label=timepoint, - lp="3061.2,221.5", - pos="e,3013.6,196.43 3241.7,257.58 3145.2,252.48 3043.2,243.69 3026.2,229 3019.6,223.36 3016.3,214.85 3014.7,206.44", + lp="2830.2,221.5", + pos="e,2764.6,195.97 3008.8,261.99 2922.4,258.12 2832.3,249.11 2795.2,229 2784.9,223.43 2776.5,213.89 2770.1,204.63", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="3126.2,178", + pos="2868.2,178", width=1.0652]; "variant as a model of disease association" -> "original subject" [color=blue, label="original subject", - lp="3159.2,221.5", - pos="e,3110.4,194.82 3255.4,255.26 3183.9,249.78 3114.3,241.36 3103.2,229 3096.5,221.56 3099.1,211.86 3104.6,202.98", + lp="2933.2,221.5", + pos="e,2866.5,196.27 3039.3,254.97 2964.4,249.34 2889.9,240.86 2877.2,229 2871,223.25 2868.2,214.83 2867.1,206.52", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3240.2,178", + pos="2993.2,178", width=1.5887]; "variant as a model of disease association" -> "original predicate" [color=blue, label="original predicate", - lp="3285.7,221.5", - pos="e,3226.4,195.8 3281,252.37 3253.9,247.21 3231.2,239.76 3222.2,229 3216.3,222.05 3217.6,213.06 3221.5,204.62", + lp="3063.7,221.5", + pos="e,2990.9,196.02 3064.4,252.26 3035.4,247.09 3010.5,239.67 3000.2,229 2994.3,222.99 2991.9,214.49 2991.1,206.2", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3354.2,178", + pos="3122.2,178", width=1.0652]; "variant as a model of disease association" -> "original object" [color=blue, label="original object", - lp="3409.7,221.5", - pos="e,3351.6,196.07 3378.2,247.43 3370.4,242.64 3363.2,236.59 3358.2,229 3353.8,222.32 3352,214 3351.6,206.08", + lp="3191.7,221.5", + pos="e,3125.1,196.35 3163.4,247.27 3154.9,242.4 3146.6,236.35 3140.2,229 3134.6,222.53 3130.7,214.18 3128,206.16", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3487.2,178", + pos="3255.2,178", width=2.1304]; "variant as a model of disease association" -> "subject category" [color=blue, label="subject category", - lp="3533.7,221.5", - pos="e,3481.8,196.22 3447.6,247.1 3453.9,241.81 3460.3,235.61 3465.2,229 3470.4,221.97 3474.7,213.49 3478.1,205.54", + lp="3312.7,221.5", + pos="e,3255.3,196.17 3231.6,247.12 3237.6,241.98 3243.3,235.86 3247.2,229 3251,222.15 3253.2,213.99 3254.3,206.26", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3658.2,178", + pos="3426.2,178", width=2.1304]; "variant as a model of disease association" -> "object category" [color=blue, label="object category", - lp="3676.7,221.5", - pos="e,3642.1,195.91 3534.8,249.98 3556.1,244.98 3577.8,238.2 3597.2,229 3610.8,222.54 3624,212.41 3634.6,202.94", + lp="3452.7,221.5", + pos="e,3413.6,195.95 3320.1,250.14 3339.5,245.12 3358.9,238.29 3376.2,229 3387.8,222.72 3398.5,212.86 3407,203.55", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3791.2,178", + pos="3559.2,178", width=1.0652]; "variant as a model of disease association" -> "subject closure" [color=blue, label="subject closure", - lp="3813.7,221.5", - pos="e,3778.1,195.42 3565.2,252.18 3640.2,245.18 3720.1,236.29 3736.2,229 3749.4,223.04 3761.5,212.72 3771.1,203", + lp="3586.7,221.5", + pos="e,3548.5,195.4 3347.7,252.26 3420.4,245.42 3496.9,236.67 3512.2,229 3523.9,223.13 3534.2,213.1 3542.2,203.55", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3890.2,178", + pos="3672.2,178", width=1.0652]; "variant as a model of disease association" -> "object closure" [color=blue, label="object closure", - lp="3934.2,221.5", - pos="e,3888.7,196.16 3566.8,252.35 3589.3,250.54 3612.4,248.71 3634.2,247 3660.6,244.93 3851.1,245.06 3872.2,229 3879.5,223.46 3883.8,\ -214.71 3886.4,206.06", + lp="3709.2,221.5", + pos="e,3667.5,196.34 3349.1,252.39 3371.5,250.58 3394.5,248.73 3416.2,247 3467.1,242.94 3602.4,256.85 3645.2,229 3653.6,223.55 3659.5,\ +214.57 3663.7,205.72", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="4023.2,178", + pos="3805.2,178", width=2.1304]; "variant as a model of disease association" -> "subject category closure" [color=blue, label="subject category closure", - lp="4092.7,221.5", - pos="e,4016.1,196.07 3563.9,252.1 3587.4,250.27 3611.5,248.5 3634.2,247 3673.5,244.41 3953.7,248.07 3988.2,229 3997.9,223.61 4005.6,214.23 \ -4011.2,205.04", + lp="3869.7,221.5", + pos="e,3795.9,196.14 3346.2,252.1 3369.6,250.27 3393.6,248.5 3416.2,247 3454.7,244.44 3728.6,246.21 3763.2,229 3774.1,223.58 3783.2,213.94 \ +3790.1,204.55", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="4216.2,178", + pos="3998.2,178", width=2.1304]; "variant as a model of disease association" -> "object category closure" [color=blue, label="object category closure", - lp="4283.7,221.5", - pos="e,4210.2,196.1 3561.9,251.9 3586,250.05 3610.8,248.33 3634.2,247 3664.7,245.27 4157.6,244.11 4184.2,229 4193.6,223.65 4200.7,214.28 \ -4205.7,205.08", + lp="4061.7,221.5", + pos="e,3990.5,196.17 3343.9,251.9 3368,250.06 3392.8,248.33 3416.2,247 3446.4,245.28 3934.4,243.08 3961.2,229 3971.3,223.68 3979.4,214.18 \ +3985.4,204.88", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4406.2,178", + pos="4188.2,178", width=1.0652]; "variant as a model of disease association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4456.2,221.5", - pos="e,4399.2,196.18 3560.8,251.82 3585.2,249.96 3610.4,248.25 3634.2,247 3675.1,244.85 4335.1,248.36 4371.2,229 4381,223.74 4388.6,214.39 \ -4394.3,205.18", + lp="4235.2,221.5", + pos="e,4180.2,195.73 3342.8,251.82 3367.2,249.96 3392.4,248.25 3416.2,247 3456.9,244.86 4112.8,247.32 4149.2,229 4159.9,223.62 4168.5,\ +213.79 4174.9,204.26", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4565.2,178", + pos="4347.2,178", width=1.0652]; "variant as a model of disease association" -> "object namespace" [color=blue, label="object namespace", - lp="4609.2,221.5", - pos="e,4557.8,195.73 3560.2,251.78 3584.8,249.91 3610.3,248.21 3634.2,247 3683.8,244.49 4484.1,251.8 4528.2,229 4538.5,223.67 4546.7,\ -213.98 4552.7,204.55", + lp="4389.2,221.5", + pos="e,4338.9,195.76 3342.2,251.78 3366.8,249.91 3392.3,248.21 3416.2,247 3465.6,244.5 4262.8,250.9 4307.2,229 4318,223.65 4326.9,213.83 \ +4333.5,204.3", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4716.2,178", + pos="4498.2,178", width=1.0652]; "variant as a model of disease association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4769.2,221.5", - pos="e,4708.2,195.76 3559.9,251.74 3584.6,249.87 3610.2,248.18 3634.2,247 3692.1,244.16 4625.3,254.87 4677.2,229 4687.9,223.66 4696.5,\ -213.83 4702.9,204.3", + lp="4549.2,221.5", + pos="e,4489.6,195.78 3341.9,251.74 3366.6,249.87 3392.2,248.18 3416.2,247 3474,244.16 4405.1,254.19 4457.2,229 4468.2,223.68 4477.2,213.87 \ +4484,204.33", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4887.2,178", + pos="4669.2,178", width=1.0652]; "variant as a model of disease association" -> "object label closure" [color=blue, label="object label closure", - lp="4934.7,221.5", - pos="e,4878.9,195.78 3559.7,251.71 3584.4,249.84 3610.1,248.15 3634.2,247 3667.8,245.39 4816.9,243.82 4847.2,229 4858,223.68 4866.9,213.87 \ -4873.5,204.33", + lp="4716.7,221.5", + pos="e,4660.3,195.81 3341.7,251.71 3366.4,249.84 3392.1,248.15 3416.2,247 3449.8,245.39 4596.8,243.44 4627.2,229 4638.3,223.71 4647.6,\ +213.9 4654.5,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="5029.2,178", + pos="4811.2,178", width=2.347]; "variant as a model of disease association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="5090.7,221.5", - pos="e,5026.8,196.45 3559.4,251.7 3584.2,249.82 3610,248.14 3634.2,247 3672.3,245.21 4976.5,250.34 5008.2,229 5016,223.72 5020.9,214.91 \ -5024,206.14", + lp="4872.7,221.5", + pos="e,4808.8,196.45 3341.4,251.7 3366.2,249.82 3392,248.14 3416.2,247 3454.3,245.21 4758.5,250.34 4790.2,229 4798,223.72 4802.9,214.91 \ +4806,206.14", style=solid]; type [height=0.5, - pos="5163.2,178", + pos="4945.2,178", width=0.86659]; "variant as a model of disease association" -> type [color=blue, label=type, - lp="5187.2,221.5", - pos="e,5169.1,196.12 3559.1,251.69 3584,249.81 3609.9,248.13 3634.2,247 3655.4,246.02 5149.2,244.12 5164.2,229 5170.1,223.03 5171.4,214.44 \ -5170.7,206.05", + lp="4969.2,221.5", + pos="e,4951.1,196.12 3341.1,251.69 3366,249.81 3391.9,248.13 3416.2,247 3437.4,246.02 4931.2,244.12 4946.2,229 4952.1,223.03 4953.4,214.44 \ +4952.7,206.05", style=solid]; category [height=0.5, - pos="5264.2,178", + pos="5046.2,178", width=1.4263]; "variant as a model of disease association" -> category [color=blue, label=category, - lp="5263.7,221.5", - pos="e,5251.2,195.44 3559.1,251.69 3584,249.81 3609.9,248.12 3634.2,247 3677.8,244.99 5166.4,244.63 5207.2,229 5221.3,223.6 5234.2,212.99 \ -5244.2,202.93", + lp="5045.7,221.5", + pos="e,5033.2,195.44 3341.1,251.69 3366,249.81 3391.9,248.12 3416.2,247 3459.8,244.99 4948.4,244.63 4989.2,229 5003.3,223.6 5016.2,212.99 \ +5026.2,202.93", style=solid]; predicate [height=0.5, - pos="5388.2,178", + pos="5170.2,178", width=1.5165]; "variant as a model of disease association" -> predicate [color=blue, label=predicate, - lp="5370.2,221.5", - pos="e,5367.2,194.81 3559.1,251.68 3584,249.8 3609.9,248.11 3634.2,247 3726.6,242.77 5209.8,252.9 5299.2,229 5320.4,223.32 5342,211.41 \ -5358.5,200.63", + lp="5152.2,221.5", + pos="e,5149.2,194.81 3341.1,251.68 3366,249.8 3391.9,248.11 3416.2,247 3508.6,242.77 4991.8,252.9 5081.2,229 5102.4,223.32 5124,211.41 \ +5140.5,200.63", style=solid]; object [height=0.5, - pos="5975.2,91", + pos="5757.2,91", width=1.0832]; "variant as a model of disease association" -> object [color=blue, label=object, - lp="5510.2,178", - pos="e,5936.5,94.237 3559.1,251.66 3584,249.78 3609.9,248.11 3634.2,247 3683.4,244.76 5361.5,244.82 5408.2,229 5431.3,221.15 5433.7,212.02 \ -5452.2,196 5469.3,181.17 5467.9,170.09 5488.2,160 5564.5,121.97 5818.5,101.88 5926.2,94.891", + lp="5292.2,178", + pos="e,5718.5,94.237 3341.1,251.66 3366,249.78 3391.9,248.11 3416.2,247 3465.4,244.76 5143.5,244.82 5190.2,229 5213.3,221.15 5215.7,212.02 \ +5234.2,196 5251.3,181.17 5249.9,170.09 5270.2,160 5346.5,121.97 5600.5,101.88 5708.2,94.891", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="5626.2,178", + pos="5408.2,178", width=2.3651]; "variant as a model of disease association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="5614.2,221.5", - pos="e,5594,194.73 3558.8,251.67 3583.8,249.79 3609.8,248.1 3634.2,247 3737.4,242.33 5391.7,247.96 5493.2,229 5524.9,223.08 5558.9,210.15 \ -5584.6,198.93", + lp="5396.2,221.5", + pos="e,5376,194.73 3340.8,251.67 3365.8,249.79 3391.8,248.1 3416.2,247 3519.4,242.33 5173.7,247.96 5275.2,229 5306.9,223.08 5340.9,210.15 \ +5366.6,198.93", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="5805.2,178", + pos="5587.2,178", width=2.1123]; "variant as a model of disease association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="5795.2,221.5", - pos="e,5776.4,194.86 3558.8,251.66 3583.8,249.77 3609.8,248.09 3634.2,247 3748.1,241.9 5574.5,252.01 5686.2,229 5714.5,223.16 5744.6,\ -210.47 5767.4,199.35", + lp="5577.2,221.5", + pos="e,5558.4,194.86 3340.8,251.66 3365.8,249.77 3391.8,248.09 3416.2,247 3530.1,241.9 5356.5,252.01 5468.2,229 5496.5,223.16 5526.6,\ +210.47 5549.4,199.35", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="5935.2,178", + pos="5717.2,178", width=1.011]; "variant as a model of disease association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="5942.7,221.5", - pos="e,5918.8,194.07 3558.8,251.64 3583.8,249.76 3609.8,248.08 3634.2,247 3696,244.25 5801.1,247.16 5860.2,229 5878.8,223.29 5897,211.35 \ -5910.8,200.57", + lp="5724.7,221.5", + pos="e,5700.8,194.07 3340.8,251.64 3365.8,249.76 3391.8,248.08 3416.2,247 3478,244.25 5583.1,247.16 5642.2,229 5660.8,223.29 5679,211.35 \ +5692.8,200.57", style=solid]; subject [height=0.5, - pos="6046.2,178", + pos="5828.2,178", width=1.2277]; "variant as a model of disease association" -> subject [color=blue, label=subject, - lp="6045.2,221.5", - pos="e,6035.4,195.89 3558.5,251.65 3583.7,249.76 3609.7,248.08 3634.2,247 3699.8,244.1 5937.9,254.98 5998.2,229 6010.4,223.72 6021.1,\ -213.63 6029.2,203.88", + lp="5827.2,221.5", + pos="e,5817.4,195.89 3340.5,251.65 3365.7,249.76 3391.7,248.08 3416.2,247 3481.8,244.1 5719.9,254.98 5780.2,229 5792.4,223.72 5803.1,\ +213.63 5811.2,203.88", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3681.2,265", + pos="3463.2,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3812.2,265", + pos="3594.2,265", width=2.0762]; "variant to disease association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3983.2,265", + pos="3765.2,265", width=2.1665]; relation [height=0.5, - pos="6010.2,18", + pos="5792.2,18", width=1.2999]; - object -> relation [pos="e,6001.7,36.198 5983.5,73.174 5987.6,64.896 5992.6,54.723 5997.2,45.438", + object -> relation [pos="e,5783.7,36.198 5765.5,73.174 5769.6,64.896 5774.6,54.723 5779.2,45.438", style=dotted]; "variant to disease association_object" [color=blue, height=0.5, label="named thing", - pos="4149.2,265", + pos="3931.2,265", width=1.9318]; subject -> object [label=relation, - lp="6004.2,134.5", - pos="e,5971.4,109.01 6009.8,167.42 5997,162.12 5983.8,154.06 5976.2,142 5971.9,135.26 5970.6,126.93 5970.6,119.01"]; - subject -> relation [pos="e,6014.4,36.005 6042.5,160.05 6038.1,139.44 6030.3,103.63 6023.2,73 6021.2,64.183 6018.9,54.574 6016.8,45.938", + lp="5786.2,134.5", + pos="e,5753.4,109.01 5791.8,167.42 5779,162.12 5765.8,154.06 5758.2,142 5753.9,135.26 5752.6,126.93 5752.6,119.01"]; + subject -> relation [pos="e,5796.4,36.005 5824.5,160.05 5820.1,139.44 5812.3,103.63 5805.2,73 5803.2,64.183 5800.9,54.574 5798.8,45.938", style=dotted]; "variant as a model of disease association_subject" [color=blue, height=0.5, label="sequence variant", - pos="4327.2,265", + pos="4109.2,265", width=2.5095]; } diff --git a/graphviz/variant_as_a_model_of_disease_association.svg b/graphviz/variant_as_a_model_of_disease_association.svg index b6676f6881..45e5d18232 100644 --- a/graphviz/variant_as_a_model_of_disease_association.svg +++ b/graphviz/variant_as_a_model_of_disease_association.svg @@ -4,16 +4,16 @@ - + %3 - + variant as a model of disease association - -variant as a model of disease association + +variant as a model of disease association @@ -24,9 +24,9 @@ variant as a model of disease association->variant to disease association - + -is_a +is_a @@ -37,9 +37,9 @@ variant as a model of disease association->model to disease association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ variant as a model of disease association->entity to disease association mixin - - -uses + + +uses @@ -63,9 +63,9 @@ variant as a model of disease association->id - - -id + + +id @@ -76,9 +76,9 @@ variant as a model of disease association->iri - - -iri + + +iri @@ -89,9 +89,9 @@ variant as a model of disease association->name - - -name + + +name @@ -102,9 +102,9 @@ variant as a model of disease association->description - - -description + + +description @@ -115,9 +115,9 @@ variant as a model of disease association->has attribute - - -has attribute + + +has attribute @@ -128,9 +128,9 @@ variant as a model of disease association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ variant as a model of disease association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ variant as a model of disease association->publications - - -publications + + +publications @@ -167,402 +167,402 @@ variant as a model of disease association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string variant as a model of disease association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string variant as a model of disease association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string variant as a model of disease association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type variant as a model of disease association->timepoint - - -timepoint + + +timepoint original subject - -string + +string variant as a model of disease association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie variant as a model of disease association->original predicate - - -original predicate + + +original predicate original object - -string + +string variant as a model of disease association->original object - - -original object + + +original object subject category - -ontology class + +ontology class variant as a model of disease association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class variant as a model of disease association->object category - - -object category + + +object category subject closure - -string + +string variant as a model of disease association->subject closure - - -subject closure + + +subject closure object closure - -string + +string variant as a model of disease association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class variant as a model of disease association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class variant as a model of disease association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string variant as a model of disease association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string variant as a model of disease association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string variant as a model of disease association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string variant as a model of disease association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source variant as a model of disease association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type variant as a model of disease association->type - - -type + + +type category - -category + +category variant as a model of disease association->category - - -category + + +category predicate - -predicate + +predicate variant as a model of disease association->predicate - - -predicate + + +predicate object - -object + +object variant as a model of disease association->object - - -object + + +object frequency qualifier - -frequency value + +frequency value variant as a model of disease association->frequency qualifier - - -frequency qualifier + + +frequency qualifier severity qualifier - -severity value + +severity value variant as a model of disease association->severity qualifier - - -severity qualifier + + +severity qualifier onset qualifier - -onset + +onset variant as a model of disease association->onset qualifier - - -onset qualifier + + +onset qualifier subject - -subject + +subject variant as a model of disease association->subject - - -subject + + +subject association_type - -string + +string association_category - -category type + +category type variant to disease association_predicate - -predicate type + +predicate type relation - -relation + +relation object->relation - - + + variant to disease association_object - -named thing + +named thing subject->object - - -relation + + +relation subject->relation - - + + variant as a model of disease association_subject - -sequence variant + +sequence variant diff --git a/graphviz/variant_to_disease_association.gv b/graphviz/variant_to_disease_association.gv index 71a6595ce9..dc0b57f4c6 100644 --- a/graphviz/variant_to_disease_association.gv +++ b/graphviz/variant_to_disease_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,5927.4,283"]; + graph [bb="0,0,5709.4,283"]; node [label="\N"]; "variant to disease association" [height=0.5, label="variant to disease association", - pos="3248.4,265", + pos="3030.4,265", width=4.1163]; association [height=0.5, pos="62.394,178", width=1.7332]; "variant to disease association" -> association [label=is_a, - lp="623.39,221.5", - pos="e,106.48,190.75 3100.7,263.13 2619.6,260.13 1100.1,249.25 609.39,229 397.51,220.26 343.01,228.13 133.39,196 127.91,195.16 122.23,\ + lp="622.39,221.5", + pos="e,106.48,190.75 2882.2,264.69 2503.4,265.83 1469.2,265.09 608.39,229 396.96,220.13 342.57,228.08 133.39,196 127.91,195.16 122.23,\ 194.11 116.58,192.95"]; "variant to entity association mixin" [height=0.5, pos="312.39,178", width=4.7121]; "variant to disease association" -> "variant to entity association mixin" [label=uses, - lp="839.89,221.5", - pos="e,418.88,192.02 3100.4,263.48 2645.3,261.62 1269.9,254.03 823.39,229 687.74,221.4 532.47,205.12 429.03,193.2"]; + lp="838.89,221.5", + pos="e,419.16,192.04 2882.6,263.24 2455.5,260.78 1224.8,251.88 822.39,229 687.22,221.32 532.53,205.1 429.3,193.21"]; "entity to disease association mixin" [height=0.5, pos="671.39,178", width=4.7482]; "variant to disease association" -> "entity to disease association mixin" [label=uses, - lp="994.89,221.5", - pos="e,745.77,194.24 3100.3,264.54 2664.6,265.69 1392.3,265.7 978.39,229 902.6,222.28 817.24,207.81 755.8,196.16"]; + lp="993.89,221.5", + pos="e,745.84,194.27 2882.1,264.26 2475.2,264.54 1347.3,262.2 977.39,229 901.98,222.23 817.05,207.8 755.83,196.18"]; id [color=blue, height=0.5, label=string, @@ -31,9 +31,9 @@ digraph { width=1.0652]; "variant to disease association" -> id [color=blue, label=id, - lp="1112.4,221.5", - pos="e,927.38,189.98 3100.8,263.2 2648.8,260.52 1301.9,250.8 1105.4,229 1033.7,221.04 1015.9,215.43 946.39,196 943.29,195.13 940.09,194.17 \ -936.89,193.15", + lp="1111.4,221.5", + pos="e,927.38,189.97 2883.1,262.92 2463.1,259.61 1278.9,248.63 1104.4,229 1033.1,220.98 1015.5,215.35 946.39,196 943.29,195.13 940.09,\ +194.16 936.89,193.14", style=solid]; iri [color=blue, height=0.5, @@ -42,9 +42,9 @@ digraph { width=1.2277]; "variant to disease association" -> iri [color=blue, label=iri, - lp="1225.4,221.5", - pos="e,1032.3,190.19 3100.9,262.99 2665.1,259.81 1402.6,248.95 1217.4,229 1143,220.99 1124.8,214.78 1052.4,196 1049,195.12 1045.5,194.16 \ -1042.1,193.14", + lp="1216.4,221.5", + pos="e,1032.3,190.13 2883.1,262.77 2479.1,259.18 1372.3,247.74 1208.4,229 1138,220.95 1120.9,214.18 1052.4,196 1049,195.11 1045.5,194.12 \ +1042.1,193.1", style=solid]; name [color=blue, height=0.5, @@ -53,8 +53,8 @@ digraph { width=1.5707]; "variant to disease association" -> name [color=blue, label=name, - lp="1332.4,221.5", - pos="e,1156.2,191.54 3100.6,263.32 2678.7,261.1 1487.3,252.79 1312.4,229 1261.6,222.09 1205,206.58 1166.1,194.65", + lp="1318.4,221.5", + pos="e,1154.7,191.99 2882.7,263.13 2492.3,260.55 1452.6,251.6 1298.4,229 1251.9,222.18 1200.4,207.07 1164.4,195.23", style=solid]; description [color=blue, height=0.5, @@ -63,8 +63,8 @@ digraph { width=2.0943]; "variant to disease association" -> description [color=blue, label=description, - lp="1452.9,221.5", - pos="e,1302.2,194.15 3100.2,263.85 2693,263.06 1576.1,258.23 1412.4,229 1377.6,222.78 1339.8,209.42 1311.7,198.07", + lp="1429.9,221.5", + pos="e,1297.7,194.75 2882.1,263.96 2505.7,263.41 1532.9,259.07 1389.4,229 1360.7,222.98 1330.1,210.3 1306.9,199.22", style=solid]; "has attribute" [color=blue, height=0.5, @@ -73,8 +73,8 @@ digraph { width=1.4443]; "variant to disease association" -> "has attribute" [color=blue, label="has attribute", - lp="1598.4,221.5", - pos="e,1443,192.95 3100.4,263.71 2715.3,262.55 1701.1,256.88 1551.4,229 1516.9,222.58 1479.6,208.62 1452.5,197.07", + lp="1561.4,221.5", + pos="e,1436.7,194.25 2882.3,264.23 2526.8,264.25 1644.5,261.04 1514.4,229 1490,222.98 1464.6,210.39 1445.4,199.35", style=solid]; negated [color=blue, height=0.5, @@ -83,8 +83,8 @@ digraph { width=1.2999]; "variant to disease association" -> negated [color=blue, label=negated, - lp="1753.4,221.5", - pos="e,1564.2,190.46 3100.1,264.56 2770.9,265.15 1987.1,262.82 1724.4,229 1671.8,222.23 1613.1,205.81 1574.2,193.62", + lp="1693.4,221.5", + pos="e,1558.4,192.55 2883,262.97 2554.4,260.29 1781.2,251.64 1664.4,229 1630.5,222.44 1593.9,208.27 1567.6,196.69", style=solid]; qualifiers [color=blue, height=0.5, @@ -93,8 +93,8 @@ digraph { width=2.1304]; "variant to disease association" -> qualifiers [color=blue, label=qualifiers, - lp="1891.9,221.5", - pos="e,1713.1,193.2 3100.2,264.68 2792.7,265.38 2094.2,263 1858.4,229 1811.7,222.26 1759.9,207.87 1722.7,196.25", + lp="1796.9,221.5", + pos="e,1694.3,195.43 2882.4,263.79 2571.2,262.77 1868.7,257.33 1763.4,229 1741.9,223.21 1719.9,211.5 1702.8,200.86", style=solid]; publications [color=blue, height=0.5, @@ -103,8 +103,8 @@ digraph { width=1.7332]; "variant to disease association" -> publications [color=blue, label=publications, - lp="2037.4,221.5", - pos="e,1864.1,192.85 3100.2,264.8 2815.6,265.52 2202.2,262.92 1993.4,229 1952,222.28 1906.6,207.95 1873.8,196.35", + lp="1888.4,221.5", + pos="e,1829.1,196.25 2882.2,264.15 2573.2,263.84 1885.2,259.68 1844.4,229 1837.2,223.56 1833.1,214.83 1830.9,206.18", style=solid]; "has evidence" [color=blue, height=0.5, @@ -113,308 +113,309 @@ digraph { width=2.0943]; "variant to disease association" -> "has evidence" [color=blue, label="has evidence", - lp="2195.9,221.5", - pos="e,2022.4,193.63 3100.3,264.08 2844,263.43 2327.8,258.35 2149.4,229 2109,222.35 2064.6,208.52 2032.1,197.09", + lp="1986.9,221.5", + pos="e,1956.3,194.88 2882.2,264.63 2591.7,265.12 1972.6,262.25 1940.4,229 1931.8,220.11 1938.1,209.91 1948.3,201.06", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2186.4,178", - width=3.015]; + label=string, + pos="2116.4,178", + width=1.0652]; "variant to disease association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2350.9,221.5", - pos="e,2211.9,195.61 3101.9,262.09 2852.1,258.33 2363,248.56 2286.4,229 2263.3,223.1 2239.3,211.34 2220.6,200.71", + lp="2104.9,221.5", + pos="e,2085.9,189.23 2882.1,264.1 2613,263.55 2069.1,258.74 2040.4,229 2035.8,224.2 2036.8,219.61 2040.4,214 2044.9,207 2060.6,199.25 \ +2076.5,192.84", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2421.4,178", - width=3.015]; + label=string, + pos="2211.4,178", + width=1.0652]; "variant to disease association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2522.4,221.5", - pos="e,2418.4,196.33 3101.4,262.61 2871.8,259.76 2451.7,251.48 2427.4,229 2421.3,223.32 2418.9,214.91 2418.3,206.59", + lp="2271.4,221.5", + pos="e,2190.8,193.24 2883,263.2 2645,261.16 2200.4,254.02 2176.4,229 2168,220.29 2174.1,209.43 2183.3,200.05", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2656.4,178", - width=3.015]; + label=string, + pos="2353.4,178", + width=1.0652]; "variant to disease association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2730.9,221.5", - pos="e,2634.6,195.87 3103.9,260.85 2924.7,256.21 2640.7,246.2 2624.4,229 2617.2,221.43 2620.7,212.05 2627.6,203.46", + lp="2491.9,221.5", + pos="e,2359.5,196.02 2883,263.04 2705.9,260.79 2427.2,253.38 2385.4,229 2376.1,223.61 2369.1,214.35 2364.1,205.26", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2838.4,178", + pos="2580.4,178", width=1.5346]; "variant to disease association" -> timepoint [color=blue, label=timepoint, - lp="2885.4,221.5", - pos="e,2837.8,196.43 3107.1,259.56 3000.7,254.9 2869.9,245.81 2850.4,229 2843.9,223.36 2840.5,214.85 2839,206.44", + lp="2654.4,221.5", + pos="e,2588.8,195.97 2882.4,263.71 2783.5,261.2 2663.7,253.01 2619.4,229 2609.1,223.43 2600.7,213.89 2594.3,204.63", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2950.4,178", + pos="2692.4,178", width=1.0652]; "variant to disease association" -> "original subject" [color=blue, label="original subject", - lp="2983.4,221.5", - pos="e,2934.6,194.82 3113.1,257.61 3031.2,252.31 2940.2,243.29 2927.4,229 2920.7,221.56 2923.3,211.86 2928.8,202.98", + lp="2757.4,221.5", + pos="e,2690.7,196.27 2896.2,257.27 2811.7,251.75 2716,242.6 2701.4,229 2695.2,223.25 2692.4,214.83 2691.3,206.52", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3064.4,178", + pos="2817.4,178", width=1.5887]; "variant to disease association" -> "original predicate" [color=blue, label="original predicate", - lp="3109.9,221.5", - pos="e,3050.6,195.8 3122.9,255.35 3088.4,250.22 3057.4,242.04 3046.4,229 3040.5,222.05 3041.9,213.06 3045.7,204.62", + lp="2887.9,221.5", + pos="e,2815.1,196.02 2906.6,255.11 2870.2,249.95 2836.8,241.82 2824.4,229 2818.6,222.99 2816.1,214.49 2815.3,206.2", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3178.4,178", + pos="2946.4,178", width=1.0652]; "variant to disease association" -> "original object" [color=blue, label="original object", - lp="3233.9,221.5", - pos="e,3175.9,196.07 3203.1,247.84 3195,242.99 3187.5,236.8 3182.4,229 3178,222.32 3176.2,214 3175.8,206.08", + lp="3015.9,221.5", + pos="e,2949.4,196.35 2988.3,247.66 2979.5,242.72 2970.9,236.54 2964.4,229 2958.8,222.53 2954.9,214.18 2952.2,206.16", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3311.4,178", + pos="3079.4,178", width=2.1304]; "variant to disease association" -> "subject category" [color=blue, label="subject category", - lp="3357.9,221.5", - pos="e,3306,196.22 3271.8,247.1 3278.1,241.81 3284.5,235.61 3289.4,229 3294.6,221.97 3298.9,213.49 3302.3,205.54", + lp="3136.9,221.5", + pos="e,3079.6,196.17 3055.8,247.12 3061.8,241.98 3067.5,235.86 3071.4,229 3075.2,222.15 3077.4,213.99 3078.5,206.26", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3482.4,178", + pos="3250.4,178", width=2.1304]; "variant to disease association" -> "object category" [color=blue, label="object category", - lp="3500.9,221.5", - pos="e,3466.3,195.91 3350.3,251.92 3374.4,246.78 3399.4,239.45 3421.4,229 3435,222.54 3448.2,212.41 3458.8,202.94", + lp="3276.9,221.5", + pos="e,3237.8,195.95 3135.8,252.23 3158,247.06 3180.6,239.65 3200.4,229 3212,222.72 3222.8,212.86 3231.2,203.55", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3615.4,178", + pos="3383.4,178", width=1.0652]; "variant to disease association" -> "subject closure" [color=blue, label="subject closure", - lp="3637.9,221.5", - pos="e,3602.3,195.42 3355.1,252.42 3444.5,242.65 3558,230.09 3560.4,229 3573.6,223.04 3585.7,212.72 3595.3,203", + lp="3410.9,221.5", + pos="e,3372.7,195.4 3135.9,252.36 3223.5,242.63 3334.1,230.16 3336.4,229 3348.1,223.13 3358.4,213.1 3366.4,203.55", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3714.4,178", + pos="3496.4,178", width=1.0652]; "variant to disease association" -> "object closure" [color=blue, label="object closure", - lp="3758.4,221.5", - pos="e,3712.9,196.21 3352.4,252.13 3370.4,250.27 3388.9,248.48 3406.4,247 3438.6,244.27 3670.6,248.37 3696.4,229 3703.7,223.51 3708.1,\ -214.77 3710.6,206.12", + lp="3533.4,221.5", + pos="e,3492,195.91 3134.4,252.16 3152.4,250.3 3170.9,248.5 3188.4,247 3219.6,244.33 3443.1,245.88 3469.4,229 3477.9,223.53 3484,214.39 \ +3488.1,205.41", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3847.4,178", + pos="3629.4,178", width=2.1304]; "variant to disease association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3916.9,221.5", - pos="e,3840.4,196.1 3351.1,252 3369.5,250.12 3388.5,248.36 3406.4,247 3451.4,243.58 3772.8,250.74 3812.4,229 3822.1,223.64 3829.8,214.27 \ -3835.4,205.08", + lp="3693.9,221.5", + pos="e,3620.1,196.17 3133.1,252.01 3151.5,250.13 3170.5,248.36 3188.4,247 3232.6,243.62 3547.6,248.65 3587.4,229 3598.3,223.62 3607.4,\ +213.98 3614.4,204.59", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="4040.4,178", + pos="3822.4,178", width=2.1304]; "variant to disease association" -> "object category closure" [color=blue, label="object category closure", - lp="4107.9,221.5", - pos="e,4034.4,196.11 3350.3,251.87 3368.9,249.98 3388.2,248.25 3406.4,247 3439.8,244.71 3979.3,245.5 4008.4,229 4017.8,223.66 4024.9,\ -214.29 4030,205.1", + lp="3885.9,221.5", + pos="e,3814.7,196.18 3132.3,251.87 3150.9,249.98 3170.2,248.25 3188.4,247 3221.5,244.72 3756,244.38 3785.4,229 3795.5,223.69 3803.6,214.19 \ +3809.6,204.89", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4230.4,178", + pos="4012.4,178", width=1.0652]; "variant to disease association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4280.4,221.5", - pos="e,4223.4,196.18 3349.9,251.8 3368.6,249.91 3388.1,248.19 3406.4,247 3450.1,244.15 4156.7,249.69 4195.4,229 4205.2,223.75 4212.9,\ -214.39 4218.5,205.19", + lp="4059.4,221.5", + pos="e,4004.4,195.74 3131.9,251.81 3150.6,249.91 3170.1,248.19 3188.4,247 3231.9,244.16 3934.4,248.59 3973.4,229 3984.1,223.63 3992.7,\ +213.8 3999.1,204.27", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4389.4,178", + pos="4171.4,178", width=1.0652]; "variant to disease association" -> "object namespace" [color=blue, label="object namespace", - lp="4433.4,221.5", - pos="e,4382,195.73 3349.4,251.79 3368.3,249.89 3387.9,248.17 3406.4,247 3458.9,243.69 4305.7,253.1 4352.4,229 4362.7,223.67 4370.9,213.99 \ -4376.9,204.55", + lp="4213.4,221.5", + pos="e,4163.1,195.77 3131.4,251.79 3150.3,249.89 3169.9,248.17 3188.4,247 3240.7,243.69 4084.4,252.15 4131.4,229 4142.2,223.66 4151.1,\ +213.84 4157.7,204.3", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4540.4,178", + pos="4322.4,178", width=1.0652]; "variant to disease association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4593.4,221.5", - pos="e,4532.4,195.77 3349.4,251.75 3368.3,249.85 3387.9,248.14 3406.4,247 3467.1,243.24 4446.9,256.14 4501.4,229 4512.1,223.66 4520.8,\ -213.84 4527.2,204.3", + lp="4373.4,221.5", + pos="e,4313.8,195.79 3131.4,251.75 3150.3,249.85 3169.9,248.14 3188.4,247 3249,243.25 4226.7,255.43 4281.4,229 4292.4,223.69 4301.4,213.87 \ +4308.2,204.33", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4711.4,178", + pos="4493.4,178", width=1.0652]; "variant to disease association" -> "object label closure" [color=blue, label="object label closure", - lp="4758.9,221.5", - pos="e,4703.1,195.79 3349,251.76 3368,249.85 3387.8,248.13 3406.4,247 3441.5,244.87 4639.8,244.45 4671.4,229 4682.2,223.69 4691.1,213.87 \ -4697.7,204.33", + lp="4540.9,221.5", + pos="e,4484.5,195.81 3131,251.76 3150,249.85 3169.8,248.13 3188.4,247 3223.4,244.87 4419.7,244.05 4451.4,229 4462.5,223.71 4471.8,213.9 \ +4478.7,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4853.4,178", + pos="4635.4,178", width=2.347]; "variant to disease association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4914.9,221.5", - pos="e,4851,196.45 3349,251.74 3368,249.82 3387.8,248.11 3406.4,247 3445.9,244.63 4799.5,251.14 4832.4,229 4840.2,223.73 4845.1,214.91 \ -4848.2,206.14", + lp="4696.9,221.5", + pos="e,4633,196.45 3131,251.74 3150,249.82 3169.8,248.11 3188.4,247 3227.9,244.63 4581.5,251.14 4614.4,229 4622.2,223.73 4627.1,214.91 \ +4630.2,206.14", style=solid]; type [height=0.5, - pos="4987.4,178", + pos="4769.4,178", width=0.86659]; "variant to disease association" -> type [color=blue, label=type, - lp="5011.4,221.5", - pos="e,4993.3,196.12 3349,251.72 3368,249.81 3387.8,248.1 3406.4,247 3428.3,245.7 4972.9,244.63 4988.4,229 4994.3,223.03 4995.6,214.44 \ -4994.9,206.05", + lp="4793.4,221.5", + pos="e,4775.3,196.12 3131,251.72 3150,249.81 3169.8,248.1 3188.4,247 3210.3,245.7 4754.9,244.63 4770.4,229 4776.3,223.03 4777.6,214.44 \ +4776.9,206.05", style=solid]; category [height=0.5, - pos="5088.4,178", + pos="4870.4,178", width=1.4263]; "variant to disease association" -> category [color=blue, label=category, - lp="5087.9,221.5", - pos="e,5075.4,195.45 3349,251.71 3368,249.8 3387.8,248.1 3406.4,247 3451.5,244.33 4989.2,245.14 5031.4,229 5045.5,223.6 5058.4,213 5068.4,\ + lp="4869.9,221.5", + pos="e,4857.4,195.45 3131,251.71 3150,249.8 3169.8,248.1 3188.4,247 3233.5,244.33 4771.2,245.14 4813.4,229 4827.5,223.6 4840.4,213 4850.4,\ 202.94", style=solid]; subject [height=0.5, - pos="5202.4,178", + pos="4984.4,178", width=1.2277]; "variant to disease association" -> subject [color=blue, label=subject, - lp="5182.4,221.5", - pos="e,5184.4,194.55 3349,251.7 3368,249.79 3387.8,248.09 3406.4,247 3501.6,241.39 5031.9,256.04 5123.4,229 5142.7,223.31 5161.7,211.44 \ -5176.3,200.69", + lp="4964.4,221.5", + pos="e,4966.4,194.55 3131,251.7 3150,249.79 3169.8,248.09 3188.4,247 3283.6,241.39 4813.9,256.04 4905.4,229 4924.7,223.31 4943.7,211.44 \ +4958.3,200.69", style=solid]; predicate [height=0.5, - pos="5319.4,178", + pos="5101.4,178", width=1.5165]; "variant to disease association" -> predicate [color=blue, label=predicate, - lp="5289.4,221.5", - pos="e,5295,194.11 3349,251.7 3368,249.79 3387.8,248.09 3406.4,247 3506.6,241.13 5114.6,251.24 5212.4,229 5238.4,223.09 5265.6,210.27 \ -5286.1,199.1", + lp="5071.4,221.5", + pos="e,5077,194.11 3131,251.7 3150,249.79 3169.8,248.09 3188.4,247 3288.6,241.13 4896.6,251.24 4994.4,229 5020.4,223.09 5047.6,210.27 \ +5068.1,199.1", style=solid]; object [height=0.5, - pos="5269.4,91", + pos="5051.4,91", width=1.0832]; "variant to disease association" -> object [color=blue, label=object, - lp="5411.4,178", - pos="e,5299.2,102.71 3348.6,251.73 3367.7,249.8 3387.7,248.09 3406.4,247 3512.9,240.78 5224.6,257.56 5327.4,229 5355.2,221.27 5369.1,\ -221.08 5383.4,196 5405.7,156.94 5349.7,124.38 5308.5,106.59", + lp="5193.4,178", + pos="e,5081.2,102.71 3130.6,251.73 3149.7,249.8 3169.7,248.09 3188.4,247 3294.9,240.78 5006.6,257.56 5109.4,229 5137.2,221.27 5151.1,\ +221.08 5165.4,196 5187.7,156.94 5131.7,124.38 5090.5,106.59", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="5557.4,178", + pos="5339.4,178", width=2.3651]; "variant to disease association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="5545.4,221.5", - pos="e,5525.2,194.74 3348.6,251.72 3367.7,249.8 3387.7,248.09 3406.4,247 3518.3,240.5 5314.2,249.54 5424.4,229 5456.1,223.09 5490.1,210.17 \ -5515.8,198.94", + lp="5327.4,221.5", + pos="e,5307.2,194.74 3130.6,251.72 3149.7,249.8 3169.7,248.09 3188.4,247 3300.3,240.5 5096.2,249.54 5206.4,229 5238.1,223.09 5272.1,210.17 \ +5297.8,198.94", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="5736.4,178", + pos="5518.4,178", width=2.1123]; "variant to disease association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="5726.4,221.5", - pos="e,5707.6,194.86 3348.6,251.71 3367.7,249.79 3387.7,248.08 3406.4,247 3529,239.92 5497.1,253.76 5617.4,229 5645.8,223.16 5675.8,210.48 \ -5698.6,199.35", + lp="5508.4,221.5", + pos="e,5489.6,194.86 3130.6,251.71 3149.7,249.79 3169.7,248.08 3188.4,247 3311,239.92 5279.1,253.76 5399.4,229 5427.8,223.16 5457.8,210.48 \ +5480.6,199.35", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="5873.4,178", + pos="5655.4,178", width=1.011]; "variant to disease association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="5875.9,221.5", - pos="e,5855.5,193.85 3348.6,251.7 3367.7,249.78 3387.7,248.08 3406.4,247 3472.5,243.2 5727.7,247.15 5791.4,229 5811.6,223.23 5831.9,211 \ -5847.1,200.07", + lp="5657.9,221.5", + pos="e,5637.5,193.85 3130.6,251.7 3149.7,249.78 3169.7,248.08 3188.4,247 3254.5,243.2 5509.7,247.15 5573.4,229 5593.6,223.23 5613.9,211 \ +5629.1,200.07", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3453.4,265", + pos="3235.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3584.4,265", + pos="3366.4,265", width=2.0762]; subject -> object [label=relation, - lp="5268.4,134.5", - pos="e,5256.7,108.05 5215.3,160.61 5225.3,147.95 5239.3,130.24 5250.5,115.98"]; + lp="5050.4,134.5", + pos="e,5038.7,108.05 4997.3,160.61 5007.3,147.95 5021.3,130.24 5032.5,115.98"]; relation [height=0.5, - pos="5214.4,18", + pos="4996.4,18", width=1.2999]; - subject -> relation [pos="e,5213.1,36.188 5203.7,159.79 5205.8,132.48 5209.8,78.994 5212.3,46.38", + subject -> relation [pos="e,4995.1,36.188 4985.7,159.79 4987.8,132.48 4991.8,78.994 4994.3,46.38", style=dotted]; "variant to disease association_subject" [color=blue, height=0.5, label="named thing", - pos="3746.4,265", + pos="3528.4,265", width=1.9318]; "variant to disease association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3912.4,265", + pos="3694.4,265", width=2.1665]; - object -> relation [pos="e,5227.2,35.54 5256.9,73.889 5250,64.939 5241.2,53.617 5233.4,43.584", + object -> relation [pos="e,5009.2,35.54 5038.9,73.889 5032,64.939 5023.2,53.617 5015.4,43.584", style=dotted]; "variant to disease association_object" [color=blue, height=0.5, label="named thing", - pos="4078.4,265", + pos="3860.4,265", width=1.9318]; } diff --git a/graphviz/variant_to_disease_association.svg b/graphviz/variant_to_disease_association.svg index b93071afbc..3c7b3187b6 100644 --- a/graphviz/variant_to_disease_association.svg +++ b/graphviz/variant_to_disease_association.svg @@ -4,16 +4,16 @@ - + %3 - + variant to disease association - -variant to disease association + +variant to disease association @@ -24,9 +24,9 @@ variant to disease association->association - + -is_a +is_a @@ -37,9 +37,9 @@ variant to disease association->variant to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ variant to disease association->entity to disease association mixin - - -uses + + +uses @@ -63,9 +63,9 @@ variant to disease association->id - - -id + + +id @@ -76,9 +76,9 @@ variant to disease association->iri - - -iri + + +iri @@ -89,9 +89,9 @@ variant to disease association->name - - -name + + +name @@ -102,9 +102,9 @@ variant to disease association->description - - -description + + +description @@ -115,9 +115,9 @@ variant to disease association->has attribute - - -has attribute + + +has attribute @@ -128,9 +128,9 @@ variant to disease association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ variant to disease association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ variant to disease association->publications - - -publications + + +publications @@ -167,402 +167,402 @@ variant to disease association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string variant to disease association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string variant to disease association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string variant to disease association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type variant to disease association->timepoint - - -timepoint + + +timepoint original subject - -string + +string variant to disease association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie variant to disease association->original predicate - - -original predicate + + +original predicate original object - -string + +string variant to disease association->original object - - -original object + + +original object subject category - -ontology class + +ontology class variant to disease association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class variant to disease association->object category - - -object category + + +object category subject closure - -string + +string variant to disease association->subject closure - - -subject closure + + +subject closure object closure - -string + +string variant to disease association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class variant to disease association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class variant to disease association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string variant to disease association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string variant to disease association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string variant to disease association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string variant to disease association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source variant to disease association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type variant to disease association->type - - -type + + +type category - -category + +category variant to disease association->category - - -category + + +category subject - -subject + +subject variant to disease association->subject - - -subject + + +subject predicate - -predicate + +predicate variant to disease association->predicate - - -predicate + + +predicate object - -object + +object variant to disease association->object - - -object + + +object frequency qualifier - -frequency value + +frequency value variant to disease association->frequency qualifier - - -frequency qualifier + + +frequency qualifier severity qualifier - -severity value + +severity value variant to disease association->severity qualifier - - -severity qualifier + + +severity qualifier onset qualifier - -onset + +onset variant to disease association->onset qualifier - - -onset qualifier + + +onset qualifier association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + variant to disease association_subject - -named thing + +named thing variant to disease association_predicate - -predicate type + +predicate type object->relation - - + + variant to disease association_object - -named thing + +named thing diff --git a/graphviz/variant_to_gene_association.gv b/graphviz/variant_to_gene_association.gv index 753f64de4e..90b9a5db02 100644 --- a/graphviz/variant_to_gene_association.gv +++ b/graphviz/variant_to_gene_association.gv @@ -1,23 +1,23 @@ digraph { - graph [bb="0,0,5151,283"]; + graph [bb="0,0,4913,283"]; node [label="\N"]; "variant to gene association" [height=0.5, label="variant to gene association", - pos="2760.4,265", + pos="2522.4,265", width=3.7733]; association [height=0.5, pos="62.394,178", width=1.7332]; "variant to gene association" -> association [label=is_a, - lp="483.39,221.5", - pos="e,106.9,190.64 2624.7,263.4 2199,261.29 892.61,252.97 469.39,229 319.58,220.51 281.37,220.86 133.39,196 128,195.09 122.41,194.01 \ -116.85,192.84"]; + lp="482.39,221.5", + pos="e,106.9,190.64 2387,263.13 1991.7,260.36 843.37,250.63 468.39,229 319.03,220.39 280.93,220.81 133.39,196 128,195.09 122.42,194.01 \ +116.85,192.83"]; "variant to entity association mixin" [height=0.5, pos="312.39,178", width=4.7121]; "variant to gene association" -> "variant to entity association mixin" [label=uses, - lp="635.89,221.5", - pos="e,386.77,194.22 2624.3,264.36 2216.9,265.02 1011,263.9 619.39,229 543.6,222.24 458.24,207.78 396.8,196.14"]; + lp="634.89,221.5", + pos="e,386.84,194.24 2386.5,264.04 2010.6,263.74 961.97,260.07 618.39,229 542.98,222.18 458.05,207.76 396.84,196.15"]; id [color=blue, height=0.5, label=string, @@ -25,9 +25,9 @@ digraph { width=1.0652]; "variant to gene association" -> id [color=blue, label=id, - lp="755.39,221.5", - pos="e,567.38,190 2625.2,263.09 2204.1,260.05 933.37,249.28 748.39,229 675.35,220.99 657.2,215.65 586.39,196 583.29,195.14 580.09,194.17 \ -576.89,193.16", + lp="752.39,221.5", + pos="e,567.38,189.98 2386.6,264.57 2028.1,265.57 1062.7,264.74 745.39,229 673.68,220.92 655.9,215.43 586.39,196 583.29,195.13 580.09,\ +194.17 576.89,193.15", style=solid]; iri [color=blue, height=0.5, @@ -36,9 +36,9 @@ digraph { width=1.2277]; "variant to gene association" -> iri [color=blue, label=iri, - lp="871.39,221.5", - pos="e,672.3,190.23 2624.3,264.53 2249.1,265.52 1205,264.85 863.39,229 786.41,220.92 767.38,215.19 692.39,196 689.02,195.14 685.54,194.18 \ -682.05,193.17", + lp="864.39,221.5", + pos="e,672.31,190.19 2386.4,264.25 2043.8,264.39 1151.4,261.52 856.39,229 782.49,220.85 764.35,214.72 692.39,196 689.02,195.12 685.54,\ +194.15 682.06,193.14", style=solid]; name [color=blue, height=0.5, @@ -47,8 +47,8 @@ digraph { width=1.5707]; "variant to gene association" -> name [color=blue, label=name, - lp="982.39,221.5", - pos="e,797.01,191.24 2625.3,263.05 2235.3,260.06 1125.3,249.82 962.39,229 908.26,222.08 847.7,206.16 806.73,194.13", + lp="971.39,221.5", + pos="e,795.96,191.5 2387.5,262.78 2032.7,259.32 1091.3,248.41 951.39,229 900.88,221.99 844.58,206.49 805.89,194.59", style=solid]; description [color=blue, height=0.5, @@ -57,8 +57,8 @@ digraph { width=2.0943]; "variant to gene association" -> description [color=blue, label=description, - lp="1109.9,221.5", - pos="e,945.41,193.76 2625,263.38 2250.9,261.34 1220.7,253.57 1069.4,229 1029.9,222.58 986.59,208.74 954.87,197.24", + lp="1090.9,221.5", + pos="e,942,194.23 2387,263.21 2047.8,260.87 1179.4,252.63 1050.4,229 1016.1,222.72 979.05,209.43 951.38,198.13", style=solid]; "has attribute" [color=blue, height=0.5, @@ -67,8 +67,8 @@ digraph { width=1.4443]; "variant to gene association" -> "has attribute" [color=blue, label="has attribute", - lp="1265.4,221.5", - pos="e,1086.6,191.98 2625.4,263.03 2275.1,260.22 1354.9,250.82 1218.4,229 1175.9,222.22 1129.2,207.3 1096.3,195.52", + lp="1234.4,221.5", + pos="e,1082.4,193.02 2387.2,262.99 2071.3,260.25 1302.7,251.37 1187.4,229 1154,222.51 1117.9,208.62 1091.6,197.13", style=solid]; subject [color=blue, height=0.5, @@ -77,8 +77,8 @@ digraph { width=1.9318]; "variant to gene association" -> subject [color=blue, label=subject, - lp="1420.4,221.5", - pos="e,1235.6,192.36 2624.4,264.28 2327.5,264.28 1628.9,260.78 1394.4,229 1342.9,222.02 1285.4,206.97 1245.2,195.2", + lp="1369.4,221.5", + pos="e,1227.8,193.68 2388,262.22 2100.5,258.08 1443.7,246.81 1343.4,229 1306.7,222.49 1266.8,208.84 1237.4,197.44", style=solid]; negated [color=blue, height=0.5, @@ -87,8 +87,8 @@ digraph { width=1.2999]; "variant to gene association" -> negated [color=blue, label=negated, - lp="1557.4,221.5", - pos="e,1362.1,190.32 2625,263.46 2350.4,261.83 1736.8,255.27 1528.4,229 1473.6,222.1 1412.3,205.5 1371.9,193.31", + lp="1474.4,221.5", + pos="e,1353.2,193.22 2387.9,262.39 2119.4,258.77 1535,248.72 1445.4,229 1416.2,222.57 1385.1,209.1 1362.2,197.76", style=solid]; qualifiers [color=blue, height=0.5, @@ -97,8 +97,8 @@ digraph { width=2.1304]; "variant to gene association" -> qualifiers [color=blue, label=qualifiers, - lp="1691.9,221.5", - pos="e,1510.8,193.12 2624.8,263.51 2372.6,261.96 1840.8,255.55 1658.4,229 1611,222.1 1558.4,207.72 1520.6,196.15", + lp="1568.9,221.5", + pos="e,1484.6,195.6 2386.7,263.67 2134.8,262.41 1613.4,256.46 1535.4,229 1519.5,223.4 1504.2,212.59 1492.3,202.44", style=solid]; publications [color=blue, height=0.5, @@ -107,8 +107,8 @@ digraph { width=1.7332]; "variant to gene association" -> publications [color=blue, label=publications, - lp="1832.4,221.5", - pos="e,1661,192.88 2624.7,263.49 2396.4,261.89 1945,255.37 1788.4,229 1747.7,222.14 1702.9,207.9 1670.6,196.36", + lp="1654.4,221.5", + pos="e,1613,195.81 2386.8,263.68 2139.2,262.42 1636.8,256.47 1610.4,229 1604.1,222.48 1605,213.43 1608.5,204.83", style=solid]; "has evidence" [color=blue, height=0.5, @@ -117,235 +117,236 @@ digraph { width=2.0943]; "variant to gene association" -> "has evidence" [color=blue, label="has evidence", - lp="1982.9,221.5", - pos="e,1817.9,193.89 2625.4,262.67 2426.5,259.96 2064.6,251.96 1936.4,229 1898.8,222.27 1857.8,208.75 1827.4,197.47", + lp="1752.9,221.5", + pos="e,1735.6,192.33 2386.9,263.02 2161,260.7 1729.5,253.13 1706.4,229 1694.1,216.12 1707.6,204.8 1726.4,196.21", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="1983.4,178", - width=3.015]; + label=string, + pos="1913.4,178", + width=1.0652]; "variant to gene association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2127.9,221.5", - pos="e,2003.7,195.77 2627.9,260.94 2440.7,256.06 2115.6,245.39 2063.4,229 2044.8,223.17 2026.3,212 2011.7,201.69", + lp="1870.9,221.5", + pos="e,1884,189.64 2388.2,262.16 2186.4,258.72 1826.1,249.7 1806.4,229 1801.8,224.17 1802.4,219.36 1806.4,214 1822.7,191.97 1839.4,204.58 \ +1865.4,196 1868.3,195.04 1871.3,194.02 1874.4,192.98", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2218.4,178", - width=3.015]; + label=string, + pos="2008.4,178", + width=1.0652]; "variant to gene association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2295.4,221.5", - pos="e,2204.3,196.1 2629.3,260.28 2468.4,255.06 2214.9,244.44 2200.4,229 2194.2,222.38 2195.4,213.47 2199.3,204.99", + lp="2038.4,221.5", + pos="e,1978,189.07 2390.4,260.54 2224.3,255.54 1958.5,245.06 1943.4,229 1930.4,215.25 1948.4,202.32 1968.7,193.05", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2453.4,178", - width=3.015]; + label=string, + pos="2126.4,178", + width=1.0652]; "variant to gene association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2504.9,221.5", - pos="e,2417.2,195.05 2629.9,259.8 2532.6,255.29 2414.1,246.3 2398.4,229 2389.4,219.14 2396.6,209.11 2408.4,200.64", + lp="2255.9,221.5", + pos="e,2129.7,196.22 2395.7,258.33 2295.6,252.82 2169.4,243.2 2149.4,229 2141.6,223.46 2136.4,214.59 2132.9,205.85", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2635.4,178", + pos="2352.4,178", width=1.5346]; "variant to gene association" -> timepoint [color=blue, label=timepoint, - lp="2653.4,221.5", - pos="e,2622.3,195.65 2672.1,251.32 2647.8,245.91 2625.9,238.59 2618.4,229 2612.9,221.97 2614,213.06 2617.6,204.71", + lp="2414.4,221.5", + pos="e,2357.6,196.25 2426.2,252.17 2409.4,246.97 2393,239.55 2379.4,229 2371.7,223.04 2365.9,214.23 2361.7,205.66", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2747.4,178", + pos="2464.4,178", width=1.0652]; "variant to gene association" -> "original subject" [color=blue, label="original subject", - lp="2750.4,221.5", - pos="e,2719.7,190.76 2714.2,247.95 2706.3,243.1 2699.1,236.89 2694.4,229 2686.7,216.25 2697.3,204.67 2710.9,195.86", + lp="2512.4,221.5", + pos="e,2456.4,195.83 2476.2,247.95 2468.3,243.1 2461.1,236.89 2456.4,229 2452.2,222.01 2452.1,213.51 2453.7,205.53", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2861.4,178", + pos="2590.4,178", width=1.5887]; "variant to gene association" -> "original predicate" [color=blue, label="original predicate", - lp="2887.9,221.5", - pos="e,2843.9,195.61 2783.6,246.94 2791,241.36 2799.1,235.03 2806.4,229 2816.5,220.62 2827.2,211.01 2836.5,202.48", + lp="2640.9,221.5", + pos="e,2585.2,196.38 2549.2,247.16 2556.1,241.95 2563.1,235.78 2568.4,229 2573.8,222.12 2578.2,213.69 2581.6,205.72", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="2975.4,178", + pos="2719.4,178", width=1.0652]; "variant to gene association" -> "original object" [color=blue, label="original object", - lp="3018.9,221.5", - pos="e,2972.8,196.36 2851.8,251.67 2898.3,244.67 2946.9,235.94 2955.4,229 2962.5,223.23 2967.1,214.57 2970,206.08", + lp="2768.9,221.5", + pos="e,2720.1,196.11 2630,253.95 2664.2,248.63 2696.3,240.7 2708.4,229 2714.5,223.08 2717.6,214.61 2719,206.32", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3108.4,178", + pos="2852.4,178", width=2.1304]; "variant to gene association" -> "subject category" [color=blue, label="subject category", - lp="3149.9,221.5", - pos="e,3101.3,196.33 2857.9,252.43 2873.8,250.58 2890,248.72 2905.4,247 2942.9,242.8 3042,248.41 3074.4,229 3083.7,223.42 3091.1,214.17 \ -3096.5,205.14", + lp="2897.9,221.5", + pos="e,2847.3,196.23 2620.3,252.49 2636,250.65 2652.2,248.77 2667.4,247 2702.3,242.96 2795.2,248.46 2824.4,229 2832.8,223.41 2838.9,214.41 \ +2843.3,205.58", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3279.4,178", + pos="3023.4,178", width=2.1304]; "variant to gene association" -> "object category" [color=blue, label="object category", - lp="3294.9,221.5", - pos="e,3263.2,195.71 2855.1,252.09 2871.8,250.22 2889.1,248.43 2905.4,247 2973.7,241.01 3149.1,252.73 3213.4,229 3229,223.26 3243.9,212.54 \ -3255.6,202.49", + lp="3041.9,221.5", + pos="e,3008.4,195.69 2617.5,252.09 2634.1,250.22 2651.2,248.44 2667.4,247 2732.6,241.19 2900.4,252.66 2961.4,229 2976.1,223.29 2990.1,\ +212.71 3001,202.76", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3412.4,178", + pos="3156.4,178", width=1.0652]; "variant to gene association" -> "subject closure" [color=blue, label="subject closure", - lp="3432.9,221.5", - pos="e,3399,195.3 2854.3,251.93 2871.3,250.05 2888.8,248.3 2905.4,247 2955.2,243.09 3307.9,247.32 3354.4,229 3368.6,223.4 3381.7,212.78 \ -3391.9,202.75", + lp="3178.9,221.5", + pos="e,3143.9,195.28 2616.3,251.95 2633.3,250.06 2650.8,248.31 2667.4,247 2715.5,243.19 3056.7,247.33 3101.4,229 3115.1,223.38 3127.6,\ +212.75 3137.2,202.73", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3510.4,178", + pos="3269.4,178", width=1.0652]; "variant to gene association" -> "object closure" [color=blue, label="object closure", - lp="3552.4,221.5", - pos="e,3508.3,196.36 2853.5,251.89 2870.7,249.99 2888.6,248.24 2905.4,247 2937.8,244.6 3463.8,247.64 3490.4,229 3498.1,223.63 3502.8,\ -214.79 3505.7,206.03", + lp="3303.4,221.5", + pos="e,3263.4,196.11 2615.9,251.85 2633,249.97 2650.7,248.24 2667.4,247 2699,244.65 3209.8,244.65 3237.4,229 3246.8,223.66 3253.9,214.28 \ +3258.9,205.09", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3643.4,178", + pos="3402.4,178", width=2.1304]; "variant to gene association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3710.9,221.5", - pos="e,3635.7,196.2 2853.5,251.82 2870.7,249.92 2888.6,248.2 2905.4,247 2944.3,244.23 3571.8,246.98 3606.4,229 3616.6,223.71 3624.7,214.22 \ -3630.6,204.92", + lp="3464.9,221.5", + pos="e,3392.2,196.28 2615.5,251.82 2632.7,249.93 2650.6,248.2 2667.4,247 2705.6,244.26 3322.6,245.06 3357.4,229 3368.9,223.71 3378.7,\ +213.94 3386.2,204.44", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3833.4,178", + pos="3595.4,178", width=2.1304]; "variant to gene association" -> "object category closure" [color=blue, label="object category closure", - lp="3900.9,221.5", - pos="e,3827.7,196.13 2853.1,251.78 2870.4,249.88 2888.5,248.16 2905.4,247 2955.1,243.59 3759.1,253.68 3802.4,229 3811.6,223.75 3818.5,\ -214.52 3823.3,205.41", + lp="3657.9,221.5", + pos="e,3587.1,196.24 2615.1,251.78 2632.4,249.88 2650.5,248.16 2667.4,247 2716.7,243.62 3512.2,251.12 3556.4,229 3566.8,223.77 3575.3,\ +214.29 3581.7,204.97", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4023.4,178", + pos="3785.4,178", width=1.0652]; "variant to gene association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4073.4,221.5", - pos="e,4016.4,196.21 2852.7,251.78 2870.2,249.86 2888.3,248.14 2905.4,247 2935.4,245 3961.8,243.12 3988.4,229 3998.2,223.78 4005.9,214.43 \ -4011.5,205.22", + lp="3831.4,221.5", + pos="e,3777.1,195.78 2614.7,251.78 2632.2,249.86 2650.3,248.14 2667.4,247 2727.2,243.01 3691.6,255.4 3745.4,229 3756.2,223.67 3765.1,\ +213.85 3771.7,204.32", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4182.4,178", + pos="3944.4,178", width=1.0652]; "variant to gene association" -> "object namespace" [color=blue, label="object namespace", - lp="4226.4,221.5", - pos="e,4175,195.75 2852.7,251.75 2870.2,249.83 2888.3,248.12 2905.4,247 2939.8,244.74 4114.7,244.73 4145.4,229 4155.7,223.69 4163.9,214.01 \ -4169.9,204.58", + lp="3987.4,221.5", + pos="e,3935.8,195.8 2614.7,251.75 2632.2,249.83 2650.3,248.12 2667.4,247 2701.7,244.75 3872.5,243.91 3903.4,229 3914.4,223.7 3923.4,213.88 \ +3930.2,204.34", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4333.4,178", + pos="4095.4,178", width=1.0652]; "variant to gene association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4386.4,221.5", - pos="e,4325.4,195.78 2852.7,251.73 2870.2,249.81 2888.3,248.11 2905.4,247 2943.9,244.5 4259.8,246.15 4294.4,229 4305.1,223.68 4313.8,\ -213.86 4320.2,204.32", + lp="4147.4,221.5", + pos="e,4087.1,195.79 2614.7,251.73 2632.2,249.81 2650.3,248.11 2667.4,247 2705.9,244.5 4020.8,245.93 4055.4,229 4066.3,223.69 4075.1,\ +213.88 4081.7,204.34", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4504.4,178", + pos="4266.4,178", width=1.0652]; "variant to gene association" -> "object label closure" [color=blue, label="object label closure", - lp="4552.9,221.5", - pos="e,4496.1,195.8 2852.7,251.71 2870.2,249.8 2888.3,248.1 2905.4,247 2948.6,244.22 4425.5,247.99 4464.4,229 4475.3,223.7 4484.1,213.89 \ -4490.7,204.35", + lp="4314.9,221.5", + pos="e,4257.8,195.81 2614.7,251.71 2632.2,249.8 2650.3,248.1 2667.4,247 2710.6,244.23 4186.4,247.74 4225.4,229 4236.4,223.72 4245.4,213.9 \ +4252.2,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4657.4,178", + pos="4419.4,178", width=2.347]; "variant to gene association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4710.9,221.5", - pos="e,4651.7,196.17 2852.3,251.73 2869.9,249.81 2888.2,248.1 2905.4,247 2953.1,243.96 4584.7,252.47 4626.4,229 4635.6,223.79 4642.5,\ -214.57 4647.4,205.46", + lp="4472.9,221.5", + pos="e,4413.7,196.17 2614.3,251.73 2631.9,249.81 2650.2,248.1 2667.4,247 2715.1,243.96 4346.7,252.47 4388.4,229 4397.6,223.79 4404.5,\ +214.57 4409.4,205.46", style=solid]; type [height=0.5, - pos="4791.4,178", + pos="4553.4,178", width=0.86659]; "variant to gene association" -> type [color=blue, label=type, - lp="4809.4,221.5", - pos="e,4794.1,195.99 2852.3,251.72 2869.9,249.8 2888.2,248.09 2905.4,247 2931.4,245.35 4764.8,246.22 4784.4,229 4790.9,223.33 4793.4,\ -214.66 4794.1,206.12", + lp="4571.4,221.5", + pos="e,4556.1,195.99 2614.3,251.72 2631.9,249.8 2650.2,248.09 2667.4,247 2693.4,245.35 4526.8,246.22 4546.4,229 4552.9,223.33 4555.4,\ +214.66 4556.1,206.12", style=solid]; category [height=0.5, - pos="4892.4,178", + pos="4654.4,178", width=1.4263]; "variant to gene association" -> category [color=blue, label=category, - lp="4887.9,221.5", - pos="e,4877.7,195.49 2852.3,251.72 2869.9,249.79 2888.2,248.09 2905.4,247 2958.7,243.63 4779,246.83 4829.4,229 4844.6,223.6 4859,212.85 \ -4870.1,202.69", + lp="4649.9,221.5", + pos="e,4639.7,195.49 2614.3,251.72 2631.9,249.79 2650.2,248.09 2667.4,247 2720.7,243.63 4541,246.83 4591.4,229 4606.6,223.6 4621,212.85 \ +4632.1,202.69", style=solid]; object [height=0.5, pos="1260.4,91", width=1.0832]; "variant to gene association" -> object [color=blue, label=object, - lp="4984.4,178", - pos="e,1299.5,91.961 2852.3,251.71 2869.9,249.79 2888.2,248.08 2905.4,247 2961.3,243.48 4872.4,252.34 4923.4,229 4953.6,215.15 4975.7,\ -183.74 4952.4,160 4885.5,91.861 1743.6,91.656 1309.8,91.953", + lp="4746.4,178", + pos="e,1299.6,92.011 2614.3,251.71 2631.9,249.79 2650.2,248.08 2667.4,247 2723.3,243.48 4634.4,252.34 4685.4,229 4715.6,215.15 4737.7,\ +183.75 4714.4,160 4652,96.377 1727.6,92.278 1309.9,92.017", style=solid]; predicate [height=0.5, - pos="5096.4,178", + pos="4858.4,178", width=1.5165]; "variant to gene association" -> predicate [color=blue, label=predicate, - lp="5068.4,221.5", - pos="e,5072.6,194.36 2852.3,251.71 2869.9,249.78 2888.2,248.08 2905.4,247 3021.2,239.74 4880.5,255.48 4993.4,229 5018.3,223.16 5044.2,\ -210.57 5063.8,199.48", + lp="4830.4,221.5", + pos="e,4834.6,194.36 2614.3,251.71 2631.9,249.78 2650.2,248.08 2667.4,247 2783.2,239.74 4642.5,255.48 4755.4,229 4780.3,223.16 4806.2,\ +210.57 4825.8,199.48", style=solid]; subject -> object [label=relation, lp="1259.4,134.5", @@ -358,23 +359,23 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="2952.4,265", + pos="2714.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3083.4,265", + pos="2845.4,265", width=2.0762]; object -> relation [pos="e,1218.2,35.54 1247.9,73.889 1241,64.939 1232.2,53.617 1224.4,43.584", style=dotted]; "variant to gene association_object" [color=blue, height=0.5, label=gene, - pos="3209.4,265", + pos="2971.4,265", width=0.92075]; "variant to gene association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3338.4,265", + pos="3100.4,265", width=2.1665]; } diff --git a/graphviz/variant_to_gene_association.svg b/graphviz/variant_to_gene_association.svg index 0202a30d45..412a75c618 100644 --- a/graphviz/variant_to_gene_association.svg +++ b/graphviz/variant_to_gene_association.svg @@ -4,16 +4,16 @@ - + %3 - + variant to gene association - -variant to gene association + +variant to gene association @@ -24,9 +24,9 @@ variant to gene association->association - + -is_a +is_a @@ -37,9 +37,9 @@ variant to gene association->variant to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ variant to gene association->id - - -id + + +id @@ -63,9 +63,9 @@ variant to gene association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ variant to gene association->name - - -name + + +name @@ -89,9 +89,9 @@ variant to gene association->description - - -description + + +description @@ -102,9 +102,9 @@ variant to gene association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ variant to gene association->subject - - -subject + + +subject @@ -128,9 +128,9 @@ variant to gene association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ variant to gene association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ variant to gene association->publications - - -publications + + +publications @@ -167,269 +167,269 @@ variant to gene association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string variant to gene association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string variant to gene association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string variant to gene association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type variant to gene association->timepoint - - -timepoint + + +timepoint original subject - -string + +string variant to gene association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie variant to gene association->original predicate - - -original predicate + + +original predicate original object - -string + +string variant to gene association->original object - - -original object + + +original object subject category - -ontology class + +ontology class variant to gene association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class variant to gene association->object category - - -object category + + +object category subject closure - -string + +string variant to gene association->subject closure - - -subject closure + + +subject closure object closure - -string + +string variant to gene association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class variant to gene association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class variant to gene association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string variant to gene association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string variant to gene association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string variant to gene association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string variant to gene association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source variant to gene association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type variant to gene association->type - - -type + + +type category - -category + +category variant to gene association->category - - -category + + +category @@ -440,22 +440,22 @@ variant to gene association->object - - -object + + +object predicate - -predicate + +predicate variant to gene association->predicate - - -predicate + + +predicate @@ -479,14 +479,14 @@ association_type - -string + +string association_category - -category type + +category type @@ -497,14 +497,14 @@ variant to gene association_object - -gene + +gene variant to gene association_predicate - -predicate type + +predicate type diff --git a/graphviz/variant_to_gene_expression_association.gv b/graphviz/variant_to_gene_expression_association.gv index 2adcfe7df2..5bcaeca1e7 100644 --- a/graphviz/variant_to_gene_expression_association.gv +++ b/graphviz/variant_to_gene_expression_association.gv @@ -1,22 +1,22 @@ digraph { - graph [bb="0,0,6032.7,283"]; + graph [bb="0,0,5794.7,283"]; node [label="\N"]; "variant to gene expression association" [height=0.5, label="variant to gene expression association", - pos="3078.8,265", + pos="2840.8,265", width=5.2537]; "variant to gene association" [height=0.5, pos="135.84,178", width=3.7733]; "variant to gene expression association" -> "variant to gene association" [label=is_a, - lp="541.84,221.5", - pos="e,218.54,192.31 2889.6,264.18 2380,264.23 986.65,261.3 527.84,229 424.96,221.76 307.74,205.78 228.5,193.82"]; + lp="540.84,221.5", + pos="e,218.71,192.34 2651.7,263.87 2175.9,263.12 937.87,258.3 526.84,229 424.39,221.7 307.68,205.77 228.64,193.85"]; "gene expression mixin" [height=0.5, pos="404.84,178", width=3.1955]; "variant to gene expression association" -> "gene expression mixin" [label=uses, - lp="673.34,221.5", - pos="e,462.68,193.59 2890.3,263.25 2359.3,260.84 875.94,252.13 656.84,229 593.73,222.34 522.94,207.64 472.49,195.89"]; + lp="672.34,221.5", + pos="e,462.7,193.62 2652.8,262.93 2159.2,259.86 851.06,249.84 655.84,229 593.09,222.3 522.7,207.65 472.47,195.92"]; id [color=blue, height=0.5, label=string, @@ -24,9 +24,9 @@ digraph { width=1.0652]; "variant to gene expression association" -> id [color=blue, label=id, - lp="792.84,221.5", - pos="e,604.82,190 2890.3,263.13 2379.3,260.5 991.85,251.36 785.84,229 712.79,221.07 694.64,215.65 623.84,196 620.73,195.14 617.53,194.17 \ -614.33,193.16", + lp="789.84,221.5", + pos="e,604.83,189.98 2653,262.82 2180.2,259.56 965.24,249.3 782.84,229 711.11,221.02 693.35,215.43 623.84,196 620.73,195.13 617.53,194.17 \ +614.33,193.15", style=solid]; iri [color=blue, height=0.5, @@ -35,9 +35,9 @@ digraph { width=1.2277]; "variant to gene expression association" -> iri [color=blue, label=iri, - lp="908.84,221.5", - pos="e,709.74,190.23 2891,262.86 2398.6,259.61 1095.4,249.18 900.84,229 823.85,221.01 804.82,215.19 729.84,196 726.46,195.14 722.98,194.18 \ -719.49,193.17", + lp="901.84,221.5", + pos="e,709.75,190.19 2653.3,262.56 2199.1,258.79 1065.2,247.63 893.84,229 819.92,220.97 801.79,214.72 729.84,196 726.46,195.12 722.99,\ +194.15 719.5,193.14", style=solid]; name [color=blue, height=0.5, @@ -46,8 +46,8 @@ digraph { width=1.5707]; "variant to gene expression association" -> name [color=blue, label=name, - lp="1019.8,221.5", - pos="e,834.45,191.28 2890.4,263.17 2413.6,260.74 1183.9,252.28 999.84,229 945.7,222.15 885.14,206.22 844.17,194.17", + lp="1008.8,221.5", + pos="e,833.4,191.53 2652.7,262.95 2214.4,260.13 1150.1,251.1 988.84,229 938.31,222.08 882.02,206.56 843.33,194.64", style=solid]; description [color=blue, height=0.5, @@ -56,8 +56,8 @@ digraph { width=2.0943]; "variant to gene expression association" -> description [color=blue, label=description, - lp="1146.3,221.5", - pos="e,982.61,193.79 2889.9,263.71 2430.2,262.56 1278.4,256.91 1105.8,229 1066.5,222.64 1023.5,208.8 992.01,197.28", + lp="1128.3,221.5", + pos="e,979.44,194.26 2652.1,263.62 2230.7,262.28 1238.2,256.24 1087.8,229 1053.6,222.79 1016.5,209.49 988.81,198.17", style=solid]; "has attribute" [color=blue, height=0.5, @@ -66,8 +66,8 @@ digraph { width=1.4443]; "variant to gene expression association" -> "has attribute" [color=blue, label="has attribute", - lp="1300.8,221.5", - pos="e,1123.6,192.01 2890.2,263.35 2456.1,261.44 1411.8,254.24 1253.8,229 1211.9,222.29 1165.7,207.37 1133.2,195.56", + lp="1272.8,221.5", + pos="e,1120,193.06 2652.2,263.43 2256,261.72 1362.4,255 1225.8,229 1192.2,222.59 1155.8,208.69 1129.3,197.18", style=solid]; subject [color=blue, height=0.5, @@ -76,8 +76,8 @@ digraph { width=1.9318]; "variant to gene expression association" -> subject [color=blue, label=subject, - lp="1453.8,221.5", - pos="e,1272.6,192.54 2891.5,262.43 2489.6,258.7 1569.3,248.19 1427.8,229 1377.6,222.18 1321.6,207.24 1282.2,195.46", + lp="1408.8,221.5", + pos="e,1265.7,193.73 2653.4,262.57 2287.8,259.32 1504.6,250.01 1382.8,229 1345.7,222.59 1305.2,208.93 1275.4,197.51", style=solid]; negated [color=blue, height=0.5, @@ -86,8 +86,8 @@ digraph { width=1.2999]; "variant to gene expression association" -> negated [color=blue, label=negated, - lp="1587.8,221.5", - pos="e,1398.7,190.46 2889.5,264.6 2540.9,264.88 1810.4,261.39 1558.8,229 1506.3,222.23 1447.5,205.8 1408.6,193.62", + lp="1515.8,221.5", + pos="e,1391.1,193.03 2652.7,262.91 2307.4,260.35 1597.6,252.3 1486.8,229 1456.4,222.59 1423.9,208.89 1400.1,197.45", style=solid]; qualifiers [color=blue, height=0.5, @@ -96,8 +96,8 @@ digraph { width=2.1304]; "variant to gene expression association" -> qualifiers [color=blue, label=qualifiers, - lp="1726.3,221.5", - pos="e,1547.6,193.2 2889.7,264.74 2565.7,265.07 1917.9,261.46 1692.8,229 1646.1,222.26 1594.4,207.87 1557.2,196.25", + lp="1611.3,221.5", + pos="e,1523.5,195.66 2651.7,264.7 2324.2,265.04 1676.8,261.5 1577.8,229 1560.9,223.43 1544.3,212.47 1531.4,202.22", style=solid]; publications [color=blue, height=0.5, @@ -106,8 +106,8 @@ digraph { width=1.7332]; "variant to gene expression association" -> publications [color=blue, label=publications, - lp="1871.8,221.5", - pos="e,1698.6,192.85 2889.6,264.86 2591.6,265.16 2026.3,261.25 1827.8,229 1786.5,222.28 1741,207.95 1708.3,196.35", + lp="1697.8,221.5", + pos="e,1653.3,195.99 2654.4,261.8 2324.6,257.47 1671,246.67 1653.8,229 1647.8,222.81 1647.7,214.06 1649.9,205.61", style=solid]; "has evidence" [color=blue, height=0.5, @@ -116,274 +116,275 @@ digraph { width=2.0943]; "variant to gene expression association" -> "has evidence" [color=blue, label="has evidence", - lp="2030.3,221.5", - pos="e,1856.8,193.63 2889.9,263.92 2623.8,262.79 2152.5,256.75 1983.8,229 1943.4,222.35 1899.1,208.52 1866.5,197.09", + lp="1796.3,221.5", + pos="e,1776.4,192.95 2651.6,264.68 2347.5,264.82 1780.6,260.79 1749.8,229 1738.3,217.05 1750.2,205.96 1767.1,197.27", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2020.8,178", - width=3.015]; + label=string, + pos="1950.8,178", + width=1.0652]; "variant to gene expression association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2185.3,221.5", - pos="e,2046.4,195.61 2893.2,261.45 2635.7,257.27 2193.3,247.5 2120.8,229 2097.7,223.1 2073.8,211.34 2055.1,200.71", + lp="1914.3,221.5", + pos="e,1921.2,189.58 2651.7,264 2371.8,263.04 1877.2,257.33 1849.8,229 1845.2,224.2 1846,219.42 1849.8,214 1864.3,193.78 1879.3,204.15 \ +1902.8,196 1905.7,195 1908.7,193.97 1911.7,192.92", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2255.8,178", - width=3.015]; + label=string, + pos="2045.8,178", + width=1.0652]; "variant to gene expression association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2356.8,221.5", - pos="e,2252.8,196.33 2892.1,262.04 2658,258.71 2284.6,250.1 2261.8,229 2255.7,223.32 2253.3,214.91 2252.7,206.59", + lp="2081.8,221.5", + pos="e,2017.1,189.95 2653,262.82 2408.6,260.34 2009.6,252.67 1986.8,229 1974.9,216.54 1989.8,203.99 2007.7,194.57", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2490.8,178", - width=3.015]; + label=string, + pos="2163.8,178", + width=1.0652]; "variant to gene expression association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="2565.3,221.5", - pos="e,2469,195.87 2897.6,259.78 2720,254.74 2473.9,244.93 2458.8,229 2451.7,221.43 2455.2,212.04 2462,203.46", + lp="2302.3,221.5", + pos="e,2169.9,196.02 2653.5,262.46 2477.2,259.63 2234.6,251.61 2195.8,229 2186.6,223.61 2179.6,214.35 2174.5,205.26", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="2672.8,178", + pos="2390.8,178", width=1.5346]; "variant to gene expression association" -> timepoint [color=blue, label=timepoint, - lp="2719.8,221.5", - pos="e,2672.2,196.43 2905.1,257.84 2807.6,252.76 2702.1,243.9 2684.8,229 2678.3,223.36 2675,214.85 2673.4,206.44", + lp="2464.8,221.5", + pos="e,2399.3,195.97 2653.6,262.42 2564.2,258.81 2468.4,249.9 2429.8,229 2419.6,223.43 2411.1,213.89 2404.7,204.63", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="2784.8,178", + pos="2502.8,178", width=1.0652]; "variant to gene expression association" -> "original subject" [color=blue, label="original subject", - lp="2817.8,221.5", - pos="e,2769.1,194.82 2917.6,255.54 2845,250.05 2773.1,241.53 2761.8,229 2755.2,221.56 2757.8,211.85 2763.2,202.97", + lp="2567.8,221.5", + pos="e,2501.1,196.27 2680.4,255.46 2603.4,249.82 2525,241.2 2511.8,229 2505.7,223.25 2502.8,214.83 2501.7,206.52", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="2898.8,178", + pos="2627.8,178", width=1.5887]; "variant to gene expression association" -> "original predicate" [color=blue, label="original predicate", - lp="2944.3,221.5", - pos="e,2885.1,195.79 2941.3,252.62 2913.5,247.45 2890,239.93 2880.8,229 2875,222.04 2876.3,213.05 2880.1,204.61", + lp="2698.3,221.5", + pos="e,2625.5,196.02 2702,252.77 2671.7,247.59 2645.5,240.03 2634.8,229 2629,222.99 2626.5,214.49 2625.8,206.2", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3012.8,178", + pos="2756.8,178", width=1.0652]; "variant to gene expression association" -> "original object" [color=blue, label="original object", - lp="3068.3,221.5", - pos="e,3010.4,196.01 3036.2,247.37 3028.6,242.55 3021.6,236.5 3016.8,229 3012.5,222.26 3010.8,213.93 3010.4,206.01", + lp="2826.3,221.5", + pos="e,2759.8,196.35 2798.1,247.27 2789.5,242.4 2781.2,236.35 2774.8,229 2769.2,222.53 2765.3,214.18 2762.6,206.16", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3145.8,178", + pos="2889.8,178", width=2.1304]; "variant to gene expression association" -> "subject category" [color=blue, label="subject category", - lp="3189.3,221.5", - pos="e,3138.9,196.18 3102,246.89 3108.3,241.6 3114.7,235.45 3119.8,229 3125.5,221.84 3130.5,213.25 3134.6,205.22", + lp="2947.3,221.5", + pos="e,2890,196.17 2866.3,247.12 2872.3,241.98 2878,235.86 2881.8,229 2885.7,222.15 2887.8,213.99 2889,206.26", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3316.8,178", + pos="3060.8,178", width=2.1304]; "variant to gene expression association" -> "object category" [color=blue, label="object category", - lp="3333.3,221.5", - pos="e,3300.1,195.66 3187.6,250.21 3209.8,245.18 3232.5,238.33 3252.8,229 3267.2,222.41 3281.2,212.04 3292.4,202.44", + lp="3087.3,221.5", + pos="e,3048.3,195.95 2953.4,250.48 2973.3,245.43 2993.2,238.51 3010.8,229 3022.5,222.72 3033.2,212.86 3041.7,203.55", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3449.8,178", + pos="3193.8,178", width=1.0652]; "variant to gene expression association" -> "subject closure" [color=blue, label="subject closure", - lp="3470.3,221.5", - pos="e,3436.6,194.94 3216,252.54 3292.7,245.45 3376.2,236.33 3392.8,229 3406.7,222.9 3419.5,212.23 3429.6,202.3", + lp="3221.3,221.5", + pos="e,3183.2,195.4 2978.5,252.61 3052.3,245.73 3131.3,236.81 3146.8,229 3158.5,223.13 3168.8,213.1 3176.8,203.55", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="3547.8,178", + pos="3306.8,178", width=1.0652]; "variant to gene expression association" -> "object closure" [color=blue, label="object closure", - lp="3589.8,221.5", - pos="e,3545.6,196.23 3212.7,252.25 3234.2,250.44 3256.1,248.63 3276.8,247 3304.7,244.8 3505.3,245.49 3527.8,229 3535.3,223.53 3540,214.79 \ -3542.9,206.14", + lp="3343.8,221.5", + pos="e,3302.2,196.36 2975,252.28 2996.4,250.47 3018.2,248.66 3038.8,247 3065.6,244.85 3257.3,243.61 3279.8,229 3288.2,223.56 3294.2,214.59 \ +3298.4,205.74", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="3680.8,178", + pos="3439.8,178", width=2.1304]; "variant to gene expression association" -> "subject category closure" [color=blue, label="subject category closure", - lp="3748.3,221.5", - pos="e,3673.1,196.1 3210.3,252.03 3232.5,250.21 3255.3,248.45 3276.8,247 3317.6,244.25 3607.8,248.26 3643.8,229 3653.9,223.59 3662,214.08 \ -3668,204.79", + lp="3504.3,221.5", + pos="e,3430.5,196.14 2972.3,252.05 2994.5,250.22 3017.3,248.46 3038.8,247 3078.7,244.29 3362.1,246.77 3397.8,229 3408.7,223.59 3417.9,\ +213.95 3424.8,204.56", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="3870.8,178", + pos="3632.8,178", width=2.1304]; "variant to gene expression association" -> "object category closure" [color=blue, label="object category closure", - lp="3938.3,221.5", - pos="e,3865.1,196.09 3208.4,251.87 3231.2,250.02 3254.7,248.3 3276.8,247 3308.1,245.16 3812.7,244.65 3839.8,229 3849,223.69 3855.9,214.45 \ -3860.7,205.35", + lp="3696.3,221.5", + pos="e,3625.2,196.17 2970.4,251.87 2993.2,250.03 3016.7,248.31 3038.8,247 3069.7,245.18 3568.4,243.38 3595.8,229 3606,223.68 3614.1,214.18 \ +3620.1,204.88", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4060.8,178", + pos="3822.8,178", width=1.0652]; "variant to gene expression association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4110.8,221.5", - pos="e,4053.8,196.18 3207.6,251.78 3230.7,249.93 3254.4,248.23 3276.8,247 3318.4,244.72 3989.2,248.66 4025.8,229 4035.6,223.74 4043.3,\ -214.39 4048.9,205.18", + lp="3869.8,221.5", + pos="e,3814.8,195.73 2969.6,251.79 2992.7,249.93 3016.4,248.23 3038.8,247 3080.2,244.73 3746.9,247.61 3783.8,229 3794.5,223.62 3803.2,\ +213.79 3809.6,204.26", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4219.8,178", + pos="3981.8,178", width=1.0652]; "variant to gene expression association" -> "object namespace" [color=blue, label="object namespace", - lp="4263.8,221.5", - pos="e,4212.5,195.73 3207.1,251.75 3230.3,249.89 3254.3,248.19 3276.8,247 3327.1,244.35 4138.1,252.1 4182.8,229 4193.2,223.67 4201.3,\ -213.98 4207.4,204.55", + lp="4023.8,221.5", + pos="e,3973.5,195.76 2969.1,251.75 2992.3,249.89 3016.3,248.19 3038.8,247 3088.9,244.35 3896.8,251.19 3941.8,229 3952.7,223.66 3961.5,\ +213.83 3968.1,204.3", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4370.8,178", + pos="4132.8,178", width=1.0652]; "variant to gene expression association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4423.8,221.5", - pos="e,4362.8,195.76 3206.8,251.72 3230.1,249.85 3254.2,248.16 3276.8,247 3335.4,243.99 4279.4,255.17 4331.8,229 4342.5,223.66 4351.2,\ -213.83 4357.6,204.3", + lp="4183.8,221.5", + pos="e,4124.2,195.79 2968.8,251.72 2992.1,249.85 3016.2,248.16 3038.8,247 3097.3,244 4039.2,254.48 4091.8,229 4102.8,223.69 4111.9,213.87 \ +4118.7,204.33", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="4541.8,178", + pos="4303.8,178", width=1.0652]; "variant to gene expression association" -> "object label closure" [color=blue, label="object label closure", - lp="4589.3,221.5", - pos="e,4533.5,195.78 3206.6,251.69 3229.9,249.83 3254.1,248.14 3276.8,247 3310.8,245.29 4471.3,243.97 4501.8,229 4512.7,223.68 4521.5,\ -213.87 4528.1,204.33", + lp="4351.3,221.5", + pos="e,4294.9,195.81 2968.6,251.69 2991.9,249.83 3016.1,248.14 3038.8,247 3072.8,245.3 4231.1,243.58 4261.8,229 4273,223.71 4282.2,213.9 \ +4289.2,204.36", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="4682.8,178", + pos="4444.8,178", width=2.347]; "variant to gene expression association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="4744.3,221.5", - pos="e,4680.8,196.42 3206.3,251.68 3229.7,249.81 3254,248.13 3276.8,247 3315.3,245.1 4631.1,250.79 4662.8,229 4670.6,223.69 4675.3,214.87 \ -4678.2,206.11", + lp="4506.3,221.5", + pos="e,4442.8,196.42 2968.3,251.68 2991.7,249.81 3016,248.13 3038.8,247 3077.3,245.1 4393.1,250.79 4424.8,229 4432.6,223.69 4437.3,214.87 \ +4440.2,206.11", style=solid]; type [height=0.5, - pos="4816.8,178", + pos="4578.8,178", width=0.86659]; "variant to gene expression association" -> type [color=blue, label=type, - lp="4840.8,221.5", - pos="e,4822.8,196.12 3206.3,251.66 3229.7,249.79 3254,248.11 3276.8,247 3298.2,245.96 4802.8,244.22 4817.8,229 4823.7,223.03 4825,214.44 \ -4824.4,206.05", + lp="4602.8,221.5", + pos="e,4584.8,196.12 2968.3,251.66 2991.7,249.79 3016,248.11 3038.8,247 3060.2,245.96 4564.8,244.22 4579.8,229 4585.7,223.03 4587,214.44 \ +4586.4,206.05", style=solid]; category [height=0.5, - pos="4917.8,178", + pos="4679.8,178", width=1.4263]; "variant to gene expression association" -> category [color=blue, label=category, - lp="4917.3,221.5", - pos="e,4904.8,195.44 3206,251.67 3229.6,249.79 3253.9,248.11 3276.8,247 3320.8,244.87 4819.7,244.74 4860.8,229 4874.9,223.6 4887.9,212.99 \ -4897.8,202.93", + lp="4679.3,221.5", + pos="e,4666.8,195.44 2968,251.67 2991.6,249.79 3015.9,248.11 3038.8,247 3082.8,244.87 4581.7,244.74 4622.8,229 4636.9,223.6 4649.9,212.99 \ +4659.8,202.93", style=solid]; object [height=0.5, pos="1297.8,91", width=1.0832]; "variant to gene expression association" -> object [color=blue, label=object, - lp="5010.8,178", - pos="e,1336.8,91.963 3206,251.66 3229.5,249.78 3253.9,248.11 3276.8,247 3323.3,244.76 4911.3,249.94 4952.8,229 4982,214.33 5000.7,183.28 \ -4977.8,160 4911.2,92.08 1779.4,91.687 1347.1,91.956", + lp="4772.8,178", + pos="e,1336.9,92.014 2968,251.66 2991.5,249.78 3015.9,248.11 3038.8,247 3085.3,244.76 4673.3,249.94 4714.8,229 4744,214.33 4762.7,183.29 \ +4739.8,160 4677.7,96.596 1763.4,92.31 1347.1,92.021", style=solid]; predicate [height=0.5, - pos="5121.8,178", + pos="4883.8,178", width=1.5165]; "variant to gene expression association" -> predicate [color=blue, label=predicate, - lp="5094.8,221.5", - pos="e,5098,194.35 3206,251.65 3229.5,249.78 3253.9,248.1 3276.8,247 3373.5,242.36 4924.6,251.17 5018.8,229 5043.7,223.14 5069.6,210.55 \ -5089.2,199.47", + lp="4856.8,221.5", + pos="e,4860,194.35 2968,251.65 2991.5,249.78 3015.9,248.1 3038.8,247 3135.5,242.36 4686.6,251.17 4780.8,229 4805.7,223.14 4831.6,210.55 \ +4851.2,199.47", style=solid]; "quantifier qualifier" [height=0.5, - pos="5291.8,178", + pos="5053.8,178", width=2.7081]; "variant to gene expression association" -> "quantifier qualifier" [color=blue, label="quantifier qualifier", - lp="5262.8,221.5", - pos="e,5253.4,194.61 3206,251.64 3229.5,249.77 3253.9,248.09 3276.8,247 3482.8,237.17 4929.1,261.28 5132.8,229 5171,222.95 5212.6,209.61 \ -5243.7,198.22", + lp="5024.8,221.5", + pos="e,5015.4,194.61 2968,251.64 2991.5,249.77 3015.9,248.09 3038.8,247 3244.8,237.17 4691.1,261.28 4894.8,229 4933,222.95 4974.6,209.61 \ +5005.7,198.22", style=solid]; "expression site" [color=blue, height=0.5, label="anatomical entity", - pos="5498.8,178", + pos="5260.8,178", width=2.5456]; "variant to gene expression association" -> "expression site" [color=blue, label="expression site", - lp="5453.3,221.5", - pos="e,5459.6,194.38 3205.8,251.65 3229.4,249.76 3253.8,248.09 3276.8,247 3391,241.61 5220.9,246.25 5333.8,229 5373.8,222.9 5417.5,209.32 \ -5449.9,197.86", + lp="5215.3,221.5", + pos="e,5221.6,194.38 2967.8,251.65 2991.4,249.76 3015.8,248.09 3038.8,247 3153,241.61 4982.9,246.25 5095.8,229 5135.8,222.9 5179.5,209.32 \ +5211.9,197.86", style=solid]; "stage qualifier" [color=blue, height=0.5, label="life stage", - pos="5662.8,178", + pos="5424.8,178", width=1.4985]; "variant to gene expression association" -> "stage qualifier" [color=blue, label="stage qualifier", - lp="5623.3,221.5", - pos="e,5631.2,192.71 3205.8,251.63 3229.4,249.75 3253.8,248.08 3276.8,247 3400.9,241.18 5389.3,249.26 5511.8,229 5550,222.68 5591.7,208.3 \ -5621.5,196.57", + lp="5385.3,221.5", + pos="e,5393.2,192.71 2967.8,251.63 2991.4,249.75 3015.8,248.08 3038.8,247 3162.9,241.18 5151.3,249.26 5273.8,229 5312,222.68 5353.7,208.3 \ +5383.5,196.57", style=solid]; "phenotypic state" [color=blue, height=0.5, label="disease or phenotypic feature", - pos="5883.8,178", + pos="5645.8,178", width=4.1344]; "variant to gene expression association" -> "phenotypic state" [color=blue, label="phenotypic state", - lp="5817.8,221.5", - pos="e,5832.6,194.99 3205.8,251.62 3229.4,249.74 3253.8,248.07 3276.8,247 3543.4,234.57 5414,261.84 5678.8,229 5728,222.9 5782.5,209.27 \ -5822.9,197.79", + lp="5579.8,221.5", + pos="e,5594.6,194.99 2967.8,251.62 2991.4,249.74 3015.8,248.07 3038.8,247 3305.4,234.57 5176,261.84 5440.8,229 5490,222.9 5544.5,209.27 \ +5584.9,197.79", style=solid]; subject -> object [label=relation, lp="1296.8,134.5", @@ -396,28 +397,28 @@ digraph { association_type [color=blue, height=0.5, label=string, - pos="3323.8,265", + pos="3085.8,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3454.8,265", + pos="3216.8,265", width=2.0762]; object -> relation [pos="e,1255.7,35.54 1285.4,73.889 1278.4,64.939 1269.7,53.617 1261.9,43.584", style=dotted]; "variant to gene association_object" [color=blue, height=0.5, label=gene, - pos="3580.8,265", + pos="3342.8,265", width=0.92075]; "variant to gene expression association_predicate" [color=blue, height=0.5, label="predicate type", - pos="3709.8,265", + pos="3471.8,265", width=2.1665]; "gene expression mixin_quantifier qualifier" [color=blue, height=0.5, label="ontology class", - pos="3882.8,265", + pos="3644.8,265", width=2.1304]; } diff --git a/graphviz/variant_to_gene_expression_association.svg b/graphviz/variant_to_gene_expression_association.svg index a3314302cc..8092932f7d 100644 --- a/graphviz/variant_to_gene_expression_association.svg +++ b/graphviz/variant_to_gene_expression_association.svg @@ -4,16 +4,16 @@ - + %3 - + variant to gene expression association - -variant to gene expression association + +variant to gene expression association @@ -24,9 +24,9 @@ variant to gene expression association->variant to gene association - - -is_a + + +is_a @@ -37,9 +37,9 @@ variant to gene expression association->gene expression mixin - - -uses + + +uses @@ -50,9 +50,9 @@ variant to gene expression association->id - - -id + + +id @@ -63,9 +63,9 @@ variant to gene expression association->iri - - -iri + + +iri @@ -76,9 +76,9 @@ variant to gene expression association->name - - -name + + +name @@ -89,9 +89,9 @@ variant to gene expression association->description - - -description + + +description @@ -102,9 +102,9 @@ variant to gene expression association->has attribute - - -has attribute + + +has attribute @@ -115,9 +115,9 @@ variant to gene expression association->subject - - -subject + + +subject @@ -128,9 +128,9 @@ variant to gene expression association->negated - - -negated + + +negated @@ -141,9 +141,9 @@ variant to gene expression association->qualifiers - - -qualifiers + + +qualifiers @@ -154,9 +154,9 @@ variant to gene expression association->publications - - -publications + + +publications @@ -167,269 +167,269 @@ variant to gene expression association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string variant to gene expression association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string variant to gene expression association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string variant to gene expression association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type variant to gene expression association->timepoint - - -timepoint + + +timepoint original subject - -string + +string variant to gene expression association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie variant to gene expression association->original predicate - - -original predicate + + +original predicate original object - -string + +string variant to gene expression association->original object - - -original object + + +original object subject category - -ontology class + +ontology class variant to gene expression association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class variant to gene expression association->object category - - -object category + + +object category subject closure - -string + +string variant to gene expression association->subject closure - - -subject closure + + +subject closure object closure - -string + +string variant to gene expression association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class variant to gene expression association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class variant to gene expression association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string variant to gene expression association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string variant to gene expression association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string variant to gene expression association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string variant to gene expression association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source variant to gene expression association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type variant to gene expression association->type - - -type + + +type category - -category + +category variant to gene expression association->category - - -category + + +category @@ -440,74 +440,74 @@ variant to gene expression association->object - - -object + + +object predicate - -predicate + +predicate variant to gene expression association->predicate - - -predicate + + +predicate quantifier qualifier - -quantifier qualifier + +quantifier qualifier variant to gene expression association->quantifier qualifier - - -quantifier qualifier + + +quantifier qualifier expression site - -anatomical entity + +anatomical entity variant to gene expression association->expression site - - -expression site + + +expression site stage qualifier - -life stage + +life stage variant to gene expression association->stage qualifier - - -stage qualifier + + +stage qualifier phenotypic state - -disease or phenotypic feature + +disease or phenotypic feature variant to gene expression association->phenotypic state - - -phenotypic state + + +phenotypic state @@ -531,14 +531,14 @@ association_type - -string + +string association_category - -category type + +category type @@ -549,20 +549,20 @@ variant to gene association_object - -gene + +gene variant to gene expression association_predicate - -predicate type + +predicate type gene expression mixin_quantifier qualifier - -ontology class + +ontology class diff --git a/graphviz/variant_to_phenotypic_feature_association.gv b/graphviz/variant_to_phenotypic_feature_association.gv index 624dd095fe..ccb90ee0f2 100644 --- a/graphviz/variant_to_phenotypic_feature_association.gv +++ b/graphviz/variant_to_phenotypic_feature_association.gv @@ -1,29 +1,29 @@ digraph { - graph [bb="0,0,6615.4,283"]; + graph [bb="0,0,6350.4,283"]; node [label="\N"]; "variant to phenotypic feature association" [height=0.5, label="variant to phenotypic feature association", - pos="3665.4,265", + pos="3400.4,265", width=5.5967]; association [height=0.5, pos="62.394,178", width=1.7332]; "variant to phenotypic feature association" -> association [label=is_a, lp="661.39,221.5", - pos="e,106.48,190.79 3465,263.05 2882.8,260.08 1198.3,249.87 647.39,229 418.64,220.34 359.75,230.11 133.39,196 127.91,195.17 122.23,194.13 \ -116.57,192.98"]; + pos="e,106.48,190.79 3200.2,262.79 2653.8,259.28 1144.6,248.11 647.39,229 418.65,220.21 359.75,230.11 133.39,196 127.91,195.17 122.23,\ +194.13 116.57,192.98"]; "variant to entity association mixin" [height=0.5, pos="312.39,178", width=4.7121]; "variant to phenotypic feature association" -> "variant to entity association mixin" [label=uses, lp="924.89,221.5", - pos="e,427.32,191.24 3464.9,263.18 2917.7,260.67 1406.2,251.83 908.39,229 745.33,221.52 557.79,204.37 437.32,192.25"]; + pos="e,427.6,191.22 3200,262.87 2690.2,259.71 1352.6,249.68 908.39,229 745.46,221.42 558.08,204.31 437.6,192.23"]; "entity to phenotypic feature association mixin" [height=0.5, pos="724.39,178", width=6.2286]; "variant to phenotypic feature association" -> "entity to phenotypic feature association mixin" [label=uses, lp="1100.9,221.5", - pos="e,813.57,194.53 3463.5,264.51 2939.7,265.32 1545.3,264 1084.4,229 995.76,222.27 895.66,207.81 823.55,196.16"]; + pos="e,813.94,194.56 3198.7,264.14 2713.7,263.95 1492.1,260.28 1084.4,229 995.91,222.21 896,207.79 823.92,196.18"]; id [color=blue, height=0.5, label=string, @@ -32,7 +32,7 @@ digraph { "variant to phenotypic feature association" -> id [color=blue, label=id, lp="1218.4,221.5", - pos="e,1034.4,189.97 3464.6,263.35 2918.5,261.26 1431.9,253.38 1211.4,229 1140.1,221.12 1122.5,215.35 1053.4,196 1050.3,195.13 1047.1,\ + pos="e,1034.4,189.97 3200.2,262.97 2696.9,260.07 1405.3,250.61 1211.4,229 1140.1,221.06 1122.5,215.35 1053.4,196 1050.3,195.13 1047.1,\ 194.16 1043.9,193.14", style=solid]; iri [color=blue, @@ -43,7 +43,7 @@ digraph { "variant to phenotypic feature association" -> iri [color=blue, label=iri, lp="1315.4,221.5", - pos="e,1139.7,190.05 3464.4,263.37 2933.1,261.38 1518.1,253.79 1307.4,229 1251.9,222.47 1189.8,205.46 1149.5,193.09", + pos="e,1139.7,190.03 3200.1,262.96 2712.7,260.1 1491.6,250.84 1307.4,229 1251.9,222.42 1189.8,205.42 1149.5,193.06", style=solid]; name [color=blue, height=0.5, @@ -53,7 +53,7 @@ digraph { "variant to phenotypic feature association" -> name [color=blue, label=name, lp="1411.4,221.5", - pos="e,1259.7,192.4 3463.9,264.09 2945.6,263.85 1592.6,260.22 1391.4,229 1349.1,222.43 1302.5,207.72 1269.5,195.95", + pos="e,1259.7,192.38 3199.3,263.63 2725.6,262.32 1566.2,256.31 1391.4,229 1349.1,222.39 1302.5,207.68 1269.5,195.92", style=solid]; description [color=blue, height=0.5, @@ -63,7 +63,7 @@ digraph { "variant to phenotypic feature association" -> description [color=blue, label=description, lp="1514.9,221.5", - pos="e,1399.8,195.28 3464.9,263.23 2941.9,260.9 1569.9,252.56 1474.4,229 1451.1,223.25 1427,211.26 1408.5,200.45", + pos="e,1399.8,195.26 3200.2,262.76 2723.9,259.5 1556.9,249.45 1474.4,229 1451.1,223.23 1427,211.23 1408.5,200.43", style=solid]; "has attribute" [color=blue, height=0.5, @@ -73,7 +73,7 @@ digraph { "variant to phenotypic feature association" -> "has attribute" [color=blue, label="has attribute", lp="1634.4,221.5", - pos="e,1536,195.21 3464,263.95 2959.5,263.36 1675.1,258.93 1587.4,229 1571.2,223.48 1555.7,212.45 1543.7,202.15", + pos="e,1536,195.2 3199.5,263.41 2743.2,261.64 1662.4,254.72 1587.4,229 1571.2,223.46 1555.7,212.43 1543.7,202.13", style=solid]; predicate [color=blue, height=0.5, @@ -83,18 +83,18 @@ digraph { "variant to phenotypic feature association" -> predicate [color=blue, label=predicate, lp="1734.4,221.5", - pos="e,1674.4,196.16 3465.2,262.91 2972.6,259.92 1738.5,250.3 1700.4,229 1690.9,223.72 1683.9,214.36 1678.8,205.16", + pos="e,1674.4,196.15 3200.7,262.34 2758.5,258.33 1732.7,247.1 1700.4,229 1691,223.71 1683.9,214.35 1678.8,205.14", style=solid]; object [color=blue, height=0.5, label="named thing", - pos="5406.4,91", + pos="5141.4,91", width=1.9318]; "variant to phenotypic feature association" -> object [color=blue, label=object, lp="1813.4,178", - pos="e,5336.7,91.969 3464.8,263.06 3087.2,260.76 2283.6,253.1 2006.4,229 1906.4,220.31 1721.1,231.63 1791.4,160 1855.5,94.718 4801.1,\ -91.943 5326.6,91.968", + pos="e,5071.6,92.076 3199.2,263.74 2858.9,262.52 2183.5,256.57 1947.4,229 1872.1,220.2 1738.3,214.15 1791.4,160 1850.5,99.698 4558.8,\ +92.844 5061.5,92.09", style=solid]; negated [color=blue, height=0.5, @@ -103,8 +103,8 @@ digraph { width=1.2999]; "variant to phenotypic feature association" -> negated [color=blue, label=negated, - lp="2114.4,221.5", - pos="e,1925.2,190.47 3463.6,264.82 3099.3,265.43 2345.7,262.4 2085.4,229 2032.8,222.25 1974.1,205.82 1935.2,193.63", + lp="2020.4,221.5", + pos="e,1914.1,194 3199.1,263.85 2837.6,262.86 2105.1,257.34 1991.4,229 1967.1,222.95 1941.9,210.31 1922.9,199.26", style=solid]; qualifiers [color=blue, height=0.5, @@ -113,8 +113,8 @@ digraph { width=2.1304]; "variant to phenotypic feature association" -> qualifiers [color=blue, label=qualifiers, - lp="2253.9,221.5", - pos="e,2074.4,193.22 3467,261.79 3099.7,257.32 2340.2,246.13 2220.4,229 2173.4,222.28 2121.4,207.89 2084,196.26", + lp="2102.9,221.5", + pos="e,2040,196.19 3199.5,263.32 2839.9,261.47 2118.5,254.57 2069.4,229 2059.2,223.71 2051.1,214.22 2045.1,204.91", style=solid]; publications [color=blue, height=0.5, @@ -123,8 +123,8 @@ digraph { width=1.7332]; "variant to phenotypic feature association" -> publications [color=blue, label=publications, - lp="2400.4,221.5", - pos="e,2225.2,192.74 3467.5,261.59 3128.5,257.02 2462.7,246.03 2356.4,229 2314.2,222.25 2267.8,207.75 2234.7,196.1", + lp="2188.4,221.5", + pos="e,2161.7,194.15 3201.4,261.98 2851.9,257.95 2162.5,247.66 2144.4,229 2135.4,219.75 2142.6,209.17 2153.6,200.13", style=solid]; "has evidence" [color=blue, height=0.5, @@ -133,334 +133,337 @@ digraph { width=2.0943]; "variant to phenotypic feature association" -> "has evidence" [color=blue, label="has evidence", - lp="2559.9,221.5", - pos="e,2383.8,193.52 3464,264.14 3183.7,263.26 2690.3,257.52 2513.4,229 2472,222.32 2426.4,208.33 2393.2,196.84", + lp="2285.9,221.5", + pos="e,2291.5,190.62 3202.6,261.52 2875.5,256.93 2255.9,246.02 2239.4,229 2234.8,224.22 2235.5,219.4 2239.4,214 2245.1,206.14 2262.5,\ +199.08 2281.7,193.39", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2547.4,178", - width=3.015]; + label=string, + pos="2477.4,178", + width=1.0652]; "variant to phenotypic feature association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2715.9,221.5", - pos="e,2574,195.62 3467.6,261.54 3194.8,257.48 2728.1,247.87 2651.4,229 2627.4,223.09 2602.3,211.25 2582.9,200.58", + lp="2416.9,221.5", + pos="e,2448.4,189.86 3198.9,264.38 2902.6,263.94 2381.3,258.88 2352.4,229 2309.9,185.08 2314.6,229.63 2429.4,196 2432.5,195.09 2435.7,\ +194.1 2438.9,193.06", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2782.4,178", - width=3.015]; + label=string, + pos="2572.4,178", + width=1.0652]; "variant to phenotypic feature association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2888.4,221.5", - pos="e,2781.3,196.06 3466.4,262.1 3217,258.82 2818.8,250.28 2793.4,229 2786.7,223.4 2783.5,214.75 2782.2,206.21", + lp="2583.4,221.5", + pos="e,2542.8,189.5 3199.8,263.27 2938.8,261.31 2512.7,254.24 2488.4,229 2483.8,224.2 2484.7,219.55 2488.4,214 2491.2,209.74 2512.7,200.84 \ +2533.2,193.08", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="3017.4,178", - width=3.015]; + label=string, + pos="2667.4,178", + width=1.0652]; "variant to phenotypic feature association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="3097.9,221.5", - pos="e,2999.2,195.77 3470.6,260.37 3277.4,255.8 3007.9,246.34 2991.4,229 2984.6,221.79 2987.2,212.44 2993,203.77", + lp="2802.9,221.5", + pos="e,2672.5,195.99 3199.3,263.71 3006.5,261.88 2738.5,254.66 2696.4,229 2687.5,223.57 2681,214.31 2676.5,205.23", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="3199.4,178", + pos="2887.4,178", width=1.5346]; "variant to phenotypic feature association" -> timepoint [color=blue, label=timepoint, - lp="3254.4,221.5", - pos="e,3201.6,196.2 3477.6,258.47 3365.4,253.57 3240.7,244.66 3219.4,229 3211.9,223.5 3207.2,214.76 3204.3,206.11", + lp="2967.4,221.5", + pos="e,2897.7,196.06 3220.1,256.94 3099.5,251.12 2958.4,241.75 2932.4,229 2921,223.43 2911.2,213.62 2903.7,204.17", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="3311.4,178", + pos="2999.4,178", width=1.0652]; "variant to phenotypic feature association" -> "original subject" [color=blue, label="original subject", - lp="3353.4,221.5", - pos="e,3299.9,195.21 3482.7,257.37 3397,252.34 3310.7,243.67 3297.4,229 3291.2,222.24 3292.2,213 3295.5,204.3", + lp="3072.4,221.5", + pos="e,3000.6,196.09 3222.4,256.52 3130.2,251.09 3033.3,242.32 3016.4,229 3009.2,223.37 3005.1,214.6 3002.7,205.97", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3425.4,178", + pos="3124.4,178", width=1.5887]; "variant to phenotypic feature association" -> "original predicate" [color=blue, label="original predicate", - lp="3481.9,221.5", - pos="e,3416.9,196.2 3492.4,255.76 3458.5,250.51 3429.8,242.16 3418.4,229 3412.9,222.69 3412.5,214.16 3414.1,205.92", + lp="3205.9,221.5", + pos="e,3126.1,196.46 3233.9,254.85 3193.8,249.69 3158,241.61 3142.4,229 3135.4,223.33 3131.1,214.7 3128.5,206.2", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3539.4,178", + pos="3253.4,178", width=1.0652]; "variant to phenotypic feature association" -> "original object" [color=blue, label="original object", - lp="3610.9,221.5", - pos="e,3542.5,196.4 3589.8,248.23 3578.7,243.43 3568.1,237.16 3559.4,229 3552.9,222.9 3548.5,214.41 3545.5,206.17", + lp="3337.9,221.5", + pos="e,3260.9,196.07 3323.3,248.31 3310.2,243.48 3297.3,237.19 3286.4,229 3278,222.71 3271.1,213.6 3265.8,204.89", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3672.4,178", + pos="3386.4,178", width=2.1304]; "variant to phenotypic feature association" -> "subject category" [color=blue, label="subject category", - lp="3725.9,221.5", - pos="e,3669,196.02 3665.1,246.84 3665.1,237.17 3665.4,224.89 3666.4,214 3666.6,211.42 3667,208.75 3667.3,206.08", + lp="3453.9,221.5", + pos="e,3389.2,196.18 3397.6,246.8 3395.6,235.16 3393.1,219.55 3390.9,206.24", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3843.4,178", + pos="3557.4,178", width=2.1304]; "variant to phenotypic feature association" -> "object category" [color=blue, label="object category", - lp="3861.9,221.5", - pos="e,3827.6,195.97 3738.1,248.2 3754.2,243.24 3770.8,236.92 3785.4,229 3797.9,222.19 3810.1,212.3 3820.1,203.12", + lp="3588.9,221.5", + pos="e,3547.5,196.09 3477.1,248.35 3491.2,243.49 3505.3,237.18 3517.4,229 3526.9,222.59 3535.2,213.24 3541.8,204.35", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3976.4,178", + pos="3690.4,178", width=1.0652]; "variant to phenotypic feature association" -> "subject closure" [color=blue, label="subject closure", - lp="3993.9,221.5", - pos="e,3960.8,194.48 3804.4,251.93 3851.8,246.31 3898.2,238.69 3919.4,229 3927,225.51 3941.2,213.09 3953.5,201.5", + lp="3720.9,221.5", + pos="e,3680.9,195.75 3544.9,252.39 3588.4,247 3629.6,239.41 3648.4,229 3659,223.11 3668.1,213.39 3675.1,204.07", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="4072.4,178", + pos="3803.4,178", width=1.0652]; "variant to phenotypic feature association" -> "object closure" [color=blue, label="object closure", - lp="4113.4,221.5", - pos="e,4069.8,196.19 3805.9,252.09 3915.2,242.7 4048.8,230.87 4051.4,229 4059,223.42 4063.9,214.55 4067,205.81", + lp="3842.4,221.5", + pos="e,3799.8,196.24 3544,252.36 3649.1,243.59 3774.4,232.48 3779.4,229 3787.3,223.49 3792.7,214.62 3796.4,205.88", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="4205.4,178", + pos="3936.4,178", width=2.1304]; "variant to phenotypic feature association" -> "subject category closure" [color=blue, label="subject category closure", - lp="4271.9,221.5", - pos="e,4197.3,196.06 3807.2,252.21 3830.3,250.39 3854,248.59 3876.4,247 3908.7,244.7 4138.8,244.28 4167.4,229 4177.6,223.54 4185.9,214.02 \ -4192.1,204.74", + lp="4001.9,221.5", + pos="e,3927.7,196.07 3542.5,252.21 3565.5,250.4 3589.1,248.6 3611.4,247 3643,244.73 3868.2,243.64 3896.4,229 3907,223.5 3915.7,213.84 \ +3922.3,204.47", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="4394.4,178", + pos="4129.4,178", width=2.1304]; "variant to phenotypic feature association" -> "object category closure" [color=blue, label="object category closure", - lp="4461.9,221.5", - pos="e,4388.7,196.07 3804.4,251.94 3828.4,250.1 3853.1,248.37 3876.4,247 3903.4,245.41 4340,242.6 4363.4,229 4372.6,223.67 4379.4,214.43 \ -4384.3,205.33", + lp="4193.9,221.5", + pos="e,4122,196.14 3539.4,251.95 3563.4,250.11 3588.1,248.37 3611.4,247 3664.9,243.85 4046.2,254.32 4093.4,229 4103.4,223.64 4111.3,214.13 \ +4117.1,204.84", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4584.4,178", + pos="4319.4,178", width=1.0652]; "variant to phenotypic feature association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4634.4,221.5", - pos="e,4577.4,196.17 3802.9,251.85 3827.4,249.99 3852.6,248.27 3876.4,247 3913.7,245 4516.5,246.71 4549.4,229 4559.2,223.73 4566.8,214.37 \ -4572.5,205.17", + lp="4366.4,221.5", + pos="e,4311.7,195.71 3538.2,251.83 3562.6,249.98 3587.7,248.27 3611.4,247 3648.6,245 4248.3,245.99 4281.4,229 4291.8,223.65 4300.2,213.96 \ +4306.4,204.53", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4743.4,178", + pos="4478.4,178", width=1.0652]; "variant to phenotypic feature association" -> "object namespace" [color=blue, label="object namespace", - lp="4787.4,221.5", - pos="e,4736,195.72 3802.4,251.79 3827,249.93 3852.4,248.22 3876.4,247 3922.5,244.65 4665.4,250.2 4706.4,229 4716.7,223.66 4724.9,213.97 \ -4730.9,204.54", + lp="4520.4,221.5", + pos="e,4470.1,195.75 3537.4,251.79 3562,249.93 3587.4,248.22 3611.4,247 3657.3,244.65 4397.2,249.36 4438.4,229 4449.2,223.65 4458.1,213.82 \ +4464.7,204.29", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4894.4,178", + pos="4629.4,178", width=1.0652]; "variant to phenotypic feature association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4947.4,221.5", - pos="e,4886.4,195.76 3802.1,251.74 3826.8,249.88 3852.4,248.19 3876.4,247 3930.7,244.31 4806.7,253.31 4855.4,229 4866.1,223.65 4874.7,\ -213.83 4881.2,204.29", + lp="4680.4,221.5", + pos="e,4620.8,195.78 3537.1,251.74 3561.8,249.88 3587.4,248.19 3611.4,247 3665.6,244.32 4539.5,252.67 4588.4,229 4599.4,223.68 4608.4,\ +213.86 4615.2,204.32", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="5014.4,178", + pos="4749.4,178", width=1.0652]; "variant to phenotypic feature association" -> "object label closure" [color=blue, label="object label closure", - lp="5100.9,221.5", - pos="e,5024.7,195.5 3801.8,251.71 3826.6,249.85 3852.3,248.16 3876.4,247 3908.3,245.47 5003,251.75 5025.4,229 5031.6,222.65 5031.3,213.6 \ -5028.6,204.95", + lp="4833.9,221.5", + pos="e,4758.8,195.55 3536.8,251.71 3561.6,249.85 3587.3,248.16 3611.4,247 3643.2,245.47 4736,251.71 4758.4,229 4764.6,222.7 4764.6,213.66 \ +4762.2,205", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="5155.4,178", + pos="4890.4,178", width=2.347]; "variant to phenotypic feature association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="5248.9,221.5", - pos="e,5170.2,196.21 3801.5,251.7 3826.4,249.83 3852.2,248.14 3876.4,247 3894.4,246.15 5161.7,241.84 5174.4,229 5180.9,222.42 5179.5,\ -213.41 5175.3,204.85", + lp="4981.9,221.5", + pos="e,4903.9,195.81 3536.5,251.7 3561.4,249.83 3587.2,248.14 3611.4,247 3629.4,246.15 4894.8,241.82 4907.4,229 4913.8,222.48 4912.6,\ +213.44 4908.8,204.83", style=solid]; type [height=0.5, - pos="5289.4,178", + pos="5024.4,178", width=0.86659]; "variant to phenotypic feature association" -> type [color=blue, label=type, - lp="5343.4,221.5", - pos="e,5308.1,192.56 3801.2,251.69 3826.2,249.81 3852.1,248.13 3876.4,247 3896.5,246.07 5308.3,243.29 5322.4,229 5331,220.33 5324.8,209.13 \ -5315.5,199.52", + lp="5076.4,221.5", + pos="e,5042.5,192.88 3536.2,251.69 3561.2,249.81 3587.1,248.13 3611.4,247 3631.4,246.07 5041.3,243.27 5055.4,229 5063.7,220.63 5058.2,\ +209.67 5049.7,200.14", style=solid]; category [height=0.5, - pos="5390.4,178", + pos="5125.4,178", width=1.4263]; "variant to phenotypic feature association" -> category [color=blue, label=category, - lp="5408.9,221.5", - pos="e,5386.1,196.09 3801.2,251.68 3826.2,249.81 3852.1,248.13 3876.4,247 3917.7,245.09 5328,250.38 5363.4,229 5372.1,223.75 5378.1,214.65 \ -5382.3,205.65", + lp="5142.9,221.5", + pos="e,5120.4,196.13 3536.2,251.68 3561.2,249.81 3587.1,248.13 3611.4,247 3652.6,245.09 5060.8,249.81 5096.4,229 5105.4,223.74 5111.9,\ +214.51 5116.4,205.41", style=solid]; subject [height=0.5, - pos="5504.4,178", + pos="5239.4,178", width=1.2277]; "variant to phenotypic feature association" -> subject [color=blue, label=subject, - lp="5496.4,221.5", - pos="e,5490.5,195.46 3801.2,251.67 3826.2,249.8 3852.1,248.12 3876.4,247 3919.9,245 5403.5,244.06 5444.4,229 5459.1,223.57 5472.8,212.81 \ -5483.4,202.66", + lp="5231.4,221.5", + pos="e,5225.2,195.46 3536.2,251.67 3561.2,249.8 3587.1,248.12 3611.4,247 3654.9,245 5137.5,243.89 5178.4,229 5193.3,223.57 5207.2,212.82 \ +5218,202.66", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="5651.4,178", + pos="5386.4,178", width=2.3651]; "variant to phenotypic feature association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="5644.4,221.5", - pos="e,5621,194.84 3800.9,251.68 3826,249.8 3852,248.12 3876.4,247 3968,242.82 5436.5,246.83 5526.4,229 5556.1,223.1 5587.9,210.33 5611.9,\ + lp="5379.4,221.5", + pos="e,5356,194.84 3535.9,251.68 3561,249.8 3587,248.12 3611.4,247 3703,242.82 5171.5,246.83 5261.4,229 5291.1,223.1 5322.9,210.33 5346.9,\ 199.18", style=solid]; "severity qualifier" [color=blue, height=0.5, label="severity value", - pos="5830.4,178", + pos="5565.4,178", width=2.1123]; "variant to phenotypic feature association" -> "severity qualifier" [color=blue, label="severity qualifier", - lp="5823.4,221.5", - pos="e,5802.9,194.85 3800.9,251.66 3826,249.78 3852,248.1 3876.4,247 3978.5,242.39 5616.4,250.47 5716.4,229 5743.6,223.16 5772.2,210.57 \ -5794,199.48", + lp="5558.4,221.5", + pos="e,5537.9,194.85 3535.9,251.66 3561,249.78 3587,248.1 3611.4,247 3713.5,242.39 5351.4,250.47 5451.4,229 5478.6,223.16 5507.2,210.57 \ +5529,199.48", style=solid]; "onset qualifier" [color=blue, height=0.5, label=onset, - pos="5960.4,178", + pos="5695.4,178", width=1.011]; "variant to phenotypic feature association" -> "onset qualifier" [color=blue, label="onset qualifier", - lp="5969.9,221.5", - pos="e,5944.5,194.3 3800.9,251.64 3826,249.76 3852,248.09 3876.4,247 3932.2,244.5 5835.1,245.94 5888.4,229 5906.3,223.31 5923.7,211.49 \ -5936.9,200.77", + lp="5704.9,221.5", + pos="e,5679.5,194.3 3535.9,251.64 3561,249.76 3587,248.09 3611.4,247 3667.2,244.5 5570.1,245.94 5623.4,229 5641.3,223.31 5658.7,211.49 \ +5671.9,200.77", style=solid]; "sex qualifier" [color=blue, height=0.5, label="biological sex", - pos="6088.4,178", + pos="5823.4,178", width=2.0401]; "variant to phenotypic feature association" -> "sex qualifier" [color=blue, label="sex qualifier", - lp="6096.4,221.5", - pos="e,6073.2,195.99 3800.7,251.65 3825.8,249.77 3851.9,248.09 3876.4,247 3936,244.35 5969.1,248.89 6025.4,229 6040.4,223.68 6054.6,213.15 \ -6065.7,203.12", + lp="5831.4,221.5", + pos="e,5808.2,195.99 3535.7,251.65 3560.8,249.77 3586.9,248.09 3611.4,247 3671,244.35 5704.1,248.89 5760.4,229 5775.4,223.68 5789.6,213.15 \ +5800.7,203.12", style=solid]; "has count" [color=blue, height=0.5, label=integer, - pos="6224.4,178", + pos="5959.4,178", width=1.2277]; "variant to phenotypic feature association" -> "has count" [color=blue, label="has count", - lp="6212.4,221.5", - pos="e,6206.1,194.57 3800.7,251.64 3825.8,249.76 3851.9,248.08 3876.4,247 3939.3,244.22 6083.9,246.61 6144.4,229 6163.9,223.34 6183.2,\ -211.47 6198,200.72", + lp="5947.4,221.5", + pos="e,5941.1,194.57 3535.7,251.64 3560.8,249.76 3586.9,248.08 3611.4,247 3674.3,244.22 5818.9,246.61 5879.4,229 5898.9,223.34 5918.2,\ +211.47 5933,200.72", style=solid]; "has total" [color=blue, height=0.5, label=integer, - pos="6330.4,178", + pos="6065.4,178", width=1.2277]; "variant to phenotypic feature association" -> "has total" [color=blue, label="has total", - lp="6315.9,221.5", - pos="e,6312.4,194.57 3800.7,251.63 3825.8,249.75 3851.9,248.08 3876.4,247 3942.3,244.1 6188.1,247.61 6251.4,229 6270.7,223.34 6289.8,\ -211.47 6304.3,200.72", + lp="6050.9,221.5", + pos="e,6047.4,194.57 3535.7,251.63 3560.8,249.75 3586.9,248.08 3611.4,247 3677.3,244.1 5923.1,247.61 5986.4,229 6005.7,223.34 6024.8,\ +211.47 6039.3,200.72", style=solid]; "has quotient" [color=blue, height=0.5, label=double, - pos="6434.4,178", + pos="6169.4,178", width=1.1735]; "variant to phenotypic feature association" -> "has quotient" [color=blue, label="has quotient", - lp="6430.4,221.5", - pos="e,6415.7,194.34 3800.7,251.63 3825.8,249.75 3851.9,248.07 3876.4,247 3945.1,243.99 6285.2,247.65 6351.4,229 6371.6,223.32 6391.8,\ -211.33 6407.2,200.51", + lp="6165.4,221.5", + pos="e,6150.7,194.34 3535.7,251.63 3560.8,249.75 3586.9,248.07 3611.4,247 3680.1,243.99 6020.2,247.65 6086.4,229 6106.6,223.32 6126.8,\ +211.33 6142.2,200.51", style=solid]; "has percentage" [color=blue, height=0.5, label=double, - pos="6541.4,178", + pos="6276.4,178", width=1.1735]; "variant to phenotypic feature association" -> "has percentage" [color=blue, label="has percentage", - lp="6560.4,221.5", - pos="e,6527.4,195 3800.7,251.62 3825.8,249.74 3851.9,248.07 3876.4,247 3948.6,243.84 6411.3,253.3 6479.4,229 6494.7,223.54 6509,212.56 \ -6520,202.28", + lp="6295.4,221.5", + pos="e,6262.4,195 3535.7,251.62 3560.8,249.74 3586.9,248.07 3611.4,247 3683.6,243.84 6146.3,253.3 6214.4,229 6229.7,223.54 6244,212.56 \ +6255,202.28", style=solid]; relation [height=0.5, - pos="5455.4,18", + pos="5190.4,18", width=1.2999]; - object -> relation [pos="e,5443.9,35.705 5418,73.174 5424,64.509 5431.4,53.768 5438,44.141", + object -> relation [pos="e,5178.9,35.705 5153,73.174 5159,64.509 5166.4,53.768 5173,44.141", style=dotted]; association_type [color=blue, height=0.5, label=string, - pos="3923.4,265", + pos="3658.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="4054.4,265", + pos="3789.4,265", width=2.0762]; subject -> object [label=relation, - lp="5462.4,134.5", - pos="e,5412.8,108.97 5471.9,165.59 5459.1,159.94 5445,152.13 5434.4,142 5427.4,135.31 5421.7,126.48 5417.3,118.1"]; - subject -> relation [pos="e,5466.6,35.828 5503,159.99 5500.9,139.02 5496,102.55 5485.4,73 5481.9,63.258 5476.8,53.189 5471.8,44.423", + lp="5197.4,134.5", + pos="e,5147.8,108.97 5206.9,165.59 5194.1,159.94 5180,152.13 5169.4,142 5162.4,135.31 5156.7,126.48 5152.3,118.1"]; + subject -> relation [pos="e,5201.6,35.828 5238,159.99 5235.9,139.02 5231,102.55 5220.4,73 5216.9,63.258 5211.8,53.189 5206.8,44.423", style=dotted]; "variant to phenotypic feature association_subject" [color=blue, height=0.5, label="sequence variant", - pos="4237.4,265", + pos="3972.4,265", width=2.5095]; } diff --git a/graphviz/variant_to_phenotypic_feature_association.svg b/graphviz/variant_to_phenotypic_feature_association.svg index 5ab032189a..a5a0dde570 100644 --- a/graphviz/variant_to_phenotypic_feature_association.svg +++ b/graphviz/variant_to_phenotypic_feature_association.svg @@ -4,16 +4,16 @@ - + %3 - + variant to phenotypic feature association - -variant to phenotypic feature association + +variant to phenotypic feature association @@ -24,7 +24,7 @@ variant to phenotypic feature association->association - + is_a @@ -37,8 +37,8 @@ variant to phenotypic feature association->variant to entity association mixin - - + + uses @@ -50,8 +50,8 @@ variant to phenotypic feature association->entity to phenotypic feature association mixin - - + + uses @@ -63,7 +63,7 @@ variant to phenotypic feature association->id - + id @@ -76,8 +76,8 @@ variant to phenotypic feature association->iri - - + + iri @@ -89,8 +89,8 @@ variant to phenotypic feature association->name - - + + name @@ -102,8 +102,8 @@ variant to phenotypic feature association->description - - + + description @@ -115,8 +115,8 @@ variant to phenotypic feature association->has attribute - - + + has attribute @@ -128,21 +128,21 @@ variant to phenotypic feature association->predicate - - + + predicate object - -named thing + +named thing variant to phenotypic feature association->object - - + + object @@ -154,9 +154,9 @@ variant to phenotypic feature association->negated - - -negated + + +negated @@ -167,9 +167,9 @@ variant to phenotypic feature association->qualifiers - - -qualifiers + + +qualifiers @@ -180,9 +180,9 @@ variant to phenotypic feature association->publications - - -publications + + +publications @@ -193,429 +193,429 @@ variant to phenotypic feature association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string variant to phenotypic feature association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string variant to phenotypic feature association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string variant to phenotypic feature association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type variant to phenotypic feature association->timepoint - - -timepoint + + +timepoint original subject - -string + +string variant to phenotypic feature association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie variant to phenotypic feature association->original predicate - - -original predicate + + +original predicate original object - -string + +string variant to phenotypic feature association->original object - - -original object + + +original object subject category - -ontology class + +ontology class variant to phenotypic feature association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class variant to phenotypic feature association->object category - - -object category + + +object category subject closure - -string + +string variant to phenotypic feature association->subject closure - - -subject closure + + +subject closure object closure - -string + +string variant to phenotypic feature association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class variant to phenotypic feature association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class variant to phenotypic feature association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string variant to phenotypic feature association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string variant to phenotypic feature association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string variant to phenotypic feature association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string variant to phenotypic feature association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source variant to phenotypic feature association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type variant to phenotypic feature association->type - - -type + + +type category - -category + +category variant to phenotypic feature association->category - - -category + + +category subject - -subject + +subject variant to phenotypic feature association->subject - - -subject + + +subject frequency qualifier - -frequency value + +frequency value variant to phenotypic feature association->frequency qualifier - - -frequency qualifier + + +frequency qualifier severity qualifier - -severity value + +severity value variant to phenotypic feature association->severity qualifier - - -severity qualifier + + +severity qualifier onset qualifier - -onset + +onset variant to phenotypic feature association->onset qualifier - - -onset qualifier + + +onset qualifier sex qualifier - -biological sex + +biological sex variant to phenotypic feature association->sex qualifier - - -sex qualifier + + +sex qualifier has count - -integer + +integer variant to phenotypic feature association->has count - - -has count + + +has count has total - -integer + +integer variant to phenotypic feature association->has total - - -has total + + +has total has quotient - -double + +double variant to phenotypic feature association->has quotient - - -has quotient + + +has quotient has percentage - -double + +double variant to phenotypic feature association->has percentage - - -has percentage + + +has percentage relation - -relation + +relation object->relation - - + + association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation subject->relation - - + + variant to phenotypic feature association_subject - -sequence variant + +sequence variant diff --git a/graphviz/variant_to_population_association.gv b/graphviz/variant_to_population_association.gv index 7601a82b31..06278c8f47 100644 --- a/graphviz/variant_to_population_association.gv +++ b/graphviz/variant_to_population_association.gv @@ -1,35 +1,35 @@ digraph { - graph [bb="0,0,6331.5,283"]; + graph [bb="0,0,6073.5,283"]; node [label="\N"]; "variant to population association" [height=0.5, label="variant to population association", - pos="3494.4,265", + pos="3236.4,265", width=4.5315]; association [height=0.5, pos="62.394,178", width=1.7332]; "variant to population association" -> association [label=is_a, - lp="608.39,221.5", - pos="e,106.49,190.74 3331.6,263.31 2802.4,260.87 1133.5,251.53 594.39,229 389.16,220.42 336.4,227.35 133.39,196 127.91,195.15 122.23,\ -194.1 116.58,192.93"]; + lp="607.39,221.5", + pos="e,106.49,190.74 3073.8,263.09 2576.5,260.12 1080,249.66 593.39,229 388.61,220.31 335.96,227.3 133.39,196 127.91,195.15 122.23,194.1 \ +116.58,192.93"]; "variant to entity association mixin" [height=0.5, pos="312.39,178", width=4.7121]; "variant to population association" -> "variant to entity association mixin" [label=uses, - lp="816.89,221.5", - pos="e,415.94,192.31 3331.3,263.79 2827.1,262.84 1296.8,257.6 800.39,229 671.75,221.59 524.7,205.47 425.95,193.53"]; + lp="815.89,221.5", + pos="e,416.21,192.33 3073.7,263.53 2602.7,261.88 1243.6,254.94 799.39,229 671.22,221.51 524.74,205.45 426.19,193.54"]; "frequency quantifier" [height=0.5, pos="605.39,178", width=2.9247]; "variant to population association" -> "frequency quantifier" [label=uses, - lp="998.89,221.5", - pos="e,677.05,191.21 3331.4,264.1 2850.3,264.03 1441.4,261.01 982.39,229 880.12,221.87 763.21,204.99 687.05,192.82"]; + lp="997.89,221.5", + pos="e,677.21,191.23 3073.6,263.81 2626.8,262.9 1388.3,257.79 981.39,229 879.55,221.79 763.16,204.98 687.19,192.83"]; "frequency qualifier mixin" [height=0.5, pos="856.39,178", width=3.5386]; "variant to population association" -> "frequency qualifier mixin" [label=uses, - lp="1137.9,221.5", - pos="e,918.07,193.75 3331.9,263.22 2832.2,260.6 1339.3,251 1121.4,229 1055.3,222.33 981.1,207.7 928.05,195.98"]; + lp="1135.9,221.5", + pos="e,917.86,193.78 3074.1,262.92 2612.2,259.62 1311.3,248.68 1119.4,229 1053.9,222.28 980.39,207.7 927.77,196"]; id [color=blue, height=0.5, label=string, @@ -37,9 +37,9 @@ digraph { width=1.0652]; "variant to population association" -> id [color=blue, label=id, - lp="1257.4,221.5", - pos="e,1069.4,190 3331.8,263.21 2850.8,260.61 1455,251.24 1250.4,229 1177.3,221.06 1159.2,215.65 1088.4,196 1085.3,195.14 1082.1,194.17 \ -1078.9,193.16", + lp="1253.4,221.5", + pos="e,1069.4,189.97 3074,262.9 2631.4,259.66 1425.3,249.07 1246.4,229 1175.1,221 1157.5,215.35 1088.4,196 1085.3,195.13 1082.1,194.16 \ +1078.9,193.14", style=solid]; iri [color=blue, height=0.5, @@ -48,9 +48,9 @@ digraph { width=1.2277]; "variant to population association" -> iri [color=blue, label=iri, - lp="1374.4,221.5", - pos="e,1174.3,190.23 3332.1,262.95 2868.5,259.73 1559.4,248.95 1366.4,229 1289,221 1269.8,215.26 1194.4,196 1191,195.14 1187.5,194.18 \ -1184,193.17", + lp="1365.4,221.5", + pos="e,1174.3,190.18 3074.3,262.66 2649.5,258.92 1525.2,247.39 1357.4,229 1283.9,220.95 1265.9,214.65 1194.4,196 1191,195.12 1187.5,194.15 \ +1184.1,193.13", style=solid]; name [color=blue, height=0.5, @@ -59,8 +59,8 @@ digraph { width=1.5707]; "variant to population association" -> name [color=blue, label=name, - lp="1485.4,221.5", - pos="e,1299.2,191.28 3332,263.21 2883.3,260.76 1647.9,251.97 1465.4,229 1411,222.16 1350.1,206.23 1309,194.17", + lp="1471.4,221.5", + pos="e,1297.9,191.64 3074.2,263.01 2664.5,260.19 1609.2,250.88 1451.4,229 1401.5,222.08 1346,206.65 1307.7,194.74", style=solid]; description [color=blue, height=0.5, @@ -69,8 +69,8 @@ digraph { width=2.0943]; "variant to population association" -> description [color=blue, label=description, - lp="1612.9,221.5", - pos="e,1447.6,193.79 3331.6,263.65 2899.2,262.36 1743.3,256.37 1572.4,229 1532.6,222.63 1489.1,208.78 1457.2,197.27", + lp="1589.9,221.5", + pos="e,1443.3,194.26 3073.7,263.62 2679.7,262.27 1696.3,256.18 1549.4,229 1515.9,222.81 1479.8,209.6 1452.8,198.31", style=solid]; "has attribute" [color=blue, height=0.5, @@ -79,8 +79,8 @@ digraph { width=1.4443]; "variant to population association" -> "has attribute" [color=blue, label="has attribute", - lp="1769.4,221.5", - pos="e,1588.7,191.89 3331.9,263.3 2923.9,261.19 1878.4,253.43 1722.4,229 1679.1,222.22 1631.4,207.13 1598.1,195.29", + lp="1732.4,221.5", + pos="e,1583.7,193.17 3073.5,263.49 2703,261.87 1818.5,255.27 1685.4,229 1653.1,222.63 1618.4,208.9 1593,197.43", style=solid]; predicate [color=blue, height=0.5, @@ -89,8 +89,8 @@ digraph { width=2.1665]; "variant to population association" -> predicate [color=blue, label=predicate, - lp="1928.4,221.5", - pos="e,1746,193.24 3332.6,262.61 2954.3,259.05 2033.7,248.49 1894.4,229 1846.7,222.33 1793.9,207.93 1755.9,196.29", + lp="1869.4,221.5", + pos="e,1735,194.46 3074,263.01 2730.9,260.47 1953.9,252.22 1835.4,229 1803.8,222.81 1769.9,209.83 1744.4,198.65", style=solid]; negated [color=blue, height=0.5, @@ -99,8 +99,8 @@ digraph { width=1.2999]; "variant to population association" -> negated [color=blue, label=negated, - lp="2071.4,221.5", - pos="e,1880.6,190.46 3331.3,264.29 3006.1,264.18 2287.1,260.25 2042.4,229 1989.1,222.19 1929.5,205.66 1890.1,193.46", + lp="1976.4,221.5", + pos="e,1869.4,193.98 3073.8,263.49 2751.5,261.9 2053.8,255.41 1947.4,229 1922.8,222.89 1897.2,210.17 1878,199.09", style=solid]; qualifiers [color=blue, height=0.5, @@ -109,8 +109,8 @@ digraph { width=2.1304]; "variant to population association" -> qualifiers [color=blue, label=qualifiers, - lp="2210.9,221.5", - pos="e,2029.5,193.07 3331.1,264.36 3029.4,264.24 2395.2,260.12 2177.4,229 2129.8,222.2 2077.1,207.74 2039.2,196.11", + lp="2059.9,221.5", + pos="e,1995.7,196.21 3074.2,262.95 2755,260.39 2072.3,252.22 2026.4,229 2016,223.72 2007.5,214.23 2001.1,204.93", style=solid]; publications [color=blue, height=0.5, @@ -119,8 +119,8 @@ digraph { width=1.7332]; "variant to population association" -> publications [color=blue, label=publications, - lp="2358.4,221.5", - pos="e,2180.9,192.71 3331.3,264.32 3054.8,263.99 2505.2,259.37 2314.4,229 2271.5,222.18 2224.3,207.69 2190.5,196.06", + lp="2145.4,221.5", + pos="e,2117.8,194.29 3075.4,261.91 2766.2,257.5 2118.1,246.23 2101.4,229 2092.7,220 2099.3,209.56 2109.7,200.56", style=solid]; "has evidence" [color=blue, height=0.5, @@ -129,326 +129,328 @@ digraph { width=2.0943]; "variant to population association" -> "has evidence" [color=blue, label="has evidence", - lp="2512.9,221.5", - pos="e,2338.6,193.61 3331.6,263.57 3084.9,262.05 2627.8,255.6 2466.4,229 2425.8,222.3 2381.1,208.48 2348.4,197.06", + lp="2244.9,221.5", + pos="e,2240.8,189.21 3073.2,264.36 2788.5,264.18 2228.2,259.87 2198.4,229 2181.9,211.94 2203.4,199.87 2230.9,191.87", style=solid]; "knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2502.4,178", - width=3.015]; + label=string, + pos="2432.4,178", + width=1.0652]; "variant to population association" -> "knowledge source" [color=blue, label="knowledge source", - lp="2667.9,221.5", - pos="e,2528.2,195.59 3334.6,261.34 3097.3,256.84 2672,246.47 2603.4,229 2580.1,223.06 2555.9,211.3 2537,200.68", + lp="2374.9,221.5", + pos="e,2403.4,189.82 3073.7,263.63 2815,262.23 2336.4,255.99 2310.4,229 2269.3,186.28 2280.7,226.9 2384.4,196 2387.5,195.08 2390.7,194.07 \ +2393.9,193.03", style=solid]; "primary knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2737.4,178", - width=3.015]; + label=string, + pos="2527.4,178", + width=1.0652]; "variant to population association" -> "primary knowledge source" [color=blue, label="primary knowledge source", - lp="2839.4,221.5", - pos="e,2734.8,196.37 3333.9,261.67 3120.1,257.83 2765.8,248.54 2744.4,229 2738.2,223.35 2735.7,214.95 2734.9,206.63", + lp="2541.4,221.5", + pos="e,2498,189.9 3074.5,262.48 2849.6,259.56 2467.7,251.32 2446.4,229 2441.8,224.18 2442.7,219.57 2446.4,214 2449.1,209.93 2469.1,201.26 \ +2488.5,193.57", style=solid]; "aggregator knowledge source" [color=blue, height=0.5, - label="information resource", - pos="2972.4,178", - width=3.015]; + label=string, + pos="2622.4,178", + width=1.0652]; "variant to population association" -> "aggregator knowledge source" [color=blue, label="aggregator knowledge source", - lp="3047.9,221.5", - pos="e,2951.1,195.91 3331.3,264.77 3177.8,263.73 2967.8,257.1 2941.4,229 2934.3,221.47 2937.7,212.1 2944.3,203.51", + lp="2761.9,221.5", + pos="e,2628.8,196.01 3075.8,261.65 2916.5,258.14 2691,249.58 2655.4,229 2645.9,223.54 2638.7,214.14 2633.4,204.96", style=solid]; timepoint [color=blue, height=0.5, label="time type", - pos="3154.4,178", + pos="2849.4,178", width=1.5346]; "variant to population association" -> timepoint [color=blue, label=timepoint, - lp="3202.4,221.5", - pos="e,3154.2,196.41 3351.8,256.21 3270.5,250.46 3181.9,241.47 3167.4,229 3160.8,223.34 3157.4,214.82 3155.6,206.41", + lp="2924.4,221.5", + pos="e,2858.2,195.91 3079.7,259.91 3003.8,255.61 2922.2,246.83 2889.4,229 2879,223.36 2870.4,213.81 2863.8,204.56", style=solid]; "original subject" [color=blue, height=0.5, label=string, - pos="3266.4,178", + pos="2961.4,178", width=1.0652]; "variant to population association" -> "original subject" [color=blue, label="original subject", - lp="3300.4,221.5", - pos="e,3251.2,194.78 3341,258.83 3297.6,253.95 3258.3,245.04 3244.4,229 3238,221.59 3240.3,212 3245.4,203.21", + lp="3027.4,221.5", + pos="e,2960.1,196.24 3082.8,258.8 3034.3,254.01 2988.7,245.17 2971.4,229 2965.2,223.22 2962.3,214.78 2961,206.47", style=solid]; "original predicate" [color=blue, height=0.5, label=uriorcurie, - pos="3380.4,178", + pos="3086.4,178", width=1.5887]; "variant to population association" -> "original predicate" [color=blue, label="original predicate", - lp="3426.9,221.5", - pos="e,3367.4,195.6 3409.1,249.62 3388.2,244.3 3369.9,237.45 3363.4,229 3358,221.92 3359.1,212.99 3362.6,204.65", + lp="3157.9,221.5", + pos="e,3084.7,196.34 3146.3,249.98 3123.1,244.61 3102.3,237.64 3094.4,229 3088.8,222.91 3086.2,214.52 3085.2,206.36", style=solid]; "original object" [color=blue, height=0.5, label=string, - pos="3494.4,178", + pos="3215.4,178", width=1.0652]; "variant to population association" -> "original object" [color=blue, label="original object", - lp="3545.9,221.5", - pos="e,3494.4,196.18 3494.4,246.8 3494.4,235.16 3494.4,219.55 3494.4,206.24", + lp="3278.9,221.5", + pos="e,3219.6,196.18 3232.1,246.8 3229.3,235.16 3225.4,219.55 3222.1,206.24", style=solid]; "subject category" [color=blue, height=0.5, label="ontology class", - pos="3627.4,178", + pos="3348.4,178", width=2.1304]; "variant to population association" -> "subject category" [color=blue, label="subject category", - lp="3670.9,221.5", - pos="e,3621.2,195.97 3563.2,248.67 3575.8,243.78 3588.1,237.38 3598.4,229 3606.2,222.66 3612.3,213.66 3616.9,205.03", + lp="3402.9,221.5", + pos="e,3347.5,196.22 3306.3,248.51 3316.8,243.67 3326.6,237.32 3334.4,229 3340.2,222.79 3343.6,214.38 3345.6,206.22", style=solid]; "object category" [color=blue, height=0.5, label="ontology class", - pos="3798.4,178", + pos="3519.4,178", width=2.1304]; "variant to population association" -> "object category" [color=blue, label="object category", - lp="3814.9,221.5", - pos="e,3782.1,195.71 3612.4,252.51 3661.4,246.55 3712.1,238.52 3734.4,229 3749,222.76 3763.1,212.32 3774.4,202.6", + lp="3543.9,221.5", + pos="e,3506,196.2 3354.5,252.53 3400.1,246.74 3446.2,238.85 3466.4,229 3478.7,223.02 3490,213.21 3499,203.86", style=solid]; "subject closure" [color=blue, height=0.5, label=string, - pos="3931.4,178", + pos="3652.4,178", width=1.0652]; "variant to population association" -> "subject closure" [color=blue, label="subject closure", - lp="3948.9,221.5", - pos="e,3915.9,194.59 3610.5,252.33 3629.2,250.51 3648.3,248.68 3666.4,247 3712.6,242.72 3831.7,247.2 3874.4,229 3882.1,225.71 3896.3,\ -213.29 3908.6,201.65", + lp="3678.9,221.5", + pos="e,3641.2,195.51 3353,252.38 3371.5,250.56 3390.5,248.71 3408.4,247 3451.7,242.86 3564.1,247.68 3603.4,229 3615.6,223.21 3626.4,213.05 \ +3634.8,203.39", style=solid]; "object closure" [color=blue, height=0.5, label=string, - pos="4027.4,178", + pos="3765.4,178", width=1.0652]; "variant to population association" -> "object closure" [color=blue, label="object closure", - lp="4068.4,221.5", - pos="e,4024.9,196.31 3608.1,252.02 3627.6,250.19 3647.5,248.43 3666.4,247 3704.1,244.14 3975.5,250.77 4006.4,229 4014.1,223.57 4019,214.72 \ -4022.1,205.97", + lp="3801.4,221.5", + pos="e,3760.6,195.96 3350.1,252.05 3369.6,250.21 3389.5,248.45 3408.4,247 3444.9,244.2 3706.3,248.37 3737.4,229 3746.2,223.53 3752.4,\ +214.26 3756.8,205.18", style=solid]; "subject category closure" [color=blue, height=0.5, label="ontology class", - pos="4160.4,178", + pos="3898.4,178", width=2.1304]; "variant to population association" -> "subject category closure" [color=blue, label="subject category closure", - lp="4226.9,221.5", - pos="e,4152.4,196.15 3606.7,251.93 3626.6,250.08 3647.1,248.33 3666.4,247 3717,243.5 4077.4,252.42 4122.4,229 4132.7,223.66 4140.9,214.15 \ -4147.1,204.86", + lp="3961.9,221.5", + pos="e,3888.8,196.2 3348.7,251.95 3368.6,250.09 3389.1,248.34 3408.4,247 3458,243.55 3810.6,250.64 3855.4,229 3866.4,223.66 3875.8,214.02 \ +3882.9,204.63", style=solid]; "object category closure" [color=blue, height=0.5, label="ontology class", - pos="4349.4,178", + pos="4091.4,178", width=2.1304]; "variant to population association" -> "object category closure" [color=blue, label="object category closure", - lp="4416.9,221.5", - pos="e,4343.7,196.11 3605.8,251.83 3625.9,249.96 3646.8,248.24 3666.4,247 3702.6,244.72 4287,247.06 4318.4,229 4327.6,223.71 4334.4,214.48 \ -4339.3,205.37", + lp="4153.9,221.5", + pos="e,4083.4,196.2 3347.8,251.83 3367.9,249.96 3388.8,248.24 3408.4,247 3444.2,244.74 4021.5,245.38 4053.4,229 4063.7,223.72 4072,214.22 \ +4078.1,204.92", style=solid]; "subject namespace" [color=blue, height=0.5, label=string, - pos="4539.4,178", + pos="4281.4,178", width=1.0652]; "variant to population association" -> "subject namespace" [color=blue, label="subject namespace", - lp="4589.4,221.5", - pos="e,4532.4,196.19 3605.3,251.77 3625.6,249.89 3646.6,248.19 3666.4,247 3712.9,244.21 4463.3,250.95 4504.4,229 4514.2,223.76 4521.9,\ -214.4 4527.5,205.19", + lp="4327.4,221.5", + pos="e,4273.1,195.76 3347.3,251.77 3367.6,249.89 3388.6,248.19 3408.4,247 3454.6,244.22 4199.9,249.5 4241.4,229 4252.2,223.65 4261.1,\ +213.82 4267.7,204.29", style=solid]; "object namespace" [color=blue, height=0.5, label=string, - pos="4698.4,178", + pos="4440.4,178", width=1.0652]; "variant to population association" -> "object namespace" [color=blue, label="object namespace", - lp="4742.4,221.5", - pos="e,4691,195.74 3605.3,251.71 3625.6,249.84 3646.6,248.15 3666.4,247 3721.6,243.78 4612.3,254.33 4661.4,229 4671.7,223.68 4679.9,213.99 \ -4685.9,204.56", + lp="4481.4,221.5", + pos="e,4431.8,195.78 3347.3,251.72 3367.6,249.84 3388.6,248.15 3408.4,247 3463.4,243.79 4349.8,253 4399.4,229 4410.4,223.68 4419.4,213.86 \ +4426.2,204.32", style=solid]; "subject label closure" [color=blue, height=0.5, label=string, - pos="4849.4,178", + pos="4591.4,178", width=1.0652]; "variant to population association" -> "subject label closure" [color=blue, label="subject label closure", - lp="4902.4,221.5", - pos="e,4841.4,195.77 3604.9,251.72 3625.3,249.83 3646.5,248.14 3666.4,247 3698.1,245.19 4781.9,243.17 4810.4,229 4821.1,223.66 4829.8,\ -213.84 4836.2,204.31", + lp="4643.4,221.5", + pos="e,4582.5,195.8 3346.9,251.72 3367.3,249.83 3388.5,248.14 3408.4,247 3471.7,243.38 4492.1,256.23 4549.4,229 4560.5,223.71 4569.8,\ +213.89 4576.7,204.35", style=solid]; "object label closure" [color=blue, height=0.5, label=string, - pos="5020.4,178", + pos="4762.4,178", width=1.0652]; "variant to population association" -> "object label closure" [color=blue, label="object label closure", - lp="5067.9,221.5", - pos="e,5012.1,195.79 3604.9,251.68 3625.3,249.8 3646.5,248.12 3666.4,247 3702.8,244.95 4947.6,245.04 4980.4,229 4991.3,223.69 5000.1,\ -213.87 5006.7,204.33", + lp="4810.9,221.5", + pos="e,4753.8,195.8 3346.9,251.69 3367.3,249.8 3388.5,248.12 3408.4,247 3444.8,244.95 4688.5,244.83 4721.4,229 4732.4,223.7 4741.4,213.89 \ +4748.2,204.35", style=solid]; "retrieval source ids" [color=blue, height=0.5, label="retrieval source", - pos="5161.4,178", + pos="4903.4,178", width=2.347]; "variant to population association" -> "retrieval source ids" [color=blue, label="retrieval source ids", - lp="5222.9,221.5", - pos="e,5159.3,196.42 3604.4,251.7 3625,249.81 3646.3,248.11 3666.4,247 3707.3,244.73 5107.6,252.18 5141.4,229 5149.1,223.7 5153.9,214.88 \ -5156.8,206.11", + lp="4965.9,221.5", + pos="e,4901.7,196.4 3346.4,251.7 3367,249.81 3388.3,248.11 3408.4,247 3449.3,244.73 4850.8,252.49 4884.4,229 4891.9,223.72 4896.5,215.03 \ +4899.2,206.36", style=solid]; type [height=0.5, - pos="5295.4,178", + pos="5037.4,178", width=0.86659]; "variant to population association" -> type [color=blue, label=type, - lp="5319.4,221.5", - pos="e,5301.3,196.13 3604.4,251.68 3625,249.79 3646.3,248.1 3666.4,247 3689,245.76 5280.5,245.1 5296.4,229 5302.3,223.03 5303.6,214.44 \ -5302.9,206.06", + lp="5062.4,221.5", + pos="e,5043.7,195.64 3346.4,251.68 3367,249.79 3388.3,248.1 3408.4,247 3431,245.76 5023.5,245.11 5039.4,229 5045.4,222.94 5046.5,214.18 \ +5045.6,205.68", style=solid]; category [height=0.5, - pos="5396.4,178", + pos="5138.4,178", width=1.4263]; "variant to population association" -> category [color=blue, label=category, - lp="5395.9,221.5", - pos="e,5383.4,195.45 3604.4,251.68 3625,249.79 3646.3,248.1 3666.4,247 3712.8,244.46 5296,245.61 5339.4,229 5353.5,223.6 5366.4,213 5376.4,\ -202.94", + lp="5138.9,221.5", + pos="e,5125.7,195.44 3346.4,251.68 3367,249.79 3388.3,248.1 3408.4,247 3454.8,244.46 5039,245.81 5082.4,229 5096.3,223.59 5109,212.99 \ +5118.8,202.93", style=solid]; subject [height=0.5, - pos="5510.4,178", + pos="5252.4,178", width=1.2277]; "variant to population association" -> subject [color=blue, label=subject, - lp="5490.4,221.5", - pos="e,5492.4,194.55 3604.4,251.67 3625,249.78 3646.3,248.09 3666.4,247 3764.3,241.67 5337.4,256.78 5431.4,229 5450.7,223.31 5469.7,211.44 \ -5484.3,200.7", + lp="5233.4,221.5", + pos="e,5234.6,194.55 3346.4,251.67 3367,249.78 3388.3,248.09 3408.4,247 3506.4,241.67 5080.4,257.07 5174.4,229 5193.5,223.31 5212.3,211.44 \ +5226.7,200.69", style=solid]; object [height=0.5, - pos="5553.4,91", + pos="5295.4,91", width=1.0832]; "variant to population association" -> object [color=blue, label=object, - lp="5597.4,178", - pos="e,5566.8,108.09 3604.4,251.66 3625,249.77 3646.3,248.09 3666.4,247 3717.8,244.21 5471.7,245.79 5520.4,229 5543.2,221.14 5550.3,216.2 \ -5563.4,196 5576.8,175.3 5573.5,166.51 5576.4,142 5577.2,135.38 5578.3,133.39 5576.4,127 5575.4,123.55 5573.9,120.13 5572.1,116.85", + lp="5338.4,178", + pos="e,5308.8,108.09 3346.4,251.66 3367,249.77 3388.3,248.09 3408.4,247 3459.8,244.21 5214.8,246.08 5263.4,229 5306.6,213.84 5313,187.43 \ +5318.4,142 5319.2,135.38 5320.3,133.39 5318.4,127 5317.4,123.55 5315.9,120.13 5314.1,116.85", style=solid]; "has quotient" [height=0.5, - pos="5721.4,178", + pos="5463.4,178", width=1.9137]; "variant to population association" -> "has quotient" [color=blue, label="has quotient", - lp="5696.4,221.5", - pos="e,5693.6,194.61 3604.4,251.65 3625,249.76 3646.3,248.08 3666.4,247 3773.9,241.2 5499,251.08 5604.4,229 5632.4,223.13 5662,210.41 \ -5684.4,199.26", + lp="5438.4,221.5", + pos="e,5435.6,194.61 3346.4,251.65 3367,249.76 3388.3,248.08 3408.4,247 3515.9,241.2 5241,251.08 5346.4,229 5374.4,223.13 5404,210.41 \ +5426.4,199.26", style=solid]; "has count" [height=0.5, - pos="5864.4,178", + pos="5606.4,178", width=1.5526]; "variant to population association" -> "has count" [color=blue, label="has count", - lp="5828.4,221.5", - pos="e,5837.5,193.89 3604.4,251.64 3625,249.75 3646.3,248.08 3666.4,247 3781.7,240.81 5632.3,252.31 5745.4,229 5774.5,223 5805.4,209.78 \ -5828.4,198.44", + lp="5570.4,221.5", + pos="e,5579.5,193.89 3346.4,251.64 3367,249.75 3388.3,248.08 3408.4,247 3523.7,240.81 5374.3,252.31 5487.4,229 5516.5,223 5547.4,209.78 \ +5570.4,198.44", style=solid]; "has total" [height=0.5, - pos="5989.4,178", + pos="5731.4,178", width=1.4263]; "variant to population association" -> "has total" [color=blue, label="has total", - lp="5947.9,221.5", - pos="e,5962.7,193.41 3604.4,251.64 3625,249.75 3646.3,248.07 3666.4,247 3788.5,240.48 5747.5,253.12 5867.4,229 5897.7,222.9 5930,209.32 \ -5953.7,197.85", + lp="5689.9,221.5", + pos="e,5704.7,193.41 3346.4,251.64 3367,249.75 3388.3,248.07 3408.4,247 3530.5,240.48 5489.5,253.12 5609.4,229 5639.7,222.9 5672,209.32 \ +5695.7,197.85", style=solid]; "has percentage" [color=blue, height=0.5, label=double, - pos="6101.4,178", + pos="5843.4,178", width=1.1735]; "variant to population association" -> "has percentage" [color=blue, label="has percentage", - lp="6085.4,221.5", - pos="e,6077,192.7 3604.4,251.63 3625,249.74 3646.3,248.07 3666.4,247 3794.9,240.16 5857.3,255.11 5983.4,229 6013.3,222.81 6045,208.91 \ -6068,197.33", + lp="5827.4,221.5", + pos="e,5819,192.7 3346.4,251.63 3367,249.74 3388.3,248.07 3408.4,247 3536.9,240.16 5599.3,255.11 5725.4,229 5755.3,222.81 5787,208.91 \ +5810,197.33", style=solid]; "frequency qualifier" [color=blue, height=0.5, label="frequency value", - pos="6246.4,178", + pos="5988.4,178", width=2.3651]; "variant to population association" -> "frequency qualifier" [color=blue, label="frequency qualifier", - lp="6252.4,221.5", - pos="e,6221.2,195.35 3604.4,251.62 3625,249.73 3646.3,248.06 3666.4,247 3735.1,243.36 6077.4,244.79 6144.4,229 6168.4,223.34 6193.3,211.26 \ -6212.5,200.39", + lp="5994.4,221.5", + pos="e,5963.2,195.35 3346.4,251.62 3367,249.73 3388.3,248.06 3408.4,247 3477.1,243.36 5819.4,244.79 5886.4,229 5910.4,223.34 5935.3,211.26 \ +5954.5,200.39", style=solid]; association_type [color=blue, height=0.5, label=string, - pos="3713.4,265", + pos="3455.4,265", width=1.0652]; association_category [color=blue, height=0.5, label="category type", - pos="3844.4,265", + pos="3586.4,265", width=2.0762]; subject -> object [label=relation, - lp="5548.4,134.5", - pos="e,5535.5,107.23 5511.5,159.55 5512.7,149.57 5515.2,137.07 5520.4,127 5522.6,122.68 5525.5,118.52 5528.7,114.66"]; + lp="5290.4,134.5", + pos="e,5277.5,107.23 5253.5,159.55 5254.7,149.57 5257.2,137.07 5262.4,127 5264.6,122.68 5267.5,118.52 5270.7,114.66"]; relation [height=0.5, - pos="5498.4,18", + pos="5240.4,18", width=1.2999]; - subject -> relation [pos="e,5499.7,36.188 5509.1,159.79 5507,132.48 5503,78.994 5500.5,46.38", + subject -> relation [pos="e,5241.7,36.188 5251.1,159.79 5249,132.48 5245,78.994 5242.5,46.38", style=dotted]; "variant to population association_subject" [color=blue, height=0.5, label="sequence variant", - pos="4027.4,265", + pos="3769.4,265", width=2.5095]; - object -> relation [pos="e,5511.2,35.54 5540.9,73.889 5534,64.939 5525.2,53.617 5517.4,43.584", + object -> relation [pos="e,5253.2,35.54 5282.9,73.889 5276,64.939 5267.2,53.617 5259.4,43.584", style=dotted]; "variant to population association_object" [color=blue, height=0.5, label="population of individual organisms", - pos="4307.4,265", + pos="4049.4,265", width=4.7662]; "variant to population association_has quotient" [color=blue, height=0.5, label=double, - pos="4539.4,265", + pos="4281.4,265", width=1.1735]; "variant to population association_has count" [color=blue, height=0.5, label=integer, - pos="4643.4,265", + pos="4385.4,265", width=1.2277]; "variant to population association_has total" [color=blue, height=0.5, label=integer, - pos="4749.4,265", + pos="4491.4,265", width=1.2277]; } diff --git a/graphviz/variant_to_population_association.svg b/graphviz/variant_to_population_association.svg index 27580d1ca1..293b22502d 100644 --- a/graphviz/variant_to_population_association.svg +++ b/graphviz/variant_to_population_association.svg @@ -4,16 +4,16 @@ - + %3 - + variant to population association - -variant to population association + +variant to population association @@ -24,9 +24,9 @@ variant to population association->association - + -is_a +is_a @@ -37,9 +37,9 @@ variant to population association->variant to entity association mixin - - -uses + + +uses @@ -50,9 +50,9 @@ variant to population association->frequency quantifier - - -uses + + +uses @@ -63,9 +63,9 @@ variant to population association->frequency qualifier mixin - - -uses + + +uses @@ -76,9 +76,9 @@ variant to population association->id - - -id + + +id @@ -89,9 +89,9 @@ variant to population association->iri - - -iri + + +iri @@ -102,9 +102,9 @@ variant to population association->name - - -name + + +name @@ -115,9 +115,9 @@ variant to population association->description - - -description + + +description @@ -128,9 +128,9 @@ variant to population association->has attribute - - -has attribute + + +has attribute @@ -141,9 +141,9 @@ variant to population association->predicate - - -predicate + + +predicate @@ -154,9 +154,9 @@ variant to population association->negated - - -negated + + +negated @@ -167,9 +167,9 @@ variant to population association->qualifiers - - -qualifiers + + +qualifiers @@ -180,9 +180,9 @@ variant to population association->publications - - -publications + + +publications @@ -193,427 +193,427 @@ variant to population association->has evidence - - -has evidence + + +has evidence knowledge source - -information resource + +string variant to population association->knowledge source - - -knowledge source + + +knowledge source primary knowledge source - -information resource + +string variant to population association->primary knowledge source - - -primary knowledge source + + +primary knowledge source aggregator knowledge source - -information resource + +string variant to population association->aggregator knowledge source - - -aggregator knowledge source + + +aggregator knowledge source timepoint - -time type + +time type variant to population association->timepoint - - -timepoint + + +timepoint original subject - -string + +string variant to population association->original subject - - -original subject + + +original subject original predicate - -uriorcurie + +uriorcurie variant to population association->original predicate - - -original predicate + + +original predicate original object - -string + +string variant to population association->original object - - -original object + + +original object subject category - -ontology class + +ontology class variant to population association->subject category - - -subject category + + +subject category object category - -ontology class + +ontology class variant to population association->object category - - -object category + + +object category subject closure - -string + +string variant to population association->subject closure - - -subject closure + + +subject closure object closure - -string + +string variant to population association->object closure - - -object closure + + +object closure subject category closure - -ontology class + +ontology class variant to population association->subject category closure - - -subject category closure + + +subject category closure object category closure - -ontology class + +ontology class variant to population association->object category closure - - -object category closure + + +object category closure subject namespace - -string + +string variant to population association->subject namespace - - -subject namespace + + +subject namespace object namespace - -string + +string variant to population association->object namespace - - -object namespace + + +object namespace subject label closure - -string + +string variant to population association->subject label closure - - -subject label closure + + +subject label closure object label closure - -string + +string variant to population association->object label closure - - -object label closure + + +object label closure retrieval source ids - -retrieval source + +retrieval source variant to population association->retrieval source ids - - -retrieval source ids + + +retrieval source ids type - -type + +type variant to population association->type - - -type + + +type category - -category + +category variant to population association->category - - -category + + +category subject - -subject + +subject variant to population association->subject - - -subject + + +subject object - -object + +object variant to population association->object - - -object + + +object has quotient - -has quotient + +has quotient variant to population association->has quotient - - -has quotient + + +has quotient has count - -has count + +has count variant to population association->has count - - -has count + + +has count has total - -has total + +has total variant to population association->has total - - -has total + + +has total has percentage - -double + +double variant to population association->has percentage - - -has percentage + + +has percentage frequency qualifier - -frequency value + +frequency value variant to population association->frequency qualifier - - -frequency qualifier + + +frequency qualifier association_type - -string + +string association_category - -category type + +category type subject->object - - -relation + + +relation relation - -relation + +relation subject->relation - - + + variant to population association_subject - -sequence variant + +sequence variant object->relation - - + + variant to population association_object - -population of individual organisms + +population of individual organisms variant to population association_has quotient - -double + +double variant to population association_has count - -integer + +integer variant to population association_has total - -integer + +integer diff --git a/json-schema/biolink-model.json b/json-schema/biolink-model.json index e40749d202..e7ced9908c 100644 --- a/json-schema/biolink-model.json +++ b/json-schema/biolink-model.json @@ -13,7 +13,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -87,7 +86,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -161,7 +159,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -211,12 +208,6 @@ "title": "Agent", "type": "object" }, - "AnatomicalContextQualifierEnum": { - "description": "", - "enum": [], - "title": "AnatomicalContextQualifierEnum", - "type": "string" - }, "AnatomicalEntity": { "additionalProperties": false, "description": "A subcellular location, cell type or gross anatomical part", @@ -230,7 +221,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -306,7 +296,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -491,7 +480,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -682,7 +670,6 @@ "type": "string" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "format": { @@ -802,7 +789,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -981,7 +967,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -1060,7 +1045,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -1130,7 +1114,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "enabled_by": { @@ -1227,7 +1210,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "frequency_qualifier": { @@ -1437,7 +1419,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -1521,7 +1502,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -1597,7 +1577,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "enabled_by": { @@ -1688,7 +1667,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "enabled_by": { @@ -1779,7 +1757,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -1858,7 +1835,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -1954,7 +1930,6 @@ "type": "string" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "format": { @@ -2068,7 +2043,6 @@ "type": "string" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "format": { @@ -2174,7 +2148,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -2250,7 +2223,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "frequency_qualifier": { @@ -2447,6 +2419,227 @@ "title": "CaseToPhenotypicFeatureAssociation", "type": "object" }, + "CausalGeneToDiseaseAssociation": { + "additionalProperties": false, + "description": "", + "properties": { + "aggregator_knowledge_source": { + "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", + "items": { + "type": "string" + }, + "type": "array" + }, + "category": { + "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "type": "string" + }, + "frequency_qualifier": { + "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_count": { + "description": "number of things with a particular property", + "type": "integer" + }, + "has_evidence": { + "description": "connects an association to an instance of supporting evidence", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_percentage": { + "description": "equivalent to has quotient multiplied by 100", + "type": "number" + }, + "has_quotient": { + "type": "number" + }, + "has_total": { + "description": "total number of things in a particular reference set", + "type": "integer" + }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" + }, + "knowledge_source": { + "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", + "type": "string" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", + "type": "string" + }, + "negated": { + "description": "if set to true, then the association is negated i.e. is not true", + "type": "boolean" + }, + "object": { + "description": "disease", + "type": "string" + }, + "object_category": { + "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "type": "string" + }, + "object_category_closure": { + "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "items": { + "type": "string" + }, + "type": "array" + }, + "object_closure": { + "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "items": { + "type": "string" + }, + "type": "array" + }, + "object_direction_qualifier": { + "$ref": "#/$defs/DirectionQualifierEnum" + }, + "object_label_closure": { + "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "items": { + "type": "string" + }, + "type": "array" + }, + "object_namespace": { + "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "type": "string" + }, + "onset_qualifier": { + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "type": "string" + }, + "original_object": { + "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", + "type": "string" + }, + "original_predicate": { + "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", + "type": "string" + }, + "original_subject": { + "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", + "type": "string" + }, + "predicate": { + "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "type": "string" + }, + "primary_knowledge_source": { + "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", + "type": "string" + }, + "publications": { + "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", + "items": { + "type": "string" + }, + "type": "array" + }, + "qualifiers": { + "description": "connects an association to qualifiers that modify or qualify the meaning of that association", + "items": { + "type": "string" + }, + "type": "array" + }, + "retrieval_source_ids": { + "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", + "items": { + "type": "string" + }, + "type": "array" + }, + "severity_qualifier": { + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" + }, + "sex_qualifier": { + "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", + "type": "string" + }, + "subject": { + "$ref": "#/$defs/GeneOrGeneProduct", + "description": "gene in which variation is shown to cause the disease." + }, + "subject_aspect_qualifier": { + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum" + }, + "subject_category": { + "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "type": "string" + }, + "subject_category_closure": { + "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "items": { + "type": "string" + }, + "type": "array" + }, + "subject_closure": { + "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "items": { + "type": "string" + }, + "type": "array" + }, + "subject_label_closure": { + "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "items": { + "type": "string" + }, + "type": "array" + }, + "subject_namespace": { + "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "type": "string" + }, + "timepoint": { + "description": "a point in time", + "format": "time", + "type": "string" + }, + "type": { + "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", + "items": { + "type": "string" + }, + "type": "array" + } + }, + "required": [ + "subject", + "predicate", + "object", + "id" + ], + "title": "CausalGeneToDiseaseAssociation", + "type": "object" + }, "CausalMechanismQualifierEnum": { "description": "", "enum": [ @@ -2485,7 +2678,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -2555,7 +2747,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -2631,7 +2822,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "frequency_qualifier": { @@ -2828,7 +3018,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -3007,7 +3196,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -3077,7 +3265,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -3161,7 +3348,6 @@ "description": "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -3381,7 +3567,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -3469,7 +3654,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -3662,7 +3846,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -3844,7 +4027,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -3938,7 +4120,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -4145,7 +4326,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "drug_regulatory_status_world_wide": { @@ -4256,7 +4436,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -4445,7 +4624,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -4638,7 +4816,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -4723,7 +4900,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -4915,7 +5091,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -5100,7 +5275,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -5285,7 +5459,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -5469,7 +5642,6 @@ "type": "string" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "format": { @@ -5541,7 +5713,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -5620,7 +5791,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -5699,7 +5869,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -5762,7 +5931,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -5832,7 +6000,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -5895,7 +6062,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -5974,7 +6140,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -6053,7 +6218,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -6123,7 +6287,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -6220,7 +6383,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -6295,7 +6457,6 @@ "type": "string" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "format": { @@ -6367,7 +6528,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -6453,7 +6613,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "drug_regulatory_status_world_wide": { @@ -6559,7 +6718,6 @@ "type": "string" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "format": { @@ -6636,7 +6794,6 @@ "type": "string" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "format": { @@ -6714,7 +6871,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -6880,6 +7036,227 @@ "title": "ContributorAssociation", "type": "object" }, + "CorrelatedGeneToDiseaseAssociation": { + "additionalProperties": false, + "description": "", + "properties": { + "aggregator_knowledge_source": { + "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", + "items": { + "type": "string" + }, + "type": "array" + }, + "category": { + "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "type": "string" + }, + "frequency_qualifier": { + "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_count": { + "description": "number of things with a particular property", + "type": "integer" + }, + "has_evidence": { + "description": "connects an association to an instance of supporting evidence", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_percentage": { + "description": "equivalent to has quotient multiplied by 100", + "type": "number" + }, + "has_quotient": { + "type": "number" + }, + "has_total": { + "description": "total number of things in a particular reference set", + "type": "integer" + }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" + }, + "knowledge_source": { + "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", + "type": "string" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", + "type": "string" + }, + "negated": { + "description": "if set to true, then the association is negated i.e. is not true", + "type": "boolean" + }, + "object": { + "description": "disease", + "type": "string" + }, + "object_category": { + "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "type": "string" + }, + "object_category_closure": { + "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "items": { + "type": "string" + }, + "type": "array" + }, + "object_closure": { + "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "items": { + "type": "string" + }, + "type": "array" + }, + "object_direction_qualifier": { + "$ref": "#/$defs/DirectionQualifierEnum" + }, + "object_label_closure": { + "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "items": { + "type": "string" + }, + "type": "array" + }, + "object_namespace": { + "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "type": "string" + }, + "onset_qualifier": { + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "type": "string" + }, + "original_object": { + "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", + "type": "string" + }, + "original_predicate": { + "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", + "type": "string" + }, + "original_subject": { + "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", + "type": "string" + }, + "predicate": { + "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "type": "string" + }, + "primary_knowledge_source": { + "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", + "type": "string" + }, + "publications": { + "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", + "items": { + "type": "string" + }, + "type": "array" + }, + "qualifiers": { + "description": "connects an association to qualifiers that modify or qualify the meaning of that association", + "items": { + "type": "string" + }, + "type": "array" + }, + "retrieval_source_ids": { + "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", + "items": { + "type": "string" + }, + "type": "array" + }, + "severity_qualifier": { + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" + }, + "sex_qualifier": { + "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", + "type": "string" + }, + "subject": { + "$ref": "#/$defs/GeneOrGeneProduct", + "description": "gene in which variation is shown to correlate with the disease." + }, + "subject_aspect_qualifier": { + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum" + }, + "subject_category": { + "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "type": "string" + }, + "subject_category_closure": { + "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "items": { + "type": "string" + }, + "type": "array" + }, + "subject_closure": { + "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "items": { + "type": "string" + }, + "type": "array" + }, + "subject_label_closure": { + "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "items": { + "type": "string" + }, + "type": "array" + }, + "subject_namespace": { + "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "type": "string" + }, + "timepoint": { + "description": "a point in time", + "format": "time", + "type": "string" + }, + "type": { + "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", + "items": { + "type": "string" + }, + "type": "array" + } + }, + "required": [ + "subject", + "predicate", + "object", + "id" + ], + "title": "CorrelatedGeneToDiseaseAssociation", + "type": "object" + }, "Dataset": { "additionalProperties": false, "description": "an item that refers to a collection of data from a data source.", @@ -6898,7 +7275,6 @@ "type": "string" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "format": { @@ -6975,7 +7351,6 @@ "type": "string" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "distribution_download_url": { @@ -7055,7 +7430,6 @@ "type": "string" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "format": { @@ -7138,7 +7512,6 @@ "type": "string" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "format": { @@ -7219,7 +7592,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -7282,7 +7654,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -7356,7 +7727,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -7426,7 +7796,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -7496,7 +7865,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -7592,7 +7960,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -7777,7 +8144,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -7962,7 +8328,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -8147,7 +8512,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "frequency_qualifier": { @@ -8364,7 +8728,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "drug_regulatory_status_world_wide": { @@ -8485,7 +8848,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -8581,7 +8943,6 @@ "type": "string" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "format": { @@ -8684,7 +9045,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -8863,7 +9223,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -8971,7 +9330,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "frequency_qualifier": { @@ -8985,6 +9343,10 @@ }, "type": "array" }, + "has_count": { + "description": "number of things with a particular property", + "type": "integer" + }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { @@ -8992,6 +9354,17 @@ }, "type": "array" }, + "has_percentage": { + "description": "equivalent to has quotient multiplied by 100", + "type": "number" + }, + "has_quotient": { + "type": "number" + }, + "has_total": { + "description": "total number of things in a particular reference set", + "type": "integer" + }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" @@ -9034,6 +9407,9 @@ }, "type": "array" }, + "object_direction_qualifier": { + "$ref": "#/$defs/DirectionQualifierEnum" + }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { @@ -9094,10 +9470,17 @@ "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string" }, + "sex_qualifier": { + "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", + "type": "string" + }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", "description": "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state." }, + "subject_aspect_qualifier": { + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum" + }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string" @@ -9172,7 +9555,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -9361,7 +9743,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -9540,7 +9921,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -9624,7 +10004,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -9694,7 +10073,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -9776,7 +10154,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -9845,7 +10222,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -9913,7 +10289,6 @@ "type": "string" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "format": { @@ -9992,7 +10367,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -10095,7 +10469,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -10280,7 +10653,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -10474,7 +10846,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "frequency_qualifier": { @@ -10724,7 +11095,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "drug_regulatory_status_world_wide": { @@ -10832,7 +11202,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -10920,7 +11289,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -11099,7 +11467,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -11169,7 +11536,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -11260,7 +11626,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "frequency_qualifier": { @@ -11274,6 +11639,10 @@ }, "type": "array" }, + "has_count": { + "description": "number of things with a particular property", + "type": "integer" + }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { @@ -11281,6 +11650,17 @@ }, "type": "array" }, + "has_percentage": { + "description": "equivalent to has quotient multiplied by 100", + "type": "number" + }, + "has_quotient": { + "type": "number" + }, + "has_total": { + "description": "total number of things in a particular reference set", + "type": "integer" + }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" @@ -11323,6 +11703,9 @@ }, "type": "array" }, + "object_direction_qualifier": { + "$ref": "#/$defs/DirectionQualifierEnum" + }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { @@ -11383,10 +11766,17 @@ "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string" }, + "sex_qualifier": { + "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", + "type": "string" + }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", "description": "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." }, + "subject_aspect_qualifier": { + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum" + }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string" @@ -11451,7 +11841,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -11534,7 +11923,10 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", + "type": "string" + }, + "frequency_qualifier": { + "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string" }, "has_attribute": { @@ -11544,6 +11936,10 @@ }, "type": "array" }, + "has_count": { + "description": "number of things with a particular property", + "type": "integer" + }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { @@ -11551,6 +11947,17 @@ }, "type": "array" }, + "has_percentage": { + "description": "equivalent to has quotient multiplied by 100", + "type": "number" + }, + "has_quotient": { + "type": "number" + }, + "has_total": { + "description": "total number of things in a particular reference set", + "type": "integer" + }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" @@ -11572,7 +11979,7 @@ "type": "boolean" }, "object": { - "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", + "description": "disease", "type": "string" }, "object_category": { @@ -11593,6 +12000,9 @@ }, "type": "array" }, + "object_direction_qualifier": { + "$ref": "#/$defs/DirectionQualifierEnum" + }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { @@ -11604,6 +12014,10 @@ "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string" }, + "onset_qualifier": { + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "type": "string" + }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string" @@ -11645,10 +12059,21 @@ }, "type": "array" }, + "severity_qualifier": { + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" + }, + "sex_qualifier": { + "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", + "type": "string" + }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", "description": "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." }, + "subject_aspect_qualifier": { + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum" + }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string" @@ -11791,7 +12216,10 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", + "type": "string" + }, + "frequency_qualifier": { + "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string" }, "has_attribute": { @@ -11801,6 +12229,10 @@ }, "type": "array" }, + "has_count": { + "description": "number of things with a particular property", + "type": "integer" + }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { @@ -11808,6 +12240,17 @@ }, "type": "array" }, + "has_percentage": { + "description": "equivalent to has quotient multiplied by 100", + "type": "number" + }, + "has_quotient": { + "type": "number" + }, + "has_total": { + "description": "total number of things in a particular reference set", + "type": "integer" + }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" @@ -11829,7 +12272,7 @@ "type": "boolean" }, "object": { - "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", + "description": "disease", "type": "string" }, "object_category": { @@ -11850,6 +12293,9 @@ }, "type": "array" }, + "object_direction_qualifier": { + "$ref": "#/$defs/DirectionQualifierEnum" + }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { @@ -11861,6 +12307,10 @@ "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string" }, + "onset_qualifier": { + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "type": "string" + }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string" @@ -11902,10 +12352,21 @@ }, "type": "array" }, - "subject": { - "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", + "severity_qualifier": { + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" + }, + "sex_qualifier": { + "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string" }, + "subject": { + "$ref": "#/$defs/GeneOrGeneProduct", + "description": "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model" + }, + "subject_aspect_qualifier": { + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum" + }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string" @@ -11976,7 +12437,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "frequency_qualifier": { @@ -12198,7 +12658,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -12391,7 +12850,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "expression_site": { @@ -12592,7 +13050,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -12777,7 +13234,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -12962,7 +13418,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -13147,7 +13602,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -13332,7 +13786,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -13517,7 +13970,10 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", + "type": "string" + }, + "frequency_qualifier": { + "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string" }, "has_attribute": { @@ -13527,6 +13983,10 @@ }, "type": "array" }, + "has_count": { + "description": "number of things with a particular property", + "type": "integer" + }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { @@ -13534,6 +13994,17 @@ }, "type": "array" }, + "has_percentage": { + "description": "equivalent to has quotient multiplied by 100", + "type": "number" + }, + "has_quotient": { + "type": "number" + }, + "has_total": { + "description": "total number of things in a particular reference set", + "type": "integer" + }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" @@ -13576,6 +14047,9 @@ }, "type": "array" }, + "object_direction_qualifier": { + "$ref": "#/$defs/DirectionQualifierEnum" + }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { @@ -13587,6 +14061,10 @@ "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string" }, + "onset_qualifier": { + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "type": "string" + }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string" @@ -13628,10 +14106,21 @@ }, "type": "array" }, - "subject": { - "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", + "severity_qualifier": { + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" + }, + "sex_qualifier": { + "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string" }, + "subject": { + "$ref": "#/$defs/GeneOrGeneProduct", + "description": "gene in which variation is correlated with the phenotypic feature" + }, + "subject_aspect_qualifier": { + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum" + }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string" @@ -13696,7 +14185,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -13766,7 +14254,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -13840,7 +14327,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -13948,7 +14434,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "end_interbase_coordinate": { @@ -14147,7 +14632,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -14230,7 +14714,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "frequency_qualifier": { @@ -14427,7 +14910,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "frequency_qualifier": { @@ -14624,7 +15106,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -14809,7 +15290,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -14994,7 +15474,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "frequency_qualifier": { @@ -15210,7 +15689,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -15389,7 +15867,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -15468,7 +15945,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -15552,7 +16028,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -15623,7 +16098,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -15699,7 +16173,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -15769,7 +16242,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -15843,7 +16315,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -15912,7 +16383,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -15982,7 +16452,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -16058,7 +16527,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -16228,61 +16696,20 @@ "additionalProperties": false, "description": "A database or knowledgebase and its supporting ecosystem of interfaces and services that deliver content to consumers (e.g. web portals, APIs, query endpoints, streaming services, data downloads, etc.). A single Information Resource by this definition may span many different datasets or databases, and include many access endpoints and user interfaces. Information Resources include project-specific resources such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb.", "properties": { - "category": { - "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", - "items": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", - "type": "string" - }, - "type": "array" - }, - "creation_date": { - "description": "date on which an entity was created. This can be applied to nodes or edges", - "format": "date", - "type": "string" - }, "description": { - "description": "a human-readable description of an entity", - "type": "string" - }, - "format": { "type": "string" }, - "has_attribute": { - "description": "connects any entity to an attribute", - "items": { - "type": "string" - }, - "type": "array" - }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, - "information_resource_status": { - "$ref": "#/$defs/InformationResourceStatusEnum", - "description": "the status of the infores identifier, default is released" - }, - "iri": { - "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" - }, - "license": { - "type": "string" - }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" }, - "provided_by": { - "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", - "items": { - "type": "string" - }, - "type": "array" - }, - "rights": { - "type": "string" + "status": { + "$ref": "#/$defs/InformationResourceStatusEnum", + "description": "the status of the infores identifier, the default is \"released\"" }, "synonym": { "description": "Alternate human-readable names for a thing", @@ -16291,12 +16718,6 @@ }, "type": "array" }, - "type": { - "items": { - "type": "string" - }, - "type": "array" - }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { @@ -16306,13 +16727,12 @@ } }, "required": [ - "id", - "category" + "id" ], "title": "InformationResource", "type": "object" }, - "InformationResourceCollection": { + "InformationResourceContainer": { "additionalProperties": false, "description": "A collection of information resources", "properties": { @@ -16324,7 +16744,7 @@ "type": "array" } }, - "title": "InformationResourceCollection", + "title": "InformationResourceContainer", "type": "object" }, "InformationResourceStatusEnum": { @@ -16332,7 +16752,8 @@ "enum": [ "released", "deprecated", - "draft" + "draft", + "modified" ], "title": "InformationResourceStatusEnum", "type": "string" @@ -16350,7 +16771,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -16432,7 +16852,6 @@ "type": "string" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "format": { @@ -16546,7 +16965,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -16603,6 +17021,82 @@ "title": "LifeStage", "type": "object" }, + "LogOddsAnalysisResult": { + "additionalProperties": false, + "description": "A result of a log odds ratio analysis.", + "properties": { + "category": { + "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", + "type": "string" + }, + "type": "array" + }, + "creation_date": { + "description": "date on which an entity was created. This can be applied to nodes or edges", + "format": "date", + "type": "string" + }, + "description": { + "type": "string" + }, + "format": { + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" + }, + "license": { + "type": "string" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", + "type": "string" + }, + "provided_by": { + "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", + "items": { + "type": "string" + }, + "type": "array" + }, + "rights": { + "type": "string" + }, + "type": { + "items": { + "type": "string" + }, + "type": "array" + }, + "xref": { + "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", + "items": { + "type": "string" + }, + "type": "array" + } + }, + "required": [ + "id", + "category" + ], + "title": "LogOddsAnalysisResult", + "type": "object" + }, "LogicalInterpretationEnum": { "description": "", "enum": [ @@ -16626,7 +17120,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -16702,7 +17195,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -16887,7 +17379,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -17072,7 +17563,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -17251,7 +17741,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -17321,7 +17810,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -17390,7 +17878,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -17575,7 +18062,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -17761,7 +18247,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -17865,7 +18350,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "enabled_by": { @@ -17962,7 +18446,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -18147,7 +18630,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -18332,7 +18814,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -18518,7 +18999,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -18611,7 +19091,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "drug_regulatory_status_world_wide": { @@ -18718,7 +19197,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -18787,7 +19265,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -18973,7 +19450,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -19084,7 +19560,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -19181,7 +19656,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -19251,7 +19725,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -19337,7 +19810,6 @@ "type": "string" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "format": { @@ -19409,7 +19881,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -19488,7 +19959,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -19567,7 +20037,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -19640,7 +20109,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -19825,7 +20293,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -20010,7 +20477,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -20195,7 +20661,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "frequency_qualifier": { @@ -20392,7 +20857,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -20577,7 +21041,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -20771,7 +21234,6 @@ "type": "string" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "format": { @@ -20868,7 +21330,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -20958,7 +21419,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -21028,7 +21488,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "enabled_by": { @@ -21119,7 +21578,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -21209,7 +21667,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "enabled_by": { @@ -21310,7 +21767,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -21373,7 +21829,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -21443,7 +21898,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -21522,7 +21976,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -21601,7 +22054,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -21664,7 +22116,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "enabled_by": { @@ -21755,7 +22206,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -21818,7 +22268,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -21888,7 +22337,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -21958,7 +22406,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -22034,7 +22481,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -22213,7 +22659,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -22282,8 +22727,8 @@ "description": "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place.", "properties": { "anatomical_context_qualifier": { - "$ref": "#/$defs/AnatomicalContextQualifierEnum", - "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." + "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", + "type": "string" }, "broad_match": { "description": "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree.", @@ -22394,7 +22839,6 @@ "type": "string" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "format": { @@ -22491,7 +22935,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -22561,7 +23004,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "drug_regulatory_status_world_wide": { @@ -22662,7 +23104,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -22739,7 +23180,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -22816,7 +23256,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -22893,7 +23332,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -22982,7 +23420,6 @@ "type": "string" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "format": { @@ -23102,7 +23539,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -23213,7 +23649,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -23343,7 +23778,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -23540,7 +23974,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -23731,7 +24164,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -23805,7 +24237,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -23899,7 +24330,6 @@ "type": "string" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "format": { @@ -23986,7 +24416,6 @@ "type": "string" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "format": { @@ -24078,7 +24507,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -24272,7 +24700,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -24451,7 +24878,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -24544,7 +24970,6 @@ "type": "string" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "format": { @@ -24654,7 +25079,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -24740,7 +25164,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -24851,7 +25274,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -24937,7 +25359,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -25018,7 +25439,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -25097,7 +25517,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -25199,7 +25618,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -25262,7 +25680,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -25337,7 +25754,6 @@ "type": "string" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "format": { @@ -25415,7 +25831,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -25614,7 +26029,6 @@ "type": "string" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "format": { @@ -25693,7 +26107,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -25796,7 +26209,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -25975,7 +26387,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -26049,7 +26460,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -26144,7 +26554,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "frequency_qualifier": { @@ -26341,7 +26750,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "frequency_qualifier": { @@ -26538,7 +26946,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -26723,7 +27130,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "expression_site": { @@ -26924,7 +27330,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "frequency_qualifier": { @@ -27140,7 +27545,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "frequency_qualifier": { @@ -27339,7 +27743,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -27409,7 +27812,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -27491,7 +27893,6 @@ "type": "string" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "format": { @@ -27588,7 +27989,6 @@ "type": "array" }, "description": { - "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -27658,6 +28058,7 @@ "$id": "https://w3id.org/biolink/biolink-model", "$schema": "http://json-schema.org/draft-07/schema#", "additionalProperties": true, + "description": "A collection of information resources", "metamodel_version": "1.7.0", "properties": { "information_resources": { @@ -27670,5 +28071,5 @@ }, "title": "Biolink-Model", "type": "object", - "version": "3.3.2" + "version": "3.4.0" }